CN111445768A - A Modular Assembled Peptide Chain Spatial Structure Model - Google Patents

Abstract

The present invention provides a modular assembled peptide chain spatial structure model, the model includes a plurality of basic modules 1 and a plurality of basic modules 2 . The invention replaces the traditional ball-and-stick model by making the peptide plane into a plane structure, and makes the imino end and the carbonyl end separable, and makes the link point Cα of the adjacent peptide plane into a spherical model as the connection hub, and uses a sleeve The tube connection replaces the ball-and-stick connection, which can intuitively show the relationship between each atom and each adjacent chemical bond in the peptide plane. It can also withstand repeated rotation without loosening, and the conformation is always stable. The two dihedral angles on the peptide plane can be directly measured or the angle values can be obtained intuitively. The invention builds a realistic model for teachers in class according to theoretical data, simplifies, three-dimensional, realistic and vivid teaching, which facilitates teachers' teaching, improves students' interest in learning, and deepens the understanding and mastery of difficult knowledge.

Description

A Modular Assembled Peptide Chain Spatial Structure Model

technical field

The invention relates to a modular assembled peptide chain space structure model, belonging to the technical field of teaching and scientific research appliances.

Background technique

Proteins that are ubiquitous in the biological world are the most important biological macromolecules in living organisms, the basic material basis of life activities, and perform different physiological functions respectively. Through the study of the structure and function correlation of a large number of proteins, it is found that proteins with different biological functions contain different spatial structures; the specific spatial conformations of proteins in vivo are closely related to their special physiological functions. Therefore, studying the structure of a protein is crucial to studying its function.

角和ψ角更为抽象，缺乏直观性。Protein molecules are biological macromolecules formed by connecting many amino acids through peptide bonds, and play important biological functions in the life activities of organisms. The specific spatial structure of a protein is the structural basis for its function. Therefore, studying the structure of a protein is very important to study its function. The molecular structure of proteins is divided into four levels, namely primary, secondary, tertiary, and quaternary structures. The sequence of the amino acids that make up the protein is the primary structure of the protein, and the latter three are collectively referred to as the advanced structure or spatial conformation of the protein. . The basic building blocks of proteins are amino acids. The peptide bond is the basic way of connecting amino acids. Due to the resonance interaction between the amide nitrogen and the carboxyl oxygen, the peptide bond has the property of partial double bond and cannot rotate freely. Therefore, the six atoms Cα1, C, O, N, H, Cα2 are in one plane, called the peptide plane (or amide plane). The peptide plane (amide plane) is the basic structural unit of protein spatial structure. The conventional ball-and-stick model shows a single peptide plane, which depends on our imagination and is not really designed on the same plane entity. Therefore, it is difficult for students to truly understand and master it in teaching, and it is difficult for teachers to explain this key content thoroughly. . The existing patent technology: a modular assembly protein structure model (CN201510262260.0) discloses a peptide plane ball-and-stick structure and a method for assembling a protein space structure. knowledge points, such as

Angle and ψ angle are more abstract and lack intuition.

The peptide plane (amide plane) is the basic structural unit of protein spatial structure. The secondary structure of a protein is the relative spatial position of the backbone atoms of the protein main chain, and is the local spatial structure of a certain segment of the protein molecule, including α helix, β sheet, β turn and random coil. Alpha helix and beta sheet are the most common basic structural models of protein secondary structure.

角为-47°，ψ角为-57°，氨基酸的侧链R基团伸向螺旋的外侧。每3.6各氨基酸残基螺旋式上升一圈(即旋转360°)，螺距为0.54nm。α螺旋的每个肽键的N-H和第四个肽键的羰基氧形成氢键，氢键的方向和螺旋长轴基本平行。肽链中的所有肽键中的全部羰基氧都可以形成氢键，以稳固α螺旋结构。β折叠(β-pleated sheet)呈折纸状，多肽链充分伸展，每个肽平面(肽单元)以Cα为旋转点，依次折叠呈锯齿状结构，氨基酸残基侧链交替位于锯齿状结构的上下方，一条肽链中的若干肽段的锯齿状结构可平行排列，分子内相距较远的两个肽段可以通过折叠而形成相同走向，也可通过回折而形成相反走向。Pauling and Corey proposed that α-helix and β-pleated sheet are the main forms of protein secondary structure based on experimental data. In the α-helix structure, the main chain of the polypeptide chain spirals up around the central axis. According to the direction of the peptide chain from the amino terminus (N terminus) to the carboxyl terminus (C terminus), the direction of the helix belongs to a clockwise right-handed spiral, its

The angle is -47°, the ψ angle is -57°, and the side chain R group of the amino acid extends to the outside of the helix. Every 3.6 amino acid residues rises in a helical manner (ie, rotates 360°), and the pitch is 0.54 nm. The NH of each peptide bond of the α-helix forms a hydrogen bond with the carbonyl oxygen of the fourth peptide bond, and the direction of the hydrogen bond is substantially parallel to the long axis of the helix. All carbonyl oxygens in all peptide bonds in a peptide chain can form hydrogen bonds to stabilize the alpha helix structure. The β-pleated sheet is origami-like, the polypeptide chain is fully stretched, and each peptide plane (peptide unit) takes Cα as the rotation point, and folds in turn in a zigzag structure, and the side chains of amino acid residues are alternately located on the upper and lower sides of the zigzag structure. The zigzag structure of several peptide segments in a peptide chain can be arranged in parallel, and two peptide segments that are far apart in the molecule can form the same direction by folding, or they can form the opposite direction by folding back.

When teachers describe the secondary structure of proteins, they only rely on textbook graphics and simple two-dimensional graphics to help students understand and master it, so it is difficult for students to understand intuitively. In the current teaching and scientific research of protein structure and function, there is no basic model that can simply and intuitively display the spatial structure of peptide chains. However, the existing patent technology: a modular assembly protein structure model (CN201510262260.0) device is difficult to actually arrange and simulate the real protein space structure. Based on this, according to the amino acid structure characteristics, peptide plane characteristics and secondary structure model characteristics of the constituent protein, the present invention designs a kind of peptide that can truly simulate the peptide plane and can be assembled into protein secondary structure, especially the α-helix, β-sheet and α-turn. The model of the basic structure provides a model basis for the teaching and research of protein structure science.

