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Energy landscapes of a hairpin peptide including NMR chemical shift restraints

Joanne M. Carr, Chris S. Whittleston, David C. Wade, David J. Wales
2015 Physical Chemistry, Chemical Physics - PCCP  
Energy landscapes for trpzip1 peptide sampled as the relative weight of forcefield and NMR restraint potential contributions is systematically varied.  ...  To obtain statistics, 10 independent simulations were performed for each landscape.  ...  The CHARMM22 potential was symmetrized with respect to feasible permutations of identical atoms, 28 as was CamShift for the relevant atoms in ARG, GLU, ASP, TYR and PHE residues.  ... 
doi:10.1039/c5cp01259g pmid:26186565 fatcat:dwm3k4dprbgglhzhiba4sgiijm

The Partner Units Configuration Problem: Completing the Picture [article]

Erich Christian Teppan, Gerhard Friedrich
2013 arXiv   pre-print
The partner units problem (PUP) is an acknowledged hard benchmark problem for the Logic Programming community with various industrial application fields like surveillance, electrical engineering, computer  ...  In this paper we provide all missing complexity results making the PUP better exploitable for benchmark testing.  ...  Figure 7 : 7 Simulating bins on the basis of the graphs given inFigure 5 Figure 8 : 8 An item fitting in a bin Figure 9 : 2 Figure 10 : 9210 Bins for the PUP with UCAP = u ≥ Simulating bins for PUP  ... 
arXiv:1308.6206v3 fatcat:djzjaxg77bazhbd5n3s5sqir2y

Conformation and Domain Movement Analysis of Human Matrix Metalloproteinase-2: Role of Associated Zn2+ and Ca2+ Ions

Leah Voit-Ostricki, Sándor Lovas, Charles R. Watts
2019 International Journal of Molecular Sciences  
Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation.  ...  Its expression is associated with several inflammatory, degenerative, and malignant diseases.  ...  The results for Ca 2+ ion 1 are the same as noted in prior simulations with a shift from backbone carbonyl interactions, which may represent crystal packing forces to interactions with the carboxyl sidechains  ... 
doi:10.3390/ijms20174194 fatcat:zaepqhanibggdln2hhxltwwgpy

High-resolution protein complexes from integrating genomic information with molecular simulation

Alexander Schug, Martin Weigt, José N. Onuchic, Terence Hwa, Hendrik Szurmant
2009 Proceedings of the National Academy of Sciences of the United States of America  
By using existing structures of the individual proteins, our method combines bioinformatically derived contact residue information with molecular dynamics simulations.  ...  based simulations ͉ transient protein complexes ͉ two component system *Note that Spo0B along with SK proteins are structurally distinct from Hpt-type phosphotransferases, commonly utilized as intermediary  ...  Because the latter incorporate the details of packing best while maintaining computational tractability, we choose ref. 20 as a basis for our docking simulations.  ... 
doi:10.1073/pnas.0912100106 pmid:20018738 pmcid:PMC2799721 fatcat:xysrdmrrcbcp5fxaul4wfludsm

Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

Sang Beom Kim, Carmeline J. Dsilva, Ioannis G. Kevrekidis, Pablo G. Debenedetti
2015 Journal of Chemical Physics  
Fig. 9 (b) shows configurations visited by the Trp-cage for one of the folding trajectories, along with the time evolution of the Asp-9-Arg-16 distance.  ...  This suggests that the intermediates are incorrectly folded structures with a similar degree of packing as the folded structure.  ... 
doi:10.1063/1.4913322 pmid:25725756 fatcat:a7u7vmvbsbb2ldrc7wdakld4jq

Computational approaches to RNA structure prediction, analysis, and design

Christian Laing, Tamar Schlick
2011 Current Opinion in Structural Biology  
pools for aptamer design.  ...  Here, we review recent advances in RNA folding algorithms, RNA tertiary motif discovery, applications of graph theory approaches to RNA structure and function, and in silico generation of RNA sequence  ...  /evolution with energy landscape analysis.  ... 
doi:10.1016/j.sbi.2011.03.015 pmid:21514143 pmcid:PMC3112238 fatcat:rgqhbrxvkndrvdl6io7ew7rn24

Activation mechanism of Drosophila cryptochrome through an allosteric switch

Yingjie Wang, Gianluigi Veglia, Dongping Zhong, Jiali Gao
2021 Science Advances  
These structural features are in accord with mutations and spectroscopic experiments.  ...  Although extensive research has been performed, the mechanism for this allosteric process is still unknown.  ...  Ren for valuable discussion of FAD parameters and system setup.  ... 
doi:10.1126/sciadv.abg3815 pmid:34144991 fatcat:wl2wh4cf7vfzzp2jsdxlobrcy4

Dynamics of RNase-A and S-Protein: A Molecular Dynamics Simulation of the Transition Toward a Folding Intermediate

Simona Cotesta, Ivano Tavernelli, Ernesto E. Di Iorio
2003 Biophysical Journal  
Furthermore, we used a novel approach, described in the preceding paper, to represent graphically the energy landscape of the simulated systems.  ...  Computer simulations can contribute in achieving this goal.  ...  Ritter for stimulating discussions. This work was supported by the Eidgenössische Technische Hochschule, ETH-Zurich (grants 41-2517.5 and 0-50503-00).  ... 
doi:10.1016/s0006-3495(03)74686-4 pmid:14507726 pmcid:PMC1303487 fatcat:vpduopvoazar5msfyeev72md24

