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Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

Lars Skjaerven, Barry Grant, Arturo Muga, Knut Teigen, J. Andrew McCammon, Nathalie Reuter, Aurora Martinez, Jianpeng Ma
2011 PLoS Computational Biology  
Here we describe extensive (in total 2:2 ms long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding.  ...  We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the  ...  Here, we provide a description of the molecular basis for the conformational changes in the GroEL subunit by performing extensive molecular dynamics simulations.  ... 
doi:10.1371/journal.pcbi.1002004 pmid:21423709 pmcid:PMC3053311 fatcat:7pah6i2ranczdcxje73apo3qnu

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

C. F. Abrams, E. Vanden-Eijnden
2010 Proceedings of the National Academy of Sciences of the United States of America  
For GroEL, the method induces in about 40 ns conformational changes that recapitulate the t → r 00 transition and are not observed in unaccelerated molecular dynamics: The apical domain is displaced by  ...  It has therefore become attractive to probe the details of protein conformational dynamics using simulation methods, such as molecular dynamics (MD) and related techniques.  ...  .), and TeraGrid allocation MCB070073N (to C.F.A.). Ali Emileh is acknowledged for conducting the MD simulation of gp120.  ... 
doi:10.1073/pnas.0914540107 pmid:20194785 pmcid:PMC2841907 fatcat:ryyuyoemxbbcbbjprzevxekwwq

A survey of coarse-grained methods for modeling protein conformational transitions

Wenjun Zheng, Han Wen
2017 Current Opinion in Structural Biology  
We highlight the similarities and differences between these methods, and illustrate their usage in case of the T-to-R 00 transition of chaperonin GroEL.  ...  To this end, coarse-grained protein structural models have proven valuable by enabling cost-effective simulation/analysis of protein conformational transitions which are too slow for all-atom molecular  ...  Acknowledgement We thank funding support from American Heart Association (#14GRNT18980033) and National Science Foundation (#0952736).  ... 
doi:10.1016/ pmid:27810573 fatcat:yqzlq64r4bgg3pjxnwzczsjfwi

Identification of Elements That Dictate the Specificity of Mitochondrial Hsp60 for Its Co-Chaperonin

Avital Parnas, Shahar Nisemblat, Celeste Weiss, Galit Levy-Rimler, Amir Pri-Or, Tsaffrir Zor, Peter A. Lund, Peter Bross, Abdussalam Azem, Dhyan Chandra
2012 PLoS ONE  
increase in affinity toward co-chaperonins that is accompanied by an alteration in the allosteric signal transmitted upon nucleotide binding.  ...  Our results indicate that the phenotype of the E321K mutant is caused mainly by a profound increase in the binding affinity to all cochaperonins, while the phenotype of R264K/E358K is caused by a slight  ...  Gideon Schreiber and Ori Cohavi for their assistance with SPR experiments. Author Contributions  ... 
doi:10.1371/journal.pone.0050318 pmid:23226518 pmcid:PMC3514286 fatcat:i2tab67znbbj7p5ikwlom3tjre

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

Harish Vashisth, Georgios Skiniotis, Charles Lee Brooks
2014 Chemical Reviews  
By adding an additional angle-dependent harmonic potential to the TAMD equations, Vashisth and Brooks showed that robust conformational transitions can be observed in components of the maltose-transporter  ...  This is immediately followed by a discussion of the importance of enhanced sampling in biomolecular simulations, and how dynamics in these systems can be explored by evolving CVs via temperature acceleration  ... 
doi:10.1021/cr4005988 pmid:24446720 pmcid:PMC3983124 fatcat:xxmfeba5gbh5hoio3kph7gukqy

Chaperonin-assisted protein folding: a chronologue

Arthur L. Horwich, Wayne A. Fenton
2020 Quarterly Reviews of Biophysics (print)  
Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.  ...  This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell.  ...  We thank all of our colleagues in this field for the many stimulating discussions and good times we have had together in so many corners of the world.  ... 
doi:10.1017/s0033583519000143 pmid:32070442 fatcat:xvo54rbqhjce5jw4nn5dadma6y

The Structural Basis of ATP as an Allosteric Modulator

Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang, Guanghong Wei
2014 PLoS Computational Biology  
Nudged elastic band simulations unveiled the distinct dynamic processes of ATP binding to the corresponding allosteric and substrate binding sites of uridine monophosphate kinase, and suggested that in  ...  Through extensive analysis of ATP in solution and proteins, we found that the free ATP can exist in the compact and extended conformations in solution, and the two different conformational characteristics  ...  Here, we addressed these questions by combining bioinformatic analyses, molecular dynamics (MD) and nudged elastic band (NEB) simulations.  ... 
doi:10.1371/journal.pcbi.1003831 pmid:25211773 pmcid:PMC4161293 fatcat:aujsntbymjea7nk76aw3jlpf2u

Award Winners and Abstracts of the 31st Annual Symposium of The Protein Society, Montreal, Canada, July 24-27, 2017

2017 Protein Science  
Grouping by Topics Pages  ...  In the present study, we aimed to improve the ExM method for imaging of proteins in human clinical tissue samples, for diagnostic pathology and research.  ...  by imaging of the ACTN4 protein expression pattern with conventional light microscopy.  ... 
doi:10.1002/pro.3349 pmid:29280217 fatcat:jrxtwzblare37gxsvc5szbwuhu