SUMMARY OF THE INVENTION

Based on the theoretical data support of protein structure, the present invention overcomes the shortcomings of lack of intuition and operability in the prior art, and provides a modular assembled peptide chain space structure model through the reconstruction of the peptide plane three-dimensional model, which is used for In the teaching and scientific research of protein structure, a realistic model is built for teachers and researchers. The teaching is simplified, three-dimensional, realistic and vivid, which is convenient for teachers to teach while improving students' interest in learning and deepening the understanding and mastery of difficult knowledge.

In order to achieve the above object, the present invention adopts the following technical means:

The present invention provides a modular assembled peptide chain spatial structure model, characterized in that the model includes a plurality of basic modules 1 and a plurality of basic modules 2, wherein:

The main body of the basic module 1 is a board, the center of the board is marked with C atoms, the center of the board is marked with N atoms, the upper left corner of the board is marked with O atoms, and the lower right corner of the board is marked with H. Atomic label; there is a single bond label between the C atom label and the N atom label, there is a double bond label between the C atom label and the O atom label, and the N atom label and the H atom label have a label Single bond mark, the C atom mark and the lower left corner of the plate have a single bond mark and a triangle mark for indicating the position of the rotation angle measurement, the N atom mark and the upper right corner of the plate are marked with a single bond mark and used to indicate Triangular mark for the position of rotation angle determination; an imaginary line segment 1 in the center of the C atom mark and the center of the N atom mark, and an imaginary line segment in the center of the C atom mark and the center of the O atom mark 2. There is an imaginary line segment 3 in the center of the N atom mark and the center of the H atom mark, and there is an imaginary line segment 4 in the center of the C atom mark and the lower left corner of the plate, in the N atom mark There is an imaginary line segment 5 in the center of the board and the upper right corner of the board; the board has two through holes on the two imaginary lines where the virtual line segment 4 and the virtual line segment 5 are located, which can be plugged with the basic module 2 ;

The main body of the basic module 2 is four tubes which are issued from the center and are connected to each other in a three-dimensional space, three of which are long tubes and the other is a short tube, and the outer end of the short tube is connected to a sphere; Among the long tubes, two long tubes are respectively provided with thin discs perpendicular to the length of the tubes, and a protractor is attached to the outside; when the long tubes without thin discs are placed downward, the short tube connecting the spheres is offset to the right. When placed on the top, there is a -NH mark on the long tube with a thin disc at the front, which can be inserted into the upper right corner hole of the basic module 1, and the long tube with a thin disc at the rear has a -CO mark, which can be inserted The hole in the lower left corner of the basic module 1 is marked with -R on the long tube that is not provided with the thin disc.

Preferably, in the basic module 1, the imaginary line segment 1 has a length of 5.28 length units, the imaginary line segment 2 has a length of 4.92 length units, and the imaginary line segment 3 has a length of 4.04 length units. The length of the imaginary line segment 4 is 6.12 length units, the length of the imaginary line segment 5 is 5.88 length units, and the inner diameter of the two through holes is 1.6 length units; the imaginary line segment 1 and the imaginary line segment are The included angle of 2 is 123.5°, the included angle between the imaginary line segment 1 and the imaginary line segment 3 is 120°, the included angle between the imaginary line segment 1 and the imaginary line segment 4 is 116°, and the imaginary line segment 1 and The included angle of the imaginary line segment 5 is 122°; the unmarked top view of the basic module 1 is shown in FIG. 3 , the marked top view is shown in FIG. 4 , and the front view is shown in FIG. 5 ;

In the basic module 2, the outer diameter of the four pipes is 1.6 units of length, the angle between the long pipe with the -NH map and the long pipe with the -CO map is 111°, and the long pipe with the -R map The angle between the long tube with -NH map and the long tube with -NH map is 110.6°, the angle between the long tube with -R map and the long tube with -CO map is 110.6°, the angle between the short tube connecting the sphere and the three long tubes 108.2° respectively, the length of three long tubes is 5.6 length units, the long tube marked with -R has a ring mark at 2.24 to 2.36 length units from the center of the module, and the length of one short tube is 5 length units, The diameter of the sphere is 2.96 length units, the two thin discs are 3.5 length units away from the center of the module, and a 360° scale protractor is attached to the outside, and its 0° line is located on the plane formed by the intersection of the center lines of the two long tubes; the basic The top view and front view of the module 2 are shown in FIGS. 6 and 7 .

Preferably, the model further includes a plurality of basic modules 3 and a plurality of basic modules 4, wherein:

The basic module 3 and the basic module 4 are the left half block and the right half block of the basic module 1, respectively, and a plug-in structure that can be plugged into each other is provided at the split; the basic module 3 and the basic module 4 The top views are shown in Figures 8 and 9.

Preferably, the model further includes a plurality of special modules 1, a plurality of special modules 2 and a plurality of special modules 3, wherein:

The main body of the special module 1 is a board, the center of the board is marked with C atoms, the center of the board is marked with N atoms, and the upper left corner of the board is marked with O atoms; There is a single bond mark in the middle of the N atom mark, a double bond mark between the C atom mark and the O atom mark, and a single bond mark between the C atom mark and the lower left corner of the plate and is used to indicate the rotation angle measurement position. The triangular mark of the N atom mark and the upper right corner of the plate have a single bond mark and a triangle mark for indicating the position of the rotation angle measurement, and there is a single bond mark in the middle of the N atom mark and the lower right corner position of the plate; There is an imaginary line segment 1 in the center of the C atom mark and the center of the N atom mark, and an imaginary line segment 2 in the center of the C atom mark and the center of the O atom mark, and in the center of the N atom mark And there is an imaginary line segment 3 at the lower right corner of the plate, an imaginary line segment 4 at the center of the C atom mark and at the lower left corner of the plate, and an imaginary line segment at the center of the N atom mark and the upper right corner of the plate. 5; the board has two through holes on the two imaginary straight lines where the imaginary line segment 4 and the imaginary line segment 5 are located, which can be plugged with the special module 2; the board has a semi-penetrating hole on the imaginary line segment 3 hole, which can be plugged with the special module 3;

