Semiclassical studies of bound states and molecular dynamics

2006 ◽  
pp. 283-292 ◽  
Author(s):  
R. A. Marcus ◽  
D. W. Noid ◽  
M. L. Koszykowski
Keyword(s):  
Molecular Dynamics ◽  
Bound States

scholarly journals Solution structures of the fibronectin-like Leishmania gp63 SRYD-containing sequence in the free and antibody-bound states . Transferred NOE and molecular dynamics studies

1998 ◽  
Vol 253 (1) ◽  
pp. 184-193 ◽  
Author(s):  
Marie-Christine Petit ◽  
Piotr Orlewski ◽  
Vassilios Tsikaris ◽  
Maria Sakarellos-Daitsiotis ◽  
Constantinos Sakarellos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Bound States ◽  
Solution Structures ◽  
Transferred Noe

scholarly journals Molecular dynamics simulations reveal distinct differences in conformational dynamics and thermodynamics between the unliganded and CD4-bound states of HIV-1 gp120

2020 ◽  
Vol 22 (10) ◽  
pp. 5548-5560
Author(s):  
Yi Li ◽  
Lei Deng ◽  
Jing Liang ◽  
Guang-Heng Dong ◽  
Yuan-Ling Xia ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bound States ◽  
Conformational Dynamics ◽  
Immunological Properties ◽  
Dynamics Simulations ◽  
Hiv Gp120 ◽  
Hiv 1

Large changes in dynamics and thermodynamics of gp120 upon CD4 binding account for the functional and immunological properties of HIV/gp120.

Antigen exposure leads to rigidification of germline antibody combining site

2014 ◽  
Vol 12 (03) ◽  
pp. 1450006 ◽  
Author(s):  
Jasmita Gill ◽  
Praapti Jayaswal ◽  
Dinakar M. Salunke
Keyword(s):  
Molecular Dynamics ◽  
Immune Complexes ◽  
Structural State ◽  
Bound States ◽  
Mechanistic Model ◽  
Conformational Transitions ◽  
Affinity Maturation ◽  
Antigen Binding ◽  
Dynamics Simulations ◽  
Antigen Release

Immune complexes involving diverse antigens and corresponding antibodies were analyzed for mapping conformational transitions of an antibody before antigen binding, upon antigen binding and after antigen release. Molecular dynamics simulations of the two comprehensive datasets consisting of the antigen-free and antigen-bound structures of the germline antibodies 36-65 and BBE6.12H3 provided mechanistic model of antigen encounter by primary antibodies. While native germline antibodies exhibit substantial mobility in the antigen-combining sites, their antigen-bound states exhibit relatively rigid conformations, even in the absence of the antigen suggesting preservation of the structural state after antigen release. It is proposed that acquired rigidity by a germline antibody upon antigen binding may be the first step in affinity maturation in favor of that antigen.

Molecular dynamics simulations of the resting and hydrogen peroxide-bound states of cytochrome c peroxidase

Biochemistry ◽  
1992 ◽  
Vol 31 (45) ◽  
pp. 11166-11174 ◽  
Author(s):  
J. R. Collins ◽  
P. Du ◽  
G. H. Loew
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Peroxide ◽  
Cytochrome C ◽  
Molecular Dynamics Simulations ◽  
Bound States ◽  
Cytochrome C Peroxidase ◽  
Dynamics Simulations

scholarly journals Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 720 ◽  
Author(s):  
Rudolf Karch ◽  
Claudia Stocsits ◽  
Nevena Ilieva ◽  
Wolfgang Schreiner
Keyword(s):  
Molecular Dynamics ◽  
T Cell ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Bound States ◽  
Cell Receptor ◽  
Dynamics Simulation ◽  
Antigenic Peptides ◽  
Major Histocompatibility Complexes ◽  
Unbound States

The interaction of antigenic peptides (p) and major histocompatibility complexes (pMHC) with T-cell receptors (TCR) is one of the most important steps during the immune response. Here we present a molecular dynamics simulation study of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex to monitor differences in relative orientations and movements of domains between bound and unbound states of TCR-pMHC. We generated local coordinate systems for MHC α1- and MHC α2-helices and the variable T-cell receptor regions TCR Vα and TCR Vβ and monitored changes in the distances and mutual orientations of these domains. In comparison to unbound states, we found decreased inter-domain movements in the simulations of bound states. Moreover, increased conformational flexibility was observed for the MHC α2-helix, the peptide, and for the complementary determining regions of the TCR in TCR-unbound states as compared to TCR-bound states.

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