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Keywords: molecular dynamics
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Articles
Biochem J (2021) BCJ20210104.
Published: 26 April 2021
... combined remediation technique in PCB-contaminated soils. The present study first used a combination of molecular docking and molecular dynamics methods to calculate the effects of the plant absorption enzyme, plant degradation enzyme, and microbial mineralization enzyme on the PCBs in the soil environment...
Articles
Biochem J (2021) 478 (3): 669–684.
Published: 12 February 2021
... computational approaches to determine whether pathogenic variants share changes in structure and function, and to understand how these changes might occur. Three pathogenic variants (G41S, Y48H, A51V) cause an increase in apoptosome activation and peroxidase activity. Molecular dynamics simulations of these...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (17): 3147–3165.
Published: 04 September 2020
... considering van der Waals interactions in molecular dynamics simulations revealed a structural difference for the N-terminal peptide, with the trans -state being more exposed to solvent and more mobile than the cis -state. Affinity for lactose or glycan-inhibitable neuroblastoma cell surface contact formation...
Includes: Supplementary data
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Biochem J (2020) 477 (15): 2791–2805.
Published: 07 August 2020
... donor substrate recognition than wildtype UGTs. Molecular dynamics simulations and deep learning analysis identified structural differences, which drive substrate preferences. The design of these UGTs with broader substrate specificity may play important role in biotechnological and industrial...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (2): 407–429.
Published: 30 January 2020
... open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY-NC-ND) . allostery HtrA3 activation HtrA3 mutants molecular dynamics PDZ serine protease domain These residues...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (23): 3649–3660.
Published: 10 December 2019
... exception of Asp205 that is absent from SsuA, but the thermodynamic parameters revealed a very high enthalpic penalty cost for binding of the other alkanesulfonates relative to taurine. Our molecular dynamic simulations indicated that the different levels of hydration of the binding site contributed to the...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (21): 3161–3182.
Published: 05 November 2019
... of nucleotides. Moreover, a structural model for mGBP7 is provided by homology modeling, which shows that the GTPase possesses an elongated C-terminal (CT) tail compared with the Caa X motif-containing mGBP2 and human GBP1. Molecular dynamics simulations indicate that this tail has transmembrane...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (16): 2411–2425.
Published: 30 August 2019
... 2019 9 8 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 deafness mechanotransduction molecular dynamics single-molecule force spectroscopy single-molecule FRET Mechanical force is transduced into an electrical signal...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (11): 1679–1694.
Published: 14 June 2019
... domains of SPAG1 in the recruitment of HSP chaperones by combining biochemical assays, ITC, NMR spectroscopy and molecular dynamics (MD) simulations. First, we propose that only two, out of the three TPR domains, are able to recruit the protein chaperones HSP70 and HSP90. We then focused on one of these...
Includes: Multimedia, Supplementary data
Articles
Biochem J (2019) 476 (6): 1021–1035.
Published: 29 March 2019
..., the remodeling effects of ADS-J1 on mature seminal fibrils were unexplored. Herein, we investigated the capacity of ADS-J1 to disassemble seminal fibrils and the potential mode of action by applying several biophysical and biochemical measurements, combined with molecular dynamic (MD) simulations. We...
Articles
Biochem J (2019) 476 (5): 889–907.
Published: 15 March 2019
... hIAPP. All-atom molecular dynamics simulation studies on full-length hIAPP pentamer with AZD suggested that AZD interacted with four possible binding sites in the amyloidogenic region of hIAPP. In summary, our results suggest AZD to be a promising candidate for combating T2DM and related amyloidogenic...
Includes: Supplementary data
Articles
Biochem J (2019) 476 (4): 719–732.
Published: 28 February 2019
... 2 2019 1 2 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 density functional theory enzyme kinetics enzyme–substrate interactions molecular dynamics thermodynamics translation factors Chiral discrimination of...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (23): 3813–3826.
Published: 06 December 2018
... recruitment, and downstream receptor-mediated ERK activation. Based on molecular dynamics simulations, we proposed a molecular mechanism for biased signaling of I109A mutant receptor. We postulate that due to the extra space created by I109A mutation, the phenyl group of the last residue (Phe-13) of apelin...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (21): 3377–3391.
Published: 09 November 2018
... fluorescence quenching experiments elucidated the binding affinities of the substrates to various domains. The molecular dynamics simulation of the modeled protein showed the presence of an unstructured region between the NTD and ABD that exhibited a large number of conformations over time, and further...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (20): 3221–3238.