The main body of the special module 2 is four tubes that are issued from the center and are connected to each other in a three-dimensional space, three of which are long tubes, and the other is a short tube, and the outer end of the short tube is connected to a sphere; Among the long tubes, two long tubes are respectively provided with thin discs perpendicular to the length of the tubes, and a protractor is attached to the outside; when the long tubes without thin discs are placed downward, the short tube connecting the spheres is offset to the right. When placed on the top, there is a -NH mark on the long tube with a thin disc in the front, which can be inserted into the upper right corner hole of the special module 1, and the long tube with a thin disc in the rear has a -CO mark, which can be inserted The hole in the lower left corner of the special module 1 is marked with -R on the long tube without the thin disc, and the short and thick tube of the special module 3 can be inserted;

The main body of the special module 3 is four tubes emanating from the center and connected to each other in a three-dimensional space, one of which is slender, the other is short and thick, and the other two tubes are respectively connected to the sphere; the slender and long tubes of the special module 3 The tube can be plugged into the lower right corner hole of the special module 1 or the short and thick tube of another special module 3, and the short and thick tube of the special module 3 can be plugged into the special module 2 marked -CO long tube or another elongated tube of said special module 3.

Preferably, in the special module 1, the imaginary line segment 1 has a length of 5.28 length units, the imaginary line segment 2 has a length of 4.96 length units, and the imaginary line segment 3 has a length of 2.90 length units. The length of the imaginary line segment 4 is 2.62 length units, the length of the imaginary line segment 5 is 2.42 length units, and the inner diameter of the two through holes and one of the semi-through holes is 1.6 length units; The included angle between line segment 1 and the imaginary line segment 2 is 121°, the included angle between the imaginary line segment 1 and the imaginary line segment 3 is 124°, and the included angle between the imaginary line segment 1 and the imaginary line segment 4 is 118° , the angle between the imaginary line segment 1 and the imaginary line segment 5 is 122°; the top view of the marked special module 1 is shown in Fig. 11, and the basic theoretical data parameters of the peptide plane composed of proline are shown in Fig. 10, the distance between the N atom and the Cα atom in the upper right corner is 0.148 nm, the distance between the upper right Cα atom and the Cβ atom is 0.154 nm, the distance between the Cβ atom and the Cγ atom is 0.151 nm, and the distance between the Cγ atom and the Cδ atom is 0.151 nm. is 0.152nm; when the N atom is the center, the angle between the C atom and the upper right Cα atom is 122°, and the angle between the upper right Cα atom and the Cδ atom is 113°; when the upper right Cα atom is the center, The angle between the N atom and the CO group is 111°, and the angle between the N atom and the Cβ atom is 103°; when the Cβ atom is used as the center, the angle between the Cα atom and the Cγ atom in the upper right corner is 105°; when the Cγ atom is used as the center When the center is the Cβ atom and the Cδ atom is 106°; when the Cδ atom is the center, the angle between the Cγ atom and the N atom is 103°;

In the special module 2, the outer diameters of the four pipes are all 1.6 length units, the length of the three long pipes is 5.6 length units, and the long pipes marked with -R are 2.24 to 2.36 length units away from the center of the module. There is a ring mark at the place, the length of a short tube is 5 length units, the diameter of the sphere is 2.96 length units, the two thin discs are 3.5 length units away from the center of the module, and a 360° scale protractor is attached to the outside, its 0° line It is located on the plane formed by the intersection of the centerlines of the two long pipes; the angle between the long pipe marked with -NH and the long pipe marked with -CO is 112.3°, and the long pipe marked with -R and the long pipe marked with -CO The included angle is 111°, the angle between the long tube marked with -NH and the long tube marked with -R is 103°, and the angle between the short tube connecting the sphere and the other three long tubes is 110.1°; the The structural diagrams of the special module 2 from different perspectives are shown in Figure 12 and Figure 13 .

In the special module 3, the outer diameter of the elongated tube is 1.6 length units, the length is 5.6 length units, and there are ring marks at 2.24-2.36 length units from the center of the module. The short and thick tube has an inner diameter of 1.6 length units and a length of 3.8 length units, the other two tubes have a length of 5 length units, and the diameter of the two spheres is 2.96 length units; the clamp of the two tubes that do not connect the spheres The angle is 104°, the included angle between the two tubes connecting the spheres is 110.5°, and the plane where the two tubes that are not connected to the spheres are located is perpendicular to the plane where the two tubes that connect the spheres are located; the front view of the special module 3 and the right Views are shown in Figures 14 and 15.

Preferably, the model further includes a plurality of special modules 4, wherein:

The main body of the special module 4 is four pipes that are issued from the center and are connected to each other in a three-dimensional space; two of the pipes are long pipes, the other two are short pipes, and the outer ends of the two short pipes are respectively connected to the sphere; Each long tube is provided with a thin disc perpendicular to the length of the tube, and a protractor is attached to the outside; one of the long tubes with the thin disc is marked with -NH, which can be inserted into the upper right corner hole of the basic module 1, and the other The long tube with the thin disc is marked with -CO and can be inserted into the lower left corner hole of the basic module 1.

Preferably, in the special module 4, the outer diameters of the four tubes are all 1.6 units of length, the angle between the long tube with the -CO map and the long tube with the -NH map is 112.1°, and the angle between the other tubes is 112.1°. The included angle is 109°, the length of the two long tubes is 5.6 length units, the length of the two short tubes is 5 length units, the diameter of the sphere is 2.96 length units, and the distance between the two thin discs is 3.5 units from the center of the module Length unit, and a 360° graduated protractor is attached to the outside, and its 0° line is located on the plane formed by the intersection of the centerlines of the two long tubes; the front view of the special module 4 is shown in FIG. 16 .

