Skip Nav Destination
Close Modal
Update search
Filter
- Title
- Author
- Author Affiliations
- Full Text
- Abstract
- Keyword
- DOI
- ISSN
- EISSN
- Issue
- Volume
- References
Filter
- Title
- Author
- Author Affiliations
- Full Text
- Abstract
- Keyword
- DOI
- ISSN
- EISSN
- Issue
- Volume
- References
Filter
- Title
- Author
- Author Affiliations
- Full Text
- Abstract
- Keyword
- DOI
- ISSN
- EISSN
- Issue
- Volume
- References
Filter
- Title
- Author
- Author Affiliations
- Full Text
- Abstract
- Keyword
- DOI
- ISSN
- EISSN
- Issue
- Volume
- References
Filter
- Title
- Author
- Author Affiliations
- Full Text
- Abstract
- Keyword
- DOI
- ISSN
- EISSN
- Issue
- Volume
- References
Filter
- Title
- Author
- Author Affiliations
- Full Text
- Abstract
- Keyword
- DOI
- ISSN
- EISSN
- Issue
- Volume
- References
NARROW
Date
Availability
1-46 of 46
Keywords: molecular dynamics
Close
Follow your search
Access your saved searches in your account
Would you like to receive an alert when new items match your search?
Sort by
Articles
Jonathan Chevriau, Gerardo Zerbetto De Palma, Cintia Jozefkowicz, Victoria Vitali, Agustina Canessa Fortuna, Nicolas Ayub, Gabriela Soto, Gerd Patrick Bienert, Ari Zeida, Karina Alleva
Journal:
Biochemical Journal
Biochem J (2024) 481 (19): 1329–1347.
Published: 25 September 2024
... water (H 2 O) and H 2 O 2 . Employing a combination of unbiased and enhanced sampling molecular dynamics simulations, we investigated the key barriers and translocation mechanisms governing H 2 O 2 permeation through these AQP in both open and closed conformational states. Our findings reveal that both...
Includes: Supplementary data
Articles
In Collection
Cell signaling in the 21st century
Alexander C. Jones, Alexandr P. Kornev, Jui-Hung Weng, Gerard Manning, Susan S. Taylor, Alexandra C. Newton
Journal:
Biochemical Journal
Biochem J (2023) 480 (16): 1299–1316.
Published: 25 August 2023
..., the R42P mutant was stable and insensitive to activator-induced ubiquitination and down-regulation, an effect previously observed by deletion of the entire C1A domain. Molecular dynamics (MD) simulations and analysis of stable regions of the domain using local spatial pattern (LSP) alignment suggested...
Includes: Supplementary data
Articles
In Collection
Cell signaling in the 21st century
Eliza Störmer, Jui-Hung Weng, Jian Wu, Daniela Bertinetti, Pallavi Kaila Sharma, Wen Ma, Friedrich W. Herberg, Susan S. Taylor
Journal:
Biochemical Journal
Biochem J (2023) 480 (11): 815–833.
Published: 12 June 2023
.... Furthermore, we demonstrate that removing the NtDs leads to altered intramolecular regulation. To further investigate the crosstalk, we used Hydrogen–Deuterium exchange Mass Spectrometry (HDX-MS) to characterize the conformation of LRRK2 RCKW and Gaussian Accelerated Molecular Dynamics (GaMD) to create...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2022) 479 (8): 921–928.
Published: 29 April 2022
... ( [email protected] ) 17 12 2021 1 4 2022 6 4 2022 © 2022 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2022 MD molecular dynamics MESA molecular enhanced sampling with autoencoders QM/MM quantum mechanics/molecular...
Articles
Journal:
Biochemical Journal
Biochem J (2021) 478 (10): 1921–1941.
Published: 24 May 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
Matthias Fellner, Rinky Parakra, Kirstin O. McDonald, Itamar Kass, Guy N.L. Jameson, Sigurd M. Wilbanks, Elizabeth C. Ledgerwood
Journal:
Biochemical Journal
Biochem J (2021) 478 (3): 669–684.
