Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. (Q52027903)

20 April 2018

title

Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. (English)

1 reference

20 April 2018

2

Martin Karplus

1 reference

20 April 2018

Olivier Michielin

1

1 reference

20 April 2018

language of work or name

English

0 references

publication date

1 November 2002

1 reference

20 April 2018

Journal of Molecular Biology

published in

1 reference

20 April 2018

volume

324

1 reference

20 April 2018

issue

3

1 reference

20 April 2018

page(s)

547-569

1 reference

20 April 2018

Optimal activation of tumor-reactive T cells by selected antigenic peptide analogues.

cites work

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Induction of potent antitumor CTL responses by recombinant vaccinia encoding a melan-A peptide analogue

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Crystal structure of the beta chain of a T cell antigen receptor

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Crystal structure of the V alpha domain of a T cell antigen receptor

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Atomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Structure of the complex between human T-cell receptor, viral peptide and HLA-A2

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

T cell recognition of hapten. Anatomy of T cell receptor binding of a H-2kd-associated photoreactive peptide derivative.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Alanine scanning mutagenesis of an alphabeta T cell receptor: mapping the energy of antigen recognition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Modeling of the TCR-MHC-peptide complex

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Calculation of the relative change in binding free energy of a protein-inhibitor complex

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

23 Theoretical calculations of relative affinities of binding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Simulation analysis of the stability mutant R96H of T4 lysozyme.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Conversion of a T cell antagonist into an agonist by repairing a defect in the TCR/peptide/MHC interface: implications for TCR signaling.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

All-atom empirical potential for molecular modeling and dynamics studies of proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Decomposition of the Free Energy of a System in Terms of Specific Interactions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Free energy simulations: the meaning of the individual contributions from a component analysis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Structural response to mutation at a protein-protein interface

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Ex vivo staining of metastatic lymph nodes by class I major histocompatibility complex tetramers reveals high numbers of antigen-experienced tumor-specific cytolytic T lymphocytes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

Grafting primary human T lymphocytes with cancer-specific chimeric single chain and two chain TCR.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

MOLMOL: a program for display and analysis of macromolecular structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900880-X

10.1016/S0022-2836(02)00880-X

7 January 2021

Identifiers

DOI

1 reference

20 April 2018

PubMed ID

12445788

1 reference

20 April 2018