Preferably, the model further includes a plurality of special modules 5 and a plurality of special modules 6, wherein:

The main body of the special module 5 is four tubes emanating from the center and connected to each other in a three-dimensional space, one of which is slender, one is short and thick, and the other two are connected to the spheres respectively;

The special module 6 is composed of two tubes that are emanating from the center and connected to each other and a detachable sphere, one of which is a thick tube that can be plugged with the elongated tube of the special module 5, and the other is a thin tube, which is a thin tube. The thin tube is connected to the detachable sphere;

Preferably, in the special module 5, the included angle between the four tubes is 109°28', the outer diameter of the elongated tube is 1.6 length units, the length is 5.6 length units, and the distance from the center of the module is 3.48 There are ring marks at each length unit; the short thick tube has an inner diameter of 1.6 length units and a length of 3.8 length units, the other two tubes have a length of 5 length units, and the diameter of the two spheres is 2.96 length units.

Preferably, in the special module 6, the angle between the two tubes is 104°, the length of the thin tube is 4.1 length units, the outer diameter is 1.6 length units, and it is a solid tube with a diameter of A plug with a length of 0.35 length units and a length of 0.86 length units, with the center of its end as the center, and the left and right sides with an included angle of 86.4° with the plug, there is also a socket matching the plug, the length of the thick tube is 3.8 length units, the inner diameter is 1.6 length units, the diameter of the sphere is 2.96 length units, and there are jacks matching the plugs; the left side view of the interconnected pipes in the special module 6 is shown in Figure 17, The front view is shown in Figure 18, and the left side view of the detachable sphere is shown in Figure 19.

Preferably, the model further includes a plurality of special modules 7, wherein:

The special module 7 is the right half of the special module 1, and the splitting part is provided with the same plug-in structure that the basic module 4 can be inserted into the basic module 3; the top view of the special module 7 is shown in FIG. 20 .

Preferably, the model further includes a hydrogen bond module, and the hydrogen bond module is an elongated round stick; in the basic module 1, the basic module 3, the basic module 4, the special module 1 or the special module The center of the O atom mark and the H atom mark in the module 7 also has a circular socket matched with the elongated round rod;

Preferably, the diameter of the elongated round rod is 0.15 length units, and the length is 6.5 length units; the diameter of the circular socket is 0.15 length units.

Preferably, the marks described in the present invention may be in any form such as map, seal carving, and painting.

Compared with the prior art, the beneficial effects of the present invention are:

The invention replaces the traditional ball-and-stick model by making the peptide plane into a plane structure, and makes the imino end and the carbonyl end separable, and makes the link point Cα of the adjacent peptide plane into a spherical model as the connection hub, and uses a sleeve The tube connection replaces the ball-and-stick connection, which can intuitively show the relationship between each atom and each adjacent chemical bond in the peptide plane. It can also withstand repeated rotation without loosening, and the conformation is always stable. The two dihedral angles on the peptide plane can be directly measured or the angle values can be obtained intuitively. Based on the basic data of protein structure, the invention constructs a realistic model for teachers according to the theoretical data through the reconstruction of the peptide plane three-dimensional model, simplifies, three-dimensional, realistic and vivid teaching, which facilitates teachers' teaching and improves students' teaching. Learning interest, deepen the understanding and mastery of difficult knowledge. The invention can be used as a teaching tool for biochemistry and molecular biology, and can also be used as a scientific research tool in the research process of protein structure biology, and provides a model basis for studying protein secondary structure. The model of the invention is simple in operation, convenient in assembly, and convenient for teaching and scientific research.

The model of the present invention can assemble and display various teaching contents including:

(1) Peptide bonds, amino acid residues, and oligopeptides such as dipeptides and tripeptides;

(2) Special amino acid proline, glycine and cysteine structure;

(3) Measurement of the rotation angle of the peptide plane and the dihedral angle;

(4) Secondary structures such as α-helix, β-sheet and β-turn of proteins.

Description of drawings

Fig. 1 is the basic theoretical data diagram of the positions of the six atoms in the peptide plane and the corresponding bond angles and bond lengths;

Fig. 2 is the design drawing of basic module 1 of the present invention;

3 is an unmarked top view of the basic module 1 of the present invention;

Fig. 4 is the top view after marking of basic module 1 of the present invention;

5 is a front view of the basic module 1 of the present invention after marking;

6 is a top view of the basic module 2 of the present invention;

Fig. 7 is the front view of basic module 2 of the present invention;

8 is a top view of the basic module 3 of the present invention;

9 is a top view of the basic module 4 of the present invention;

Figure 10 is a basic theoretical data diagram of a peptide plane composed of proline;

Fig. 11 is the top view after marking the special module 1 of the present invention;

Fig. 12 is the structural diagram of the special module 2 of the present invention;

Fig. 13 is the structural diagram of the special module 2 of the present invention;

Fig. 14 is the front view of the special module 3 of the present invention;

Fig. 15 is the right side view of the special module 3 of the present invention;

Fig. 16 is the front view of the special module 4 of the present invention;

Figure 17 is a left side view of the interconnected pipes in the special module 6 of the present invention;

Figure 18 is a front view of the interconnected pipes in the special module 6 of the present invention;

Fig. 19 is the left side view of the detachable sphere in the special module 6 of the present invention;

Fig. 20 is the top view of the special module 7 of the present invention;

Figure 21 is a display diagram of peptide bond connection in Example 2 of the present invention;

Figure 22 is a diagram showing the connection of amino acid residues in Example 2 of the present invention;

Figure 23 is a diagram showing the trans connection of proline in Example 3 of the present invention;

Figure 24 is a diagram showing the cis connection of proline in Example 3 of the present invention;

Figure 25 is the basic theoretical data diagram of the cysteine side chain in Example 4 of the present invention;

Figure 26 is a diagram showing the connection of disulfide bonds in Example 4 of the present invention;

ψ＝0°时的连接展示图；Figure 27 is the rotation angle of the peptide plane in Example 6 of the present invention

Connection display diagram when ψ=0°;

和ψ均为0°的连接展示图；Fig. 28 is the dihedral angle in the seventh embodiment of the present invention

and ψ are the connection display diagram of 0°;

ψ＝-57°时的连接展示图；Fig. 29 shows the dihedral angle in Examples 7 and 8 of the present invention

Connection display diagram when ψ=-57°;

Detailed ways

The present invention will be further described below with reference to specific embodiments, and the advantages and characteristics of the present invention will become clearer with the description. However, these examples are only exemplary and do not constitute any limitation to the scope of the present invention. It should be understood by those skilled in the art that the details and forms of the technical solutions of the present invention can be modified or replaced without departing from the spirit and scope of the present invention, but these modifications and replacements all fall within the protection scope of the present invention.

