... histocompatibility complex molecular dynamics peptide loading complex Activation of the T-cell mediated adaptive arm of the immune system relies upon transport of potential antigens within our cells to the cell surface. It is a longstanding challenge of the field to generate predictive models...

...John W. Vant; Daipayan Sarkar; Jonathan Nguyen; Alexander T. Baker; Josh V. Vermaas; Abhishek Singharoy Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology...

... will be on principles and examples, and this review is, therefore, best suited for readers who are looking for a brief, conceptual overview of the field. For a more technical introduction, we refer the reader to previous literature [ 2 , 3 ]. conformational ensemble molecular dynamics protein structure...

...Alzbeta Tuerkova; Peter M. Kasson The protein–membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become...

... 2021 15 1 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 allosteric regulation computational biochemistry molecular dynamics Aromatic amino acids phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) are important...

... all-atom molecular dynamics to mean-field theories. We discuss the advantage and limit of each modeling technique, and summarize the theoretical insights that, despite certain controversy, deepened our understanding of the hairy pore. Correspondence: Igal Szleifer ( igalsz@northwestern.edu...

... simulation techniques such as molecular dynamics simulations allow characterisation of the metastable conformational states and the transitions between them, and thus free energy landscapes, to be characterised, the barriers between states can be high, precluding efficient sampling without substantial...

... site on a protein will help to indicate how likely such an interaction is to occur within a native cell membrane, rather than e.g. in a detergent-solubilised experimental environment. free energy lipid membrane protein molecular dynamics simulation Biological membranes are formed from...

... of neuroactive drugs comes from computer simulation methods and, in particular, from molecular dynamics (MD). This provides insight into structure–function relationship of a target and predicts structure, dynamics and energetics of ligand/target complexes under biologically relevant conditions like temperature...

...-binding domains by the linker, using molecular dynamics Mol. Inform. 2013 32 529 540 10.1002/minf.201200175 18 Moradi M. Tajkhorshid E. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution Proc. Natl. Acad. Sci. U.S.A. 2013 110 18916...

... drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand–protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events...

... conducted using phospho–Ser 65 (pSer 65 ) and Ser 65 to study the motion of the auto-inhibited structure that leads to an active conformation of the E3 enzyme. The molecular motion required for release of the auto-inhibitory structure was furthered using accelerated molecular dynamics and sampling...

..., I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations...

..., accomplished through the use of MD (molecular dynamics) simulations. Our pipeline for the MD simulations of GPCRs, implemented in the web service http://gpcr.usc.es , is updated in the present paper and illustrated by recent applications. Special emphasis is put on the A 2A adenosine receptor, one...

... C (bridge–helix C-terminal hinge) cause a substantial increase in specific activity (‘superactivity’). Fully atomistic molecular dynamics simulations show that kinking of the BH-H C appears to be driven by cation–π interactions and involve amino acid side chains that are exceptionally highly...

... Molecular Dynamics molecular recognition protein flexibility quantitative structure–activity relationship structure-based drug design GSK3 (glycogen synthase kinase 3), also known as TPK I (tau protein kinase I), is a serine/threonine protein kinase encoded by two isoforms in humans, termed...

... bilayer based on coarse-grained Molecular Dynamics simulations is described. This method has been used to develop a database of CG simulations (coarse-grained simulations) of membrane proteins ( http://sbcb.bioch.ox.ac.uk/cgdb ). Comparison of CG simulations and AT simulations (atomistic simulations...

... Studies: A Biochemical Society Focused Meeting in conjunction with the Molecular Graphics and Modelling Society held at Manchester Interdisciplinary Biocentre, Manchester, U.K., 10–11 September 2007. Organized and Edited by Mike Sutcliffe (Manchester, U.K.). MD Molecular Dynamics...

... modelling with energy minimization and Molecular Dynamics simulation in order to address these interesting biological phenomena from a structural angle. Thus three-dimensional models of human and mouse TLR3 and TLR4 domains were successfully generated. Apart from providing a structural framework in which...

... (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp 62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly...

.... 1 To whom correspondence should be addressed (email gunnar@dbb.su.se ). 21 7 2005 hydrophobicity scale membrane protein molecular dynamics protein–lipid interactions transmembrane The exposed surface of integral membrane proteins generally seems to reflect quite...

... from inactivation. To elucidate the role of protein structure in O 2 inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O 2 and H 2 diffusion in CpI ([Fe]-hydrogenase I from Clostridium...

... active than the parent peptide. We will also report on our progress towards understanding the dynamic character of compstatin using molecular dynamics simulations. The identification of an ensemble of interconverting conformers of compstatin with variable populations is a first step towards...