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Keywords: Molecular Dynamics
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Articles
Biochem Soc Trans (2023) BST20220782.
Published: 16 January 2023
... 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...
Articles
Biochem Soc Trans (2022) 50 (1): 569–581.
Published: 25 February 2022
...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...
Articles
Biochem Soc Trans (2022) 50 (1): 541–554.
Published: 07 February 2022
... ] and interactions with alignment media in samples for RDC experiments [ 60 ]. One must choose a computational method to sample or generate protein conformations. A common approach is to use molecular dynamics (MD) or Monte Carlo (MC) simulations [ 61–63 ], where conformations are sampled based on the energy...
Articles
Biochem Soc Trans (2021) 49 (6): 2527–2537.
Published: 16 November 2021
...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...
Includes: Supplementary data
Articles
Biochem Soc Trans (2021) 49 (1): 415–429.
Published: 05 February 2021
... 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...
Articles
Biochem Soc Trans (2020) 48 (4): 1447–1461.
Published: 14 August 2020
... 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...
Articles
Biochem Soc Trans (2020) 48 (4): 1707–1724.
Published: 05 August 2020
... 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...
Articles
Biochem Soc Trans (2020) 48 (1): 25–37.
Published: 24 December 2019
... molecular dynamics simulation Biological membranes are formed from a bilayer containing different species of lipid, into which integral transmembrane proteins are inserted, whilst peripheral membrane proteins are bound to the surface. These membrane proteins play key roles in cell function via...
Articles
Biochem Soc Trans (2019) 47 (3): 909–918.
Published: 13 May 2019
... 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...
Articles
Biochem Soc Trans (2015) 43 (5): 952–958.
Published: 09 October 2015
... selected and finally illustrate how MD simulations can be used as a means to give more confidence about models that have been generated via this approach. ATP-binding cassette (ABC) transporters computational export pump molecular dynamics multi-drug resistance simulation Though more X-ray...
Includes: Supplementary data
Articles
Biochem Soc Trans (2015) 43 (2): 151–156.
Published: 07 April 2015
... 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...
Articles
Biochem Soc Trans (2015) 43 (2): 269–274.
Published: 07 April 2015
... combined with the computational modelling to establish a complete structure for human Parkin at an all-atom resolution [ 30 ]. In combination with additional molecular dynamics simulations (MDSs), a conformational pathway of Parkin activation could be developed. Thereby, PINK1-dependent phosphorylation...
Articles
Biochem Soc Trans (2013) 41 (2): 620–624.
Published: 21 March 2013
..., 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...
Articles
Biochem Soc Trans (2013) 41 (1): 205–212.
Published: 29 January 2013
..., 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...
Articles
Biochem Soc Trans (2011) 39 (1): 31–35.
Published: 19 January 2011
... 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...
Articles
Biochem Soc Trans (2008) 36 (1): 55–58.
Published: 22 January 2008
... as composites from an ensemble of receptor conformations. A more simple approach is to use soft docking, where the ligand is allowed to penetrate into the protein surface to some extent [ 11 ]. The use of Molecular Dynamics simulations is a better method to explore receptor flexibility. However, incorporation...
Articles
Biochem Soc Trans (2008) 36 (1): 27–32.
Published: 22 January 2008
... 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...
Articles
Biochem Soc Trans (2008) 36 (1): 11–15.
Published: 22 January 2008
... 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...
Articles
Biochem Soc Trans (2007) 35 (6): 1515–1518.
Published: 23 November 2007
... 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...
Includes: Supplementary data
Articles
Biochem Soc Trans (2007) 35 (6): 1551–1557.
Published: 23 November 2007
... (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...
Articles
Biochem Soc Trans (2005) 33 (5): 1012–1015.
Published: 26 October 2005
.... With the quantitative information on transmembrane-helix integration offered by the experiments described above, a natural next step is to see whether a more detailed understanding might be arrived at through molecular dynamics simulations of bilayer-embedded transmembrane helices. As a first step in this direction, we...
Articles
Biochem Soc Trans (2005) 33 (1): 80–82.
Published: 01 February 2005
... 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...
Articles
Biochem Soc Trans (2004) 32 (1): 28–32.
Published: 01 February 2004
... 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...