Example 1 Determination of basic size data of basic module 1

According to the basic theoretical data of the positions of the six atoms in the peptide plane and the corresponding bond angles and bond lengths, the module size and data parameters of the peptide plane teaching aid model are made, so as to determine the size of the basic module 1, the bond angles are unchanged, and the bond lengths can be proportional zoom.

Figure 1 is the basic theoretical data diagram of the positions of the six atoms in the peptide plane and the corresponding bond angles and bond lengths. The distance between the atom and the H atom is 0.101 nm, the distance between the C atom and the Cα atom in the lower left corner is 0.153 nm, and the distance between the N atom and the Cα atom in the upper right corner is 0.147 nm; when the C atom is the center, the distance between the N atom and the O atom is 0.147 nm. The angle is 123.5°, and the angle between the N atom and the Cα atom in the lower left corner is 116°; when the N atom is the center, the angle between the C atom and the H atom is 120°, and the angle between the C atom and the Cα atom in the upper right corner is 120°. is 122°.

FIG. 2 is a design diagram of the basic module 1 .

Example 2 Using basic module 3, basic module 4 and basic module 5 to assemble and display peptide bonds, amino acid residues, and oligopeptides such as dipeptides and tripeptides

The peptide bond is formed by the dehydration condensation of the α amino group of one amino acid and the α carboxyl group of another amino acid, so the basic module 3 (carbonyl end module) and the basic module 4 (imino end module) are used to display and assemble through the middle plug-in structure, As shown in Figure 21. The peptide chain amino acids exist in the form of residues, so basic module 4 (imino end module), basic module 5 (Cα module), and basic module 3 (carbonyl end module) can be assembled into amino acids in the order from left to right. residues, as shown in Figure 22. The basic assembly method of oligopeptide: basic module 4 - basic module 5 - basic module 3 - basic module 4 - basic module 5 - basic module 3 - basic module 4 - basic module 5 - basic module 3..., and then display a protein level structure.

Example 3 Assembly and display of peptide bonds formed from the amino terminus of proline using basic module 3, special module 7, special module 2 and special module 3

Proline is an imino acid, and its residue model consists of a proline-specific peptide plane module, a proline alpha carbon structural module, and three proline side chain carbon structural modules. The proline-specific detachable module of the present invention can assemble and display a peptide bond structure formed by the amino terminus of proline, wherein proline can also form two types of trans-linking and cis-linking, as shown in Figure 23 and Figure 24, respectively shown.

Prepare one basic module 3, one special module 7, one special module 2 and three special modules 3, and assemble them as follows:

(1) Insert the long tube marked -NH in the special module 2 into the upper right corner hole of the special module 7;

(2) Insert the long tube marked -R in the special module 2 into the short and thick tube of the first special module 3;

(3) Insert the slender tube of the first special module 3 into the short and thick tube of the second special module 3;

(4) Insert the slender tube of the second special module 3 into the short and thick tube of the third special module 3;

(5) Insert the slender tube of the third special module 3 into the hole in the lower right corner of the special module 7. At this time, it is necessary to rotate the aforementioned connections, and gradually fine-tune the direction and depth until it is inserted into the ring mark;

(6) If the special module 7 is inserted into the basic module 3 from the front, the trans configuration as shown in Fig. 23 can be obtained; cis configuration.

Example 4 Assembly and display of peptide bonds formed from the amino terminus of glycine using basic module 1 and special module 4

Glycine has no side chain carbon structure, but hydrogen atoms, and the carbon-hydrogen bond length is short, so the exclusive module C of glycine is specially designed.

Prepare a basic module 1 and special module 4 and assemble as follows:

Insert the long tube marked -NH in special module 4 into the upper right hole of base module 1.

Example 5 Assembling and Displaying Cysteine Side Chains Using Basic Module 2, Special Module 5, Special Module 6

The main structural parameters of the cysteine side chain are shown in Figure 25, where the distance between Cα atom and Cβ atom is 0.154nm, the distance between Cβ atom and S atom is 0.182nm, and the distance between S atom and H atom is 0.135nm ; When the Cβ atom is the center, the angle between the Cα atom and the S atom is 109°28'; when the S atom is the center, the angle between the Cβ atom and the H atom is 104.

Prepare a basic module 2, a special module 5, and two special modules 6, and assemble them as follows:

(1) Insert the long tube marked -R in the basic module 2 into the short thick tube of the special module 5 to the ring mark of the -R tube;

(2) Insert the slender tube of the special module 5 into the thick tube of the first special module 6 to the circular mark of the slender tube, and insert the plug at the end of the thin tube into the socket of the sphere representing the hydrogen atom to form a half Cystine side chain;

(3) When two cysteines are required for connection, the spheres representing hydrogen atoms in the two special modules 6 are removed, and then the ends of the two thin tubes are inserted into each other to form a disulfide bond. There is a plug at the end of each thin tube and two sockets, which can be inserted into two rotation directions, and the two sockets are spaced 86.4° from the plug, and the two bonds of the S atom have a bond angle of 104°. It can ensure that the S-C bonds on both sides are in a vertical relationship with each other. As shown in Figure 26.

Example 6 Assembling and Displaying the Rotation Angle of the Peptide Plane Using Base Module 1 and Base Module 2

角和ψ角。将两个相邻的肽单位从氨基(N)末端到羧基(C)末端，从第一个α-碳原子开始将肽链上的原子编为Cα1-C1-N1-Cα2-C2-N2，这些原子属于肽链的主链骨架原子。当Cα2-C2键与C1-N1键呈顺式结构时，

反式结构时

沿N1-Cα2键轴从Cα2端观察，键以顺时针旋转时

增大，以逆时针旋转时

减小。当N1-Cα2键与C2-N2键呈顺式时ψ＝0°，反式时ψ＝±180°；沿Cα2-C2键轴从Cα2端观察，键以顺时针旋转ψ增大，逆时针旋转ψ减小。Using the disk protractor equipped in the model of the present invention, the adjacent peptide planes can be displayed.

angle and ψ angle. Two adjacent peptide units from the amino (N) terminus to the carboxyl (C) terminus, coding the atoms on the peptide chain as Cα1-C1-N1-Cα2-C2-N2 starting from the first α-carbon atom, These atoms belong to the backbone atoms of the peptide chain. When the Cα2-C2 bond is in a cis structure with the C1-N1 bond,

in trans

Viewed from the Cα2 end along the N1-Cα2 bond axis, when the bond rotates clockwise

increase, when rotated counterclockwise

decrease. When the N1-Cα2 bond and the C2-N2 bond are in cis form, ψ=0°, and in trans form, ψ=±180°; when viewed from the Cα2 end along the Cα2-C2 bond axis, the bond rotates clockwise to increase ψ, and counterclockwise Rotation ψ decreases.