Abstracts of the 29th Annual Symposium of The Protein Society

2015 Protein Science  
Overall, the results illustrate the power of 19F-NMR for monitoring ligand binding and conformational changes.  ...  The interactions of SPM-1 with various potential inhibitors were reported by 19F-NMR, which enabled monitoring SPM-1 conformational changes on ligand binding and informed on binding strength by enabling  ...  The structure of the C-terminal domain until residue 1629 has been solved by crystallography, while the structure and function of the remaining 130 residues remained undetermined [2].  ... 
doi:10.1002/pro.2823 pmid:26452528 pmcid:PMC4632850 fatcat:ejmksoqj3zbsrkabl4jyp7emgi

Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis

Stefano Donini, Davide M. Ferraris, Riccardo Miggiano, Alberto Massarotti, Menico Rizzi
2017 Scientific Reports  
(UMP), the precursor of all pyrimidine nucleotides 10 .  ...  In this context, also the de novo and salvage synthesis of purine and pyrimidine nucleotides, the key precursors of DNA and RNA, have been reported as essential for mycobacterial survival both in vitro  ...  Acknowledgements The authors would like to thank Giorgia Bolognesi for technical support and assistance. Author Contributions  ... 
doi:10.1038/s41598-017-01057-z pmid:28446777 pmcid:PMC5430920 fatcat:cmzm7p75hnhitixqikzvg77lqu


2019 Seibutsu Butsuri  
We have studied the HA binding on CD44 HABD by using molecular dynamics (MD) simulation. Two conformations of HABD, O and PD forms showed different binding manner and binding affinity.  ...  The structural dynamics and energetics features revealed from our atomistic molecular dynamics (MD) simulations and related analyses on the single-subunit T7 RNAP thus provided detailed and quantitative  ...  To conquer this problem, we employed the particle-filter molecular dynamics (MD) simulation, in which the AFM cantilever probes the surface sequentially pixel by pixel.  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

Molecular knots in biology and chemistry

Nicole C H Lim, Sophie E Jackson
2015 Journal of Physics: Condensed Matter  
We would also like to thank many people in the field for interesting discussions and useful advice. N C H Lim is supported by a UBD Chancellor scholarship from the Brunei Government.  ...  We would also like to thank Dr Gokhan Barin and Prof J Fraser Stoddart for sending us the x-ray crystal structures in figures 13(b) and (d), and Dr G Dan Pantoş for sending us the structures shown in  ...  (f) Conformations of packed P4 phage genomes as determined by coarse-grained molecular dynamics simulations. Reprinted from [49] , with permission from Elsevier.  ... 
doi:10.1088/0953-8984/27/35/354101 pmid:26291690 fatcat:aih4t62urvg53f3ie7i4jmxn4y

Macromolecular electron microscopy in the era of structural genomics

W Baumeister
2000 TIBS -Trends in Biochemical Sciences. Regular ed  
Cryo-electron microscopy (cryo-EM) is emerging as a powerful method for studying the structure, assembly and dynamics of such macromolecules, and their interactions with substrates.  ...  Moreover, cryo-EM can be combined in several ways with X-ray diffraction to enhance the resolution of cryo-EM and the applicability of crystallography.  ...  Bohm for help with graphics, and D. Rees and P. Bjorkman for helpful comments.  ... 
doi:10.1016/s0968-0004(00)01720-5 pmid:11116190 fatcat:klq2rcxuebadpbgdoe6jlgzcci

Evolutionary and cellular analysis of the dark pseudokinase PSKH2 [article]

Dominic P Byrne, Safal Shrestha, Leonard A Daly, Vanessa Marensi, Krithika Ramakrishnan, Claire E Eyers, Natarajan Kannan, Patrick A Eyers
2022 bioRxiv   pre-print
molecular chaperone system.  ...  Primates encode PSKH2 in the form of a pseudokinase, which is predicted to be catalytically inactive due to loss of the invariant catalytic Asp residue.  ...  Molecular dynamics (MD) simulation of full-length PSKH2 and molecular modelling of the PSKH2/HSP90/Cdc37 complex Unbiased full atom MD simulation of the full length AF2 model of human PSKH2 (Uniprot ID  ... 
doi:10.1101/2022.09.10.507278 fatcat:rpk42mhwyve4fmdidwx6lofl7a

2017 ASCB Annual Meeting Abstracts

David G. Drubin
2017 Molecular Biology of the Cell  
A thorough understanding of the molecular mechanisms by which key regulators and mediators of ubiquitination regulate GPCR signaling and trafficking is essential for understanding dysregulated mechanisms  ...  ESCRT binding also depends on the presence of a specific phosphoinositide lipid in the endosomal membrane, PI3P (generated by the Vps34 PI3-kinase), which serves as an additional docking site for the ESCRT  ...  In a resting cell membrane, about ~40% of GPI-APs form transient (<1 sec) nanoclusters driven by the dynamics of the contractile actin machinery operating close to the inner leaflet of the plasma membrane  ... 
doi:10.1091/mbc.e17-10-0618 pmid:29237772 pmcid:PMC5739290 fatcat:3msjrn3omzcybfanlagykayauy
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