The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY)

Mark S. Formaneck, Qiang Cui
2006 Journal of Computational Chemistry  
to phosphorylation, when compared with explicit solvent simulations.  ...  signaling protein, chemotaxis protein Y (CheY), with different combinations of the phosphorylation state and conformation of the system; the results were compared to explicit solvent simulations using  ...  Computational resources from the National Center for Supercomputing Applications at the University of Illinois are greatly appreciated.  ... 
doi:10.1002/jcc.20489 pmid:17019722 fatcat:mrbaz7jvcnf7dbuofpkxdy6cpa

Computational re-engineering of Amylin sequence with reduced amyloidogenic potential

Mohamed R Smaoui, Jérôme Waldispühl
2015 BMC Structural Biology  
Results: To unravel sequence mutations that destabilize amyloid fibrils yet simultaneously conserve native fold, we analyze the structural landscape of amyloid proteins and search for potential areas that  ...  In this paper, we explore destabilizing amyloid proteins through the manipulation of genetic code to create beneficial substitute molecules for patients with certain deficiencies.  ...  We then run a full MD simulation and plot RMSD and RMSF graphs to verify any structure deviations caused by the mutation.  ... 
doi:10.1186/s12900-015-0034-4 pmid:25903685 pmcid:PMC4428086 fatcat:uttrvaq4v5eb7ocfh7qolth57y

Hidden complexity of free energy surfaces for peptide (protein) folding

S. V. Krivov, M. Karplus
2004 Proceedings of the National Academy of Sciences of the United States of America  
The ␤-hairpin used for this study has the sequence Gly-Glu-Trp-Thr-Tyr-Asp-Asp-Ala-Thr-Lys-Thr-Phe-Thr-Val-Thr-Glu with no blocking groups for the terminal residues; the model is the same as that used  ...  The ␤-hairpin was simulated at 360 K for 4 s to obtain a sufficient number of folding͞unfolding events for analysis. Structures were recorded every 20 ps.  ...  We thank Aaron Dinner for helpful discussions and assistance in the comparison with the results in ref. 13 and William Eaton for helpful comments on the manuscript.  ... 
doi:10.1073/pnas.0406234101 pmid:15466711 pmcid:PMC522040 fatcat:ixq4lrxwiza47mhrolg3onydb4

Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding

Raju Dash, Md. Chayan Ali, Nayan Dash, Md. Abul Kalam Azad, S. M. Zahid Hosen, Md. Abdul Hannan, Il Soo Moon
2019 International Journal of Molecular Sciences  
Accumulating data indicates that the polymorphism rs9282861 (R213H) is responsible for inefficient enzymatic activity and associated with cancer progression.  ...  Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous and exogenous compounds.  ...  with lowest energy minima, calculated from the free energy landscape.  ... 
doi:10.3390/ijms20246256 pmid:31835852 pmcid:PMC6969939 fatcat:c25xy2ep3bgjbgmdkbsqto2xnm

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation [article]

Kirill Shmilovich, Rachael A. Mansbach, Hythem Sidky, Olivia E. Dunne, Sayak Subhra Panda, John D. Tovar, Andrew L. Ferguson
2020 arXiv   pre-print
capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically-active π-cores.  ...  Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport.  ...  The terminal residues are constrained to be Asp to endow each terminus of the molecule with two carboxyl groups and provide a pH trigger for assembly: at pH>5 the four carboxyls are deprotonated endowing  ... 
arXiv:2002.01563v1 fatcat:uvxbwpabmbg6pobgdr5xx5uaiu

Kinetics and Thermodynamics of Type VIII β-Turn Formation: A CD, NMR, and Microsecond Explicit Molecular Dynamics Study of the GDNP Tetrapeptide

Patrick F.J. Fuchs, Alexandre M.J.J. Bonvin, Brigida Bochicchio, Antonietta Pepe, Alain J.P. Alix, Antonio M. Tamburro
2006 Biophysical Journal  
Extensive MD simulations give a description of the free energy landscape of the peptide in which we retrieve the same two main conformations suggested by the experiments.  ...  This important finding may help for peptide design and is in line with recent studies on bioactive elastin peptides.  ...  Pakdaman is also acknowledged for fruitful discussion on the kinetic aspect. P.F. dedicates this work to the memory of Prof. S. Hazout.  ... 
doi:10.1529/biophysj.105.074401 pmid:16443656 pmcid:PMC1414573 fatcat:wosjvlx5ljh65nozajeumrre5q

Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues

Rebecca Strawn, Milan Melichercik, Michael Green, Thomas Stockner, Jannette Carey, Rüdiger Ettrich, Ruth Nussinov
2010 PLoS Computational Biology  
Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote  ...  An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism  ...  Acknowledgments We thank Ladislav Luley for his early contributions to this work; Prof. D. Peter Tieleman for sharing his expertise and for hosting R.E. and L.  ... 
doi:10.1371/journal.pcbi.1000801 pmid:20532206 pmcid:PMC2880562 fatcat:sci2tbkn7bgulnjqo2ehi3t2mq
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