A method for assembling and displaying the rotation angle of the peptide plane using one base module 1 and two base modules 2:

(1) Insert the long tube marked -NH in the first basic module 2 into the upper right corner hole of the basic module 1;

(2) Insert the long tube marked -CO in the second basic module 2 into the hole in the lower left corner of the basic module 1.

表示Cα-N单键的旋转角；基本模块1的板平面左下角三角标记尖端对应第二个基本模块2上-CO端的量角器的角度即为ψ，表示Cα-C单键的旋转角。The tip of the triangle mark in the upper right corner of the board plane of the basic module 1 corresponds to the angle of the protractor on the -NH end of the first basic module 2, which is

Represents the rotation angle of the Cα-N single bond; the angle of the triangle mark in the lower left corner of the board plane of the basic module 1 corresponds to the angle of the protractor at the -CO end of the second basic module 2, which is ψ, which represents the rotation angle of the Cα-C single bond.

Looking from the Cα structure to the peptide plane, the clockwise rotation of the plane is positive, and the counterclockwise is negative, and the scale corresponding to the intersection of the peptide plane and the protractor can be viewed from a specific angle.

ψ＝0°时，如图27所示。when

When ψ=0°, as shown in Figure 27.

和ψ二面角的测量Example 7 Assembling and displaying using basic module 1 and basic module 2

and ψ dihedral angle measurement

A method for assembling and displaying the rotation angle of the peptide plane using two basic modules 1 and one basic module 2:

(1) Insert the long tube marked -NH in the basic module 2 into the upper right corner hole of the first basic module 1;

(2) Insert the long tube marked -CO in basic module 2 into the hole in the lower left corner of the second basic module 1.

时，如果其两端的N-C与Cα-C共面且在其同侧(顺式)，则此时

为0°，从α碳原子向N望去，顺时针旋转为正角度，逆时针为负值。同理可知ψ的定义方式。当旋转基本模块1时，其插管端口处的边将贴着量角器盘面旋转，从前文所述0°位置开始，顺时针为正逆时针为负，该边对应的刻度即为旋转角。First of all, it is necessary to clarify the definition of 0°, which is shown in Figure 28. When determining the rotation angle of Cα-N

, if the NCs at both ends are coplanar with Cα-C and on the same side (cis), then

is 0°, looking from the α carbon atom to N, the clockwise rotation is a positive angle, and the counterclockwise is a negative value. Similarly, we can know how ψ is defined. When the basic module 1 is rotated, the edge at the intubation port will rotate against the protractor disk. Starting from the 0° position mentioned above, clockwise is positive and counterclockwise is negative, and the scale corresponding to this edge is the rotation angle.

ψ＝-57°时，如图29所示。when

When ψ=-57°, as shown in Figure 29.

Example 8 Assembly and Display of Protein Secondary Structure Alpha Helix and Beta Sheet Using Basic Module 1, Basic Module 2 and Hydrogen Bonding Modules

Pauling and Corey proposed that α-helix and β-pleated sheet are the main forms of protein secondary structure based on experimental data.

1. The secondary structure of the protein α helix

角为-47°，ψ角为-57°，氨基酸的侧链R基团伸向螺旋的外侧。每3.6个氨基酸残基螺旋式上升一圈(即旋转360°)，螺距为0.54nm。α螺旋的每个肽键的N-H和第四个肽键的羰基氧形成氢键，氢键的方向和螺旋长轴基本平行。肽链中的所有肽键中的全部羰基氧都可以形成氢键，以稳固α螺旋结构。In the α helix structure, the main chain of the polypeptide chain spirals up around the central axis. According to the direction of the peptide chain from the amino terminus (N terminus) to the carboxyl terminus (C terminus), the direction of the helix belongs to a clockwise right-hand helix.

The angle is -47°, the ψ angle is -57°, and the side chain R group of the amino acid extends to the outside of the helix. Every 3.6 amino acid residues spirals up one turn (ie, rotates 360°), and the pitch is 0.54 nm. The NH of each peptide bond of the α-helix forms a hydrogen bond with the carbonyl oxygen of the fourth peptide bond, and the direction of the hydrogen bond is substantially parallel to the long axis of the helix. All carbonyl oxygens in all peptide bonds in a peptide chain can form hydrogen bonds to stabilize the alpha helix structure.

A method for assembling and displaying the secondary structure alpha helix of a protein using multiple base modules 1, multiple base modules 2 and multiple hydrogen bond modules:

(1) Insert a long tube marked -NH in a basic module 2 into the upper right corner hole of a basic module 1;

(2) Insert the long tube marked -CO in one basic module 2 into the lower left corner hole of another basic module 1;

角为-47°，ψ角为-57°(如图29所示)；(3) Adjustment

The angle is -47°, and the ψ angle is -57° (as shown in Figure 29);

(4) repeat steps (1) to (3), continue to extend;

(5) Insert a hydrogen bond module between the circular hole on the H atom mark in each basic module 1 and the round hole on the O atom mark in the fourth basic module 1 from it to stabilize α Spiral structure.

2, the secondary structure of protein β-sheet

The β-fold is origami-like, and the polypeptide chain is fully extended. Each peptide plane (peptide unit) takes Cα as the rotation point, and folds in turn in a zigzag structure. The side chains of amino acid residues are alternately located above and below the zigzag structure. The zigzag structure of several peptide segments can be arranged in parallel, and the two peptide segments that are far apart in the molecule can form the same direction by folding, or they can form the opposite direction by folding back.