Published: 12 February 2021
... 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 variants...
Includes: Supplementary data
Articles
Michelle C. Miller, Irina V. Nesmelova, Vladimir A. Daragan, Hans Ippel, Malwina Michalak, Aurelio Dregni, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H. Mayo
Journal:
Biochemical Journal
Biochem J (2020) 477 (17): 3147–3165.
Published: 04 September 2020
... and 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
Articles
Aishat Akere, Serena H. Chen, Xiaohan Liu, Yanger Chen, Sarath Chandra Dantu, Alessandro Pandini, Debsindhu Bhowmik, Shozeb Haider
Journal:
Biochemical Journal
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
Journal:
Biochemical Journal
Biochem J (2020) 477 (2): 407–429.
Published: 30 January 2020
...) . allostery HtrA3 activation HtrA3 mutants molecular dynamics PDZ serine protease domain Correspondence: Kakoli Bose ( [email protected] ) Reaction rates V 0 (mM/min) were determined by linear regression analysis corresponding to the maximum reaction rates for individual assay condition...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2019) 476 (23): 3649–3660.
Published: 10 December 2019
..., with the 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...
Includes: Supplementary data
Articles
Larissa Legewie, Jennifer Loschwitz, Nora Steffens, Martin Prescher, Xue Wang, Sander H. J. Smits, Lutz Schmitt, Birgit Strodel, Daniel Degrandi, Klaus Pfeffer
Journal:
Biochemical Journal
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 characteristics...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
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
Marie-Eve Chagot, Raphael Dos Santos Morais, Sana Dermouche, Dorian Lefebvre, Xavier Manival, Christophe Chipot, François Dehez, Marc Quinternet
Journal:
Biochemical Journal
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...
Includes: Multimedia, Supplementary data
Articles
Jinqing Li, Zichao Yang, Han Liu, Mengjie Qiu, Tingting Zhang, Wenjuan Li, Zhaofeng Li, Tao Qi, Yurong Qiu, Lin Li, Xuefeng Zhou, Shuwen Liu, Suiyi Tan
Journal:
Biochemical Journal
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 found...
Articles
Richa Dubey, Ketaki Patil, Sarath C. Dantu, Devika M. Sardesai, Parnika Bhatia, Nikita Malik, Jhankar D. Acharya, Soham Sarkar, Soumadwip Ghosh, Rajarshi Chakrabarti, Shilpy Sharma, Ashutosh Kumar
Journal:
Biochemical Journal
Biochem J (2019) 476 (5): 889–907.
Published: 15 March 2019
...-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 disorders...
Includes: Supplementary data
Articles
Mykola M. Ilchenko, Mariia Yu. Rybak, Alex V. Rayevsky, Oksana P. Kovalenko, Igor Ya. Dubey, Michael A. Tukalo
Journal:
Biochemical Journal
Biochem J (2019) 476 (4): 719–732.
Published: 28 February 2019
... mode’, and the replacement of ‘ChemScore’ with ‘ASP’ as a restoring function. density functional theory enzyme kinetics enzyme–substrate interactions molecular dynamics thermodynamics translation factors Chiral discrimination of amino acids is essential for the two connected steps...
Includes: Supplementary data
Articles
Ting Ban, Xun Li, Xiaochuan Ma, Hui Yang, Yunpeng Song, Yaping Sun, Michelle Shen, Na Li, Mei-Yun Zhang, Yingli Ma, Wenge Zhong, Mingqiang Zhang, Liaoyuan A. Hu
Journal:
Biochemical Journal
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
Journal:
Biochemical Journal
Biochem J (2018) 475 (21): 3377–3391.