Published: 23 October 2018
... that inhibited wild-type (WT) IDH1 were effective against R132Q. This suggests that patients with a R132Q mutation may have a poor response to mutant IDH1 therapies. Molecular dynamics simulations revealed that near the NADP + /NADPH-binding site in R132Q IDH1, a pair of α-helices switches between...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (10): 1701–1719.
Published: 18 May 2018
...-like structure with the increase in α-helical content was observed. The molecular dynamics simulation results illustrate distinct structural dynamics for different regions of SOD1 variants and show uniform local unfolding of β-strands. The strands protected by the zinc-binding and electrostatic loops...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (5): 905–921.
Published: 09 March 2018
... determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved...
Articles
Biochem J (2017) 474 (13): 2203–2217.
Published: 16 June 2017
... small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (6): 971–982.
Published: 07 March 2017
... rational design of a substrate-mimic, peptidic inhibitor of PRDM9 automethylation. The discovery of automethylation in PRDM9 adds a new dimension to our understanding of PRDM9 enzymology. automethylation histone methyltransferase molecular dynamics substrate-mimic inhibitor Automodification...
Includes: Multimedia, Supplementary data
Articles
Biochem J (2017) 474 (4): 539–556.
Published: 03 February 2017
... Creative Commons Attribution License 4.0 (CC BY) . Here, we report the crystal structure of the kindlin-3 PH domain together with molecular dynamics-based and biophysical characterisation of its inositol phosphate lipid-binding properties. We show that the kindlin-3 PH domain has a hydrogen bond-based...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (20): 3705–3724.
Published: 11 October 2016
.... Correspondence: Jacek Czub ( jacczub@pg.gda.pl ) * B.A. and M.W. contributed equally to this work. 16 6 2016 25 7 2016 16 8 2016 17 8 2016 © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2016 molecular dynamics osmolytes...
Includes: Supplementary data
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Biochem J (2016) 473 (14): 2097–2107.
Published: 12 July 2016
..., abolishing kinetic co-operativity in wild-type dh PPase, but restoring it in the variant dh PPase. A reverse serine-to-asparagine replacement restored kinetic co-operativity in eh PPase. Molecular dynamics simulations revealed that the asparagine substitution resulted in a change in the hydrogen-bonding...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (12): 1651–1662.
Published: 10 June 2016
... determine temporal complex structures in which the biomolecules are weakly interacting. Then an all-atom computer simulation such as molecular dynamics (MD) is a useful technique for quantifying those complex structures because the all-atom simulations can trace biomolecular motions at an atomic resolution...
Articles
Biochem J (2016) 473 (11): 1523–1536.
Published: 27 May 2016
...–nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison with the pancreatic RNase type, its structure includes lineage-specific features that facilitate...
Includes: Supplementary data
Articles
Biochem J (2015) 465 (1): 175–184.
Published: 12 December 2014
...-cholen-3-one being a pure antagonist in vitro and in vivo . Caenorhabditis elegans daf-9 mutant DAF-12 receptor dafachronic acid molecular dynamics Many biological processes, such as the mechanisms that govern developmental transitions, pathways that regulate lifespan and those...
Includes: Supplementary data
Articles
Biochem J (2012) 448 (3): 417–423.
Published: 21 November 2012
..., distribution and reproduction in any medium, provided the original work is properly cited. cancer epidermal growth factor receptor (EGFR) erlotinib gefitinib inhibitor molecular dynamics receptor tyrosine kinase (RTK) X-ray crystallography Activating mutations in the EGFR (epidermal growth...
Includes: Supplementary data
Articles
Biochem J (2011) 438 (3): 415–426.
Published: 26 August 2011
... computer simulation integrative biology molecular dynamics Parkinson's disease Amyloid-related diseases comprise a group of several dozen pathologies. The most common among the human amyloid-related diseases are AD (Alzheimer's disease), PD (Parkinson's disease) and T2DM (Type 2 diabetes...
Includes: Multimedia, Supplementary data
Articles
Biochem J (2011) 436 (2): 241–251.
Published: 13 May 2011
... elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of three members of the ErbB family (those with known kinase activity), namely EGFR, ErbB2 (HER2) and ErbB4 (HER4), in different...
Includes: Supplementary data
Articles
Biochem J (2011) 435 (3): 783–789.
Published: 13 April 2011
... interactions is highly unlikely. 1 To whom correspondence should be addressed (email roesch@unibt.de ). 13 10 2010 2 2 2011 23 2 2011 23 2 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 antitermination molecular dynamics NMR N-utilization...
Includes: Supplementary data
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Biochem J (2011) 435 (2): 391–399.