A method for assembling and displaying the secondary structure β-sheet of a protein using multiple base modules 1, multiple base modules 2 and multiple hydrogen bond modules:

(1) Insert a long tube marked -NH in a basic module 2 into the upper right corner hole of a basic module 1;

(2) Insert the long tube marked -CO in one basic module 2 into the lower left corner hole of another basic module 1;

角为-140°，ψ角为130°；(3) Adjustment

The angle is -140°, and the ψ angle is 130°;

(4) repeat steps (1) to (3), continue to extend;

(5) Insert a hydrogen bond module between the circular hole on the H atom mark in each basic module 1 and the circular hole on the H atom mark in the adjacent basic module 1 to demonstrate the hydrogen bond pair stable β The role of the folded structure.

Claims (10)

1. A model of a spatial structure of a modularly assembled peptide chain, said model comprising a plurality of base modules 1 and a plurality of base modules 2, wherein:

the main body of the basic module 1 is a plate, the position of the center of the plate, which is towards the left, is provided with a C atom mark, the position of the center of the plate, which is towards the right, is provided with a N atom mark, the position of the upper left corner of the plate is provided with an O atom mark, and the position of the lower right corner of the plate is provided with an H atom mark; a single bond mark is arranged between the C atom mark and the N atom mark, a double bond mark is arranged between the C atom mark and the O atom mark, a single bond mark is arranged between the N atom mark and the H atom mark, a single bond mark and a triangular mark are arranged at the left lower corner of the C atom mark and the plate, and a single bond mark and a triangular mark are arranged at the right upper corner of the N atom mark and the plate; an imaginary line segment 1 is arranged at the center of the C atom mark and the center of the N atom mark, an imaginary line segment 2 is arranged at the center of the C atom mark and the center of the O atom mark, an imaginary line segment 3 is arranged at the center of the N atom mark and the center of the H atom mark, an imaginary line segment 4 is arranged at the center of the C atom mark and the lower left corner of the plate, and an imaginary line segment 5 is arranged at the center of the N atom mark and the upper right corner of the plate; the plate has two through holes on two imaginary straight lines of the imaginary line segment 4 and the imaginary line segment 5;

the main body of the basic module 2 is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein three pipes are long pipes, the other pipe is a short pipe, and the outer end of the short pipe is connected with a sphere; two long tubes of the three long tubes are respectively provided with a thin disc vertical to the length direction of the tubes, and a protractor is externally attached; when the long pipe without the thin disc is placed downwards and the short pipe connected with the sphere is placed upwards towards the right side, the long pipe with the thin disc in the front is provided with an-NH mark, the long pipe with the thin disc in the rear is provided with a-CO mark, and the long pipe without the thin disc is provided with an-R mark.

2. The model of claim 1, wherein:

in the base module 1, the length of the virtual line segment 1 is 5.28 length units, the length of the virtual line segment 2 is 4.92 length units, the length of the virtual line segment 3 is 4.04 length units, the length of the virtual line segment 4 is 6.12 length units, the length of the virtual line segment 5 is 5.88 length units, and the inner diameters of the two through holes are 1.6 length units; an included angle between the imaginary line segment 1 and the imaginary line segment 2 is 123.5 degrees, an included angle between the imaginary line segment 1 and the imaginary line segment 3 is 120 degrees, an included angle between the imaginary line segment 1 and the imaginary line segment 4 is 116 degrees, and an included angle between the imaginary line segment 1 and the imaginary line segment 5 is 122 degrees;

in the basic module 2, the outer diameters of four pipes are 1.6 length units, the included angle between a long pipe with a-NH mark and a long pipe with a-CO mark is 111 degrees, the included angle between a long pipe with a-R mark and a long pipe with a-NH mark is 110.6 degrees, the included angle between a long pipe with a-R mark and a long pipe with a-CO mark is 110.6 degrees, the included angles between a short pipe connecting a sphere and three long pipes are 108.2 degrees respectively, the lengths of the three long pipes are 5.6 length units, the long pipe with a-R mark is provided with annular marks at the positions 2.24-2.36 length units away from the center of the module, the length of one short pipe is 5 length units, the diameter of the sphere is 2.96 length units, the two thin disks are 3.5 length units away from the center of the module, and a 360-degree scale protractor is attached to the outside, and the 0-degree line of the long pipe is positioned on the plane formed by.

3. The model of claim 1, further comprising a plurality of base modules 3 and a plurality of base modules 4, wherein:

the basic module 3 and the basic module 4 are respectively a left half block and a right half block of the basic module 1, and the division positions are provided with inserting structures which can be inserted into each other.

4. The model of claim 1, further comprising a plurality of special modules 1, a plurality of special modules 2, and a plurality of special modules 3, wherein:

the main body of the special module 1 is a plate, the position of the center of the plate, which is deviated to the left, is provided with a C atom mark, the position of the center of the plate, which is deviated to the right, is provided with an N atom mark, and the position of the upper left corner of the plate is provided with an O atom mark; a single bond mark is arranged between the C atom mark and the N atom mark, a double bond mark is arranged between the C atom mark and the O atom mark, a single bond mark and a triangular mark are arranged at the left lower corner of the C atom mark and the plate, a single bond mark and a triangular mark are arranged at the right upper corner of the N atom mark and the plate, and a single bond mark is arranged between the N atom mark and the right lower corner of the plate; an imaginary line segment 1 is arranged at the center of the C atom mark and the center of the N atom mark, an imaginary line segment 2 is arranged at the center of the C atom mark and the center of the O atom mark, an imaginary line segment 3 is arranged at the center of the N atom mark and the lower right corner of the plate, an imaginary line segment 4 is arranged at the center of the C atom mark and the lower left corner of the plate, and an imaginary line segment 5 is arranged at the center of the N atom mark and the upper right corner of the plate; the plate has two through holes on two imaginary straight lines of the imaginary line segment 4 and the imaginary line segment 5; the plate has semi-through holes on the imaginary line segment 3;

the main body of the special module 2 is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein three pipes are long pipes, the other pipe is a short pipe, and the outer end of the short pipe is connected with a sphere; two long tubes of the three long tubes are respectively provided with a thin disc vertical to the length direction of the tubes, and a protractor is externally attached; when the long pipe without the thin disc is placed downwards and the short pipe connected with the sphere is placed upwards towards the right side, the long pipe with the thin disc in the front is provided with an-NH mark, the long pipe with the thin disc in the rear is provided with a-CO mark, and the long pipe without the thin disc is provided with an-R mark;

the main body of the special module 3 is four tubes which are emitted from the center and are mutually connected in a three-dimensional space, wherein one tube is long and thin, the other tube is short and thick, and the other two tubes are respectively connected with a sphere.