Published: 09 November 2018
... and 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
Diego Avellaneda Matteo, Grace A. Wells, Lucas A. Luna, Adam J. Grunseth, Olga Zagnitko, David A. Scott, An Hoang, Amit Luthra, Manal A. Swairjo, Jamie M. Schiffer, Christal D. Sohl
Journal:
Biochemical Journal
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 conformations...
Includes: Supplementary data
Articles
TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies
Journal:
Biochemical Journal
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
Journal:
Biochemical Journal
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
Kenneth T. Walker, Ruodan Nan, David W. Wright, Jayesh Gor, Anthony C. Bishop, George I. Makhatadze, Barbara Brodsky, Stephen J. Perkins
Journal:
Biochemical Journal
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
Xiaoying Koh-Stenta, Anders Poulsen, Rong Li, John Liang Kuan Wee, Perlyn Zekui Kwek, Sin Yin Chew, Jianhe Peng, Liling Wu, Ernesto Guccione, Joma Joy, Jeffrey Hill
Journal:
Biochemical Journal
Biochem J (2017) 474 (6): 971–982.
Published: 07 March 2017
...); published by Portland Press Limited on behalf of the Biochemical Society 2017 automethylation histone methyltransferase molecular dynamics substrate-mimic inhibitor We have previously characterised the histone lysine methyltransferase activities of PRDM9, one of 17 members of the PRDM...
Includes: Multimedia, Supplementary data
Articles
Tao Ni, Antreas C. Kalli, Fiona B. Naughton, Luke A. Yates, Omar Naneh, Mirijam Kozorog, Gregor Anderluh, Mark S.P. Sansom, Robert J.C. Gilbert
Journal:
Biochemical Journal
Biochem J (2017) 474 (4): 539–556.
Published: 03 February 2017
..., but with a pleckstrin homology (PH) domain inserted in the F2 subdomain that enables membrane association. We present the crystal structure of murine kindlin-3 PH domain determined at a resolution of 2.23 Å and characterise its lipid binding using biophysical and computational approaches. Molecular dynamics simulations...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2016) 473 (20): 3705–3724.
Published: 11 October 2016
...: Jacek Czub ( [email protected] ) * 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 protein...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
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
Journal:
Biochemical Journal
Biochem J (2016) 473 (12): 1651–1662.
Published: 10 June 2016
... on behalf of the Biochemical Society and distributed under the Creative Commons Attribution Licence 4.0 (CC BY-NC-ND) . all-atom model free energy generalized ensemble molecular binding molecular dynamics molecular interaction A protein–protein or protein–ligand complex is stabilized...
Articles
Guillem Prats-Ejarque, Javier Arranz-Trullén, Jose A. Blanco, David Pulido, M. Victòria Nogués, Mohammed Moussaoui, Ester Boix
Journal:
Biochemical Journal
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
María V. Dansey, Lautaro D. Alvarez, Gisela Samaja, Daiana S. Escudero, Adriana S. Veleiro, Adalí Pecci, Olga A. Castro, Gerardo Burton
Journal:
Biochemical Journal
Biochem J (2015) 465 (1): 175–184.
Published: 12 December 2014
... 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 involved in a number...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2012) 448 (3): 417–423.
Published: 21 November 2012
... epidermal growth factor receptor (EGFR) erlotinib gefitinib inhibitor molecular dynamics receptor tyrosine kinase (RTK) X-ray crystallography Activating mutations in the EGFR (epidermal growth factor receptor) are now well accepted as oncogenic drivers in such cancers as NSCLC (non-small-cell...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 438 (3): 415–426.
Published: 26 August 2011
[email protected] 28 2 2011 28 4 2011 4 5 2011 26 8 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 Alzheimer's disease computer simulation integrative biology molecular dynamics Parkinson's disease Amyloid-related diseases comprise a group...
Includes: Multimedia, Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 436 (2): 241–251.
Published: 13 May 2011
.... To 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
Journal:
Biochemical Journal
Biochem J (2011) 435 (3): 783–789.