Published: 29 March 2011
... 2011 26 1 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 calcium-binding protein calsequestrin catecholaminergic polymorphic ventricular tachycardia (CPVT) metal ion molecular dynamics protein folding proteolysis Purified WT and mutants of CASQ2...
Includes: Supplementary data
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Biochem J (2007) 405 (2): 277–286.
Published: 27 June 2007
... model was refined using molecular dynamics calculations and validated by virtual screening methods, with an enrichment factor of 5. Furthermore, mutational analyses of Arg 106 , Glu 186 , Arg 268 , Arg 307 and Ala 313 confirmed the adequacy of our h P2Y 11 -R model and the computed ligand recognition...
Includes: Supplementary data
Articles
Biochem J (2005) 386 (3): 471–478.
Published: 08 March 2005
... flavonoid incorporation into cells. 1 To whom correspondences should be addressed (email pstrobel@bio.puc.cl ). 29 4 2004 27 9 2004 7 10 2004 7 10 2004 The Biochemical Society, London 2005 catechin-gallate flavonoid glucose transporter molecular dynamics...
Articles
Biochem J (2004) 382 (1): 293–305.
Published: 10 August 2004
... long-term molecular dynamics simulations in an explicit solvent; similar calculations were performed for the ATP-binding domain of Ca 2+ -ATPase. In both cases, we found large-scale motions that lead to significant changes of distances between several functionally important residues. The ATP docking...
Articles
Biochem J (2004) 378 (2): 421–433.
Published: 01 March 2004
... enzyme kinetic, X-ray crystallographic and molecular dynamics studies indicate that the effect of His 182 is due to interactions with Asp 181 and with Gln 262 . We conclude that residue 182 can modulate the functionality of both Asp 181 and Gln 262 and therefore affect the E- P hydrolysis step of PTP...
Articles
Biochem J (2003) 374 (1): 109–115.
Published: 15 August 2003
.... Molecular dynamics simulations of the polar head group of selected NAPEs reveal a substantially increased conformational variability as the N-acyl chain grows. This larger conformational space represents an increased impairment limiting the access of these molecules to the active site. Our data indicate...
Articles
Biochem J (2001) 360 (3): 539–548.
Published: 10 December 2001
...Allan M. TORRES; R. Manjunatha KINI; Nirthanan SELVANAYAGAM; Philip W. KUCHEL A high-resolution solution structure of bucandin, a neurotoxin from Malayan krait ( Bungarus candidus ), was determined by 1 H-NMR spectroscopy and molecular dynamics. The average backbone root-mean-square deviation for...
Includes: Supplementary data
Articles
Biochem J (2001) 359 (1): 65–75.
Published: 24 September 2001
... protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data. The Biochemical...
Articles
Biochem J (2001) 358 (1): 101–110.
Published: 08 August 2001
..., London ©2001 2001 essential dynamics herbicide detoxification molecular dynamics protein engineering Abbreviations used: CDNB, 1-chloro-2,4-dinitrobenzene; G-site, GSH binding site; GST, glutathione S-transferase; H-site, electrophile binding site; Ni-NTA, Ni 2+ -nitrilotriacetate...
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Biochem J (2000) 346 (1): 193–199.
Published: 08 February 2000
... correspondence should be addressed (e-mail b.giardina@;uniserv.ccr.rm.cnr.it). 26 7 1999 11 10 1999 18 11 1999 The Biochemical Society, London © 2000 2000 Hb variants α 1 β 1 interface molecular dynamics oxygen affinity Biochem. J. (2000) 346, 193 199 (Printed in Great Britain...
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Biochem J (1999) 344 (2): 585–592.
Published: 24 November 1999
... compared to wild type. This double substitution catalysed the phosphorolysis of adenosine with a K m of 42 μ M and a k cat / K m twice that of the single Asn-243-Asp substitution. Molecular dynamics simulation of the engineered proteins with adenine as substrate revealed favourable hydrogen bond distances...
Articles
Biochem J (1999) 343 (2): 361–369.
Published: 08 October 1999
... participation of water in the aging process. Molecular dynamics simulations performed on the active-site gorge of the wild-type DIP adduct showed that the isopropyl chain involved in aging was highly solvated, supporting the idea that water is important for stabilizing the transition state of the dealkylation...
Articles
Biochem J (1999) 339 (2): 309–317.
Published: 08 April 1999
... deleted. The mutants were constructed on the basis of molecular dynamic studies and the prediction of the structure of thioredoxin from B. acidocaldarius , performed by a comparative molecular modelling technique using Escherichia coli thioredoxin as the reference protein. The mutants obtained by PCR...