5. The model of claim 4, wherein:

in the special module 1, the length of the virtual line segment 1 is 5.28 length units, the length of the virtual line segment 2 is 4.96 length units, the length of the virtual line segment 3 is 2.90 length units, the length of the virtual line segment 4 is 2.62 length units, the length of the virtual line segment 5 is 2.42 length units, and the inner diameters of the two through holes and the one semi-through hole are 1.6 length units; an included angle between the imaginary line segment 1 and the imaginary line segment 2 is 121 °, an included angle between the imaginary line segment 1 and the imaginary line segment 3 is 124 °, an included angle between the imaginary line segment 1 and the imaginary line segment 4 is 118 °, and an included angle between the imaginary line segment 1 and the imaginary line segment 5 is 122 °;

in the special module 2, the outer diameters of four pipes are 1.6 length units, the lengths of three long pipes are 5.6 length units, the long pipe with the R mark is provided with an annular mark at a position 2.24-2.36 length units away from the center of the module, the length of a short pipe is 5 length units, the diameter of a sphere is 2.96 length units, two thin discs are 3.5 length units away from the center of the module, a 360-degree scale protractor is externally attached, and the 0-degree line of the protractor is positioned on a plane formed by intersecting central lines of the two long pipes; the included angle between the long tube with the-NH mark and the long tube with the-CO mark is 112.3 degrees, the included angle between the long tube with the-R mark and the long tube with the-CO mark is 111 degrees, the included angle between the long tube with the-NH mark and the long tube with the-R mark is 103 degrees, and the included angles between the short tube for connecting the ball body and the other three long tubes are 110.1 degrees;

in the special module 3, the outer diameter of the slender pipe is 1.6 length units, the length of the slender pipe is 5.6 length units, the annular mark is arranged at a position 2.24-2.36 length units away from the center of the module, the inner diameter of the short and thick pipe is 1.6 length units, the length of the short and thick pipe is 3.8 length units, the lengths of the other two pipes are 5 length units, and the diameters of the two spheres are 2.96 length units; the included angle of the two tubes not connected with the spheres is 104 degrees, the included angle of the two tubes connected with the spheres is 110.5 degrees, and the plane where the two tubes not connected with the spheres are located is perpendicular to the plane where the two tubes connected with the spheres are located.

6. The model according to claim 1, characterized in that it further comprises a plurality of special modules 4, wherein:

the main body of the special module 4 is four tubes which are emitted from the center and are mutually connected in a three-dimensional space; wherein two of the tubes are long tubes, the other two of the tubes are short tubes, and the outer ends of the two short tubes are respectively connected with the ball body; the two long pipes are respectively provided with a thin disc which is vertical to the length direction of the pipes, and a protractor is attached to the outside; one of the long tubes with the thin disks is provided with a-NH mark, and the other long tube with the thin disks is provided with a-CO mark.

7. The model of claim 6, wherein:

in the special module 4, the outer diameters of four pipes are all 1.6 length units, the included angle between the long pipe with the-CO mapping and the long pipe with the-NH mapping is 112.1 degrees, the included angles between the other pipes are 109 degrees, the lengths of the two long pipes are 5.6 length units, the lengths of the two short pipes are 5 length units, the diameter of the sphere is 2.96 length units, the distance between the two thin discs and the center of the module is 3.5 length units, the 360-degree scale protractor is externally attached, and the 0-degree line of the protractor is located on a plane formed by intersecting center lines of the two long pipes.

8. The model of claim 3, further comprising a plurality of special modules 5 and a plurality of special modules 6, wherein:

the main body of the special module 5 is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein one pipe is long and thin, the other pipe is short and thick, and the other two pipes are respectively connected with a sphere;

the special module 6 consists of two pipes which are emitted from the center and are connected with each other and a detachable sphere, wherein one pipe is a thick pipe, the other pipe is a thin pipe, and the thin pipe is connected with the detachable sphere;

preferably, in said special module 5, the four tubes are mutually inclined at an angle of 109 ° 28', the outer diameter of the elongated tube is 1.6 length units, the length is 5.6 length units, and there is a ring mark at a distance of 3.48 length units from the center of the module; the inner diameter of the short and thick tube is 1.6 length units, the length is 3.8 length units, the length of the other two tubes is 5 length units, and the diameter of the two spheres is 2.96 length units.

Preferably, in the special module 6, the included angle between the two tubes is 104 °, the length of the thin tube is 4.1 length units, the outer diameter is 1.6 length units, the tube is a solid tube, the end of the tube is provided with a plug with the diameter of 0.35 length unit and the length of 0.86 length unit, the center of the end of the tube is used as the center, the left side and the right side of the included angle of 86.4 ° with the plug are respectively provided with a jack matched with the plug, the length of the thick tube is 3.8 length units, the inner diameter is 1.6 length units, the diameter of the sphere is 2.96 length units, and the jacks matched with the plug are arranged.

9. The model according to claim 4, characterized in that it further comprises a plurality of special modules 7, wherein:

the special module 7 is a right half block of the special module 1, and a splicing structure which is the same as the basic module 4 and can be inserted into the basic module 3 is arranged at the splitting position.

10. A model according to any of claims 1-9, further comprising a hydrogen bonding module, said hydrogen bonding module being an elongated round stick; the centers of the O atom mark and the H atom mark in the basic module 1, the basic module 3, the basic module 4, the special module 1 or the special module 7 are also provided with circular jacks matched with the elongated round sticks;

preferably, the diameter of the slender round stick is 0.15 length units, and the length of the slender round stick is 6.5 length units; the diameter of the circular jack is 0.15 length units.

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