A study on the structural features of SELK, an over-expressed protein in hepatocellular carcinoma, by molecular dynamics simulations in a lipid–water system

2016 ◽  
Vol 12 (10) ◽  
pp. 3209-3222 ◽  
Author(s):  
Andrea Polo ◽  
Stefano Guariniello ◽  
Giovanni Colonna ◽  
Gennaro Ciliberto ◽  
Susan Costantini
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Dynamics ◽  
Water System ◽  
Structural Features ◽  
System P ◽  
Dynamics Simulations

Terminal regions in SELK present different conformational dynamics being coupled complicatedly through the membrane.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

Unraveling cGAS catalytic mechanism upon DNA activation through molecular dynamics simulations

2021 ◽  
Author(s):  
Jordi Soler ◽  
Pedro Paiva ◽  
Maria Joao Joao Ramos ◽  
Pedro Alexandrino Fernandes ◽  
Marie Brut
Keyword(s):  
Molecular Dynamics ◽  
Dna Binding ◽  
Molecular Dynamics Simulations ◽  
Cyclic Gmp ◽  
Catalytic Mechanism ◽  
System P ◽  
Dynamics Simulations ◽  
Cyclic Dinucleotide

Cyclic GMP-AMP Synthase (cGAS) is activated upon DNA binding and catalyzes the synthesis of 2’,3’-cGAMP from GTP and ATP. This cyclic dinucleotide is a messenger that triggers the autoimmune system...

Cluster, Surface and Bulk Properties of ZnCd Binary Alloys: Molecular-Dynamics Simulations

2005 ◽  
Vol 502 ◽  
pp. 51-56 ◽  
Author(s):  
Sakir Erkoc
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Structural Features ◽  
Bulk Materials ◽  
Bulk Properties ◽  
Atom Clusters ◽  
Dynamics Simulations ◽  
Mixed Clusters ◽  
Stable Structures

The structural and electronic properties of isolated neutral ZnmCdn clusters for m+n £ 3 have been investigated by performing density functional theory calculations at B3LYP level. The optimum geometries, vibrational frequencies, electronic structures, and the possible dissosiation channels of the clusters considered have been obtained. An empirical many-body potential energy function (PEF), which comprices two- and three-body atomic interactions, has been developed to investigate the structural features and energetics of ZnmCdn (m+n=3,4) microclusters. The most stable structures were found to be triangular for the three-atom clusters and tetrahedral for the four-atom clusters. On the other hand, the structural features and energetics of Znn-mCdm (n=7,8) microclusters, and Zn50, Cd50, Zn25Cd25, Zn12Cd38, and Zn38Cd12 nanoparticles have been investigated by performing molecular-dynamics computer simulations using the developed PEF. The most stable structures were found to be compact and three-dimensional for all elemental and mixed clusters. An interesting structural feature of the mixed clusters is that Zn and Cd atoms do not mix in mixed clusters, they come together almost without mixing. Surface and bulk properties of Zn, Cd, and ZnCd systems have been investigated too by performing molecular-dynamics simulations using the developed PEF. Surface reconstruction and multilayer relaxation on clean surfaces, adatom on surface, substitutional atom on surface and bulk materials, and vacancy on surface and bulk materials have been studied extensively.

Thermal boundary conductance between Al films and GaN nanowires investigated with molecular dynamics

2014 ◽  
Vol 16 (20) ◽  
pp. 9403-9410 ◽  
Author(s):  
Xiao-wang Zhou ◽  
Reese E. Jones ◽  
Patrick E. Hopkins ◽  
Thomas E. Beechem
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermal Transport ◽  
Thermal Boundary Conductance ◽  
Gan Nanowires ◽  
System P ◽  
Dynamics Simulations ◽  
Important System

Using molecular dynamics simulations, we studied the thermal boundary conductance between GaN nanowires and Al films and showed how it may be possible to enhance interfacial thermal transport in this important system.

scholarly journals Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3261
Author(s):  
Sousa ◽  
Laurent ◽  
Quéméner ◽  
Mortier ◽  
Questel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Features ◽  
Cellular Functions ◽  
Α Subunit ◽  
X Ray Crystallography ◽  
Receptor Complexes ◽  
Protein Interfaces ◽  
Dynamics Simulations ◽  
Comparison Of The Results

Interleukin 15 (IL-15), a four-helix bundle cytokine, is involved in a plethora of different cellular functions and, particularly, plays a key role in the development and activation of immune responses. IL-15 forms receptor complexes by binding with IL-2Rβ- and common γ(γc)-signaling subunits, which are shared with other members of the cytokines family (IL-2 for IL-2Rβ- and all other γc- cytokines for γc). The specificity of IL-15 is brought by the non-signaling α-subunit, IL-15Rα. Here we present the results of molecular dynamics simulations carried out on four relevant forms of IL-15: its monomer, IL-15 interacting individually with IL-15Rα (IL-15/IL-15Rα), with IL-2Rβ/γc subunits (IL-15/IL-2Rβ/γc) or with its three receptors simultaneously (IL-15/IL-15Rα/IL-2Rβ/γc). Through the analyses of the various trajectories, new insights on the structural features of the interfaces are highlighted, according to the considered form. The comparison of the results with the experimental data, available from X-ray crystallography, allows, in particular, the rationalization of the importance of IL-15 key residues (e.g. Asp8, Lys10, Glu64). Furthermore, the pivotal role of water molecules in the stabilization of the various protein-protein interfaces and their H-bonds networks are underlined for each of the considered complexes.

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.

scholarly journals Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

2014 ◽  
Vol 111 (50) ◽  
pp. 17887-17892 ◽  
Author(s):  
Michael E. Wall ◽  
Andrew H. Van Benschoten ◽  
Nicholas K. Sauter ◽  
Paul D. Adams ◽  
James S. Fraser ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Dynamics ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering
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