Published: 13 April 2011
... as the ribosome-interaction domain [ 4 ]. 1 To whom correspondence should be addressed (email [email protected] ). 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...
Includes: Supplementary data
Articles
Naresh C. Bal, Nivedita Jena, Danesh Sopariwala, Tuniki Balaraju, Sana Shaikh, Chandralata Bal, Ashoke Sharon, Sandor Gyorke, Muthu Periasamy
Journal:
Biochemical Journal
Biochem J (2011) 435 (2): 391–399.
Published: 29 March 2011
... the conservation of sequences around the CPVT mutations were generated using Weblogo 3.0 [ 33 ]. To examine further the effect of the mutations on the 3D (3-dimensional) structure and surface charge, we used MD/FEP (molecular dynamics/free energy perturbation) simulations. For this, the initial 3D co-ordinates...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
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
Pablo STROBEL, Claudio ALLARD, Tomás PEREZ-ACLE, Rosario CALDERON, Rebeca ALDUNATE, Federico LEIGHTON
Journal:
Biochemical Journal
Biochem J (2005) 386 (3): 471–478.
Published: 08 March 2005
... in flavonoid incorporation into cells. catechin-gallate flavonoid glucose transporter molecular dynamics myricetin quercetin 1 To whom correspondences should be addressed (email [email protected] ). 29 4 2004 27 9 2004 7 10 2004 7 10 2004 The Biochemical...
Articles
Roman G. EFREMOV, Yuri A. KOSINSKY, Dmitry E. NOLDE, Ruslan TSIVKOVSKII, Alexander S. ARSENIEV, Svetlana LUTSENKO
Journal:
Biochemical Journal
Biochem J (2004) 382 (1): 293–305.
Published: 10 August 2004
... to 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
Anja K. PEDERSEN, Xiao-Ling GUO, Karin B. MØLLER, Günther H. PETERS, Henrik S. ANDERSEN, Jette S. KASTRUP, Steen B. MORTENSEN, Lars F. IVERSEN, Zhong-Yin ZHANG, Niels Peter H. MØLLER
Journal:
Biochemical Journal
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
Journal:
Biochemical Journal
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
Journal:
Biochemical Journal
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...
Includes: Supplementary data
Articles
Valeria MENCHISE, Catherine CORBIER, Claude DIDIERJEAN, Michele SAVIANO, Ettore BENEDETTI, Jean-Pierre JACQUOT, André AUBRY
Journal:
Biochemical Journal
Biochem J (2001) 359 (1): 65–75.
Published: 24 September 2001
... that 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. Biochem. J. (2001...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 358 (1): 101–110.
Published: 08 August 2001
...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. Biochem...
Articles
Adult and fetal haemoglobin J-Sardegna [α50(CE8)His→Asp]: functional and molecular modelling studies
Marcella CORDA, Maria C. DE ROSA, Maria G. PELLEGRINI, Maria T. SANNA, Alessandra OLIANAS, Antonella FAIS, Laura MANCA, Bruno MASALA, Bruno ZAPPACOSTA, Silvana FICARRA, Massimo CASTAGNOLA, Bruno GIARDINA
Journal:
Biochemical Journal
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...
Articles
Jason T. MAYNES, W.-S. YAM, Jack P. JENUTH, R. Gang YUAN, Steven A. LITSTER, Barry M. PHIPPS, Floyd F. SNYDER
Journal:
Biochemical Journal
Biochem J (1999) 344 (2): 585–592.
Published: 24 November 1999
... as 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
Patrick MASSON, Cécile CLÉRY, Patrice GUERRA, Arnaud REDSLOB, Christine ALBARET, Pierre-Louis FORTIER
Journal:
Biochemical Journal
Biochem J (1999) 343 (2): 361–369.
Published: 08 October 1999
... 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 reaction...
Articles
Journal:
Biochemical Journal
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...
