(Q30333153)

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Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

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Europe PubMed Central

PubMed publication ID

18 June 2017

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (English)

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Europe PubMed Central

PubMed publication ID

18 June 2017

author name string

Holger Gohlke

1

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Europe PubMed Central

PubMed publication ID

18 June 2017

Christina Kiel

2

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Europe PubMed Central

PubMed publication ID

18 June 2017

David A Case

3

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Europe PubMed Central

PubMed publication ID

18 June 2017

language of work or name

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publication date

1 July 2003

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Europe PubMed Central

PubMed publication ID

18 June 2017

Journal of Molecular Biology

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Europe PubMed Central

PubMed publication ID

18 June 2017

330

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Europe PubMed Central

PubMed publication ID

18 June 2017

4

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Europe PubMed Central

PubMed publication ID

18 June 2017

891-913

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

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Selective inhibition of Ras interaction with its particular effector by synthetic peptides corresponding to the Ras effector region

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Anatomy of hot spots in protein interfaces

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Mini-review: computational structure-based design of inhibitors that target protein surfaces

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Principles of protein-protein interactions

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Interactions of protein antigens with antibodies

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Stability of macromolecular complexes

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Dominant forces in protein folding

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Conservation of polar residues as hot spots at protein interfaces

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Comparison of a structural and a functional epitope

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Rational design of faster associating and tighter binding protein complexes.

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Unraveling hot spots in binding interfaces: progress and challenges

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Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

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The GTPase superfamily: conserved structure and molecular mechanism

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How Ras-related proteins talk to their effectors

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Regulation of Ras-mediated signalling: more than one way to skin a cat.

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Mammalian Ras interacts directly with the serine/threonine kinase Raf

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Increasing complexity of Ras signaling.

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Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface

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Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation

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Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis

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Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins

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Structural and biochemical analysis of Ras-effector signaling via RalGDS

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Structural basis for the interaction of Ras with RalGDS

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The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue

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Ras/Rap effector specificity determined by charge reversal

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Transient Kinetic Studies on the Interaction of Ras and the Ras-Binding Domain of c-Raf-1 Reveal Rapid Equilibration of the Complex†

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Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP.

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Interactions between Ras proteins and their effectors

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Purification of a Ras-dependent mitogen-activated protein kinase kinase kinase from bovine brain cytosol and its identification as a complex of B-Raf and 14-3-3 proteins

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Regulation of the Raf kinase by phosphorylation

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Thermodynamics of Ras/effector and Cdc42/effector interactions probed by isothermal titration calorimetry

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Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations.

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Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding

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Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction

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2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.

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Three-dimensional structure of the Ras-interacting domain of RalGDS

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Free energy decomposition of protein-protein interactions.

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Empirical scale of side-chain conformational entropy in protein folding

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Quantitative analysis of the complex between p21ras and the Ras-binding domain of the human Raf-1 protein kinase

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Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

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Protein folding intermediates: native-state hydrogen exchange

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Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors.

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Observation of signal transduction in three-dimensional domain swapping

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Can allosteric regulation be predicted from structure?

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Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble

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Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: general thermodynamic models and data for the binding of nucleotides to ribonuclease A.

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Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies.

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Identifiers

10.1016/S0022-2836(03)00610-7

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

ResearchGate publication ID

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