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Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks

Gregg Lois, Jerzy Blawzdziewicz, Corey S. O'Hern
2010 Physical Review E  
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct "first-passage" networks as the system transitions from unfolded to native states.  ...  We show that these scalings are determined by the fractal properties of first-passage networks.  ...  and depends on global properties of first-passage networks.  ... 
doi:10.1103/physreve.81.051907 pmid:20866261 fatcat:yr6hojv52jcgdoz5776b6zxvna

Network Structure of Protein Folding Pathways [article]

Erzsebet Ravasz, S. Gnanakaran, Zoltan Toroczkai
2007 arXiv   pre-print
Folding can be interpreted as a biased random walk on the conformation network.  ...  Here we introduce a network approach to capture the statistical properties of the structure of conformation spaces.  ...  Acknowledgments This work was supported in part by the Department of Energy under contract No. W-7405-ENG-36. Note For supporting information please e-mail: eregan@bidmc.harvard.edu.  ... 
arXiv:0705.0912v1 fatcat:deltwwgyibholghlyre62prkn4

Uncovering the Properties of Energy-Weighted Conformation Space Networks with a Hydrophobic-Hydrophilic Model

Zaizhi Lai, Jiguo Su, Weizu Chen, Cunxin Wang
2009 International Journal of Molecular Sciences  
The vertices (nodes) of the network are the conformations and the links are the transitions between them.  ...  Moreover, the modular (community) structure of weighted CSNs is also studied. These results are helpful to understand the topological properties of the CSN and the underlying free-energy landscapes.  ...  On the other hand, the properties of some dynamical processes, such as protein folding, are determined not by the spectrum but also by the connectivity of the conformations [53] .  ... 
doi:10.3390/ijms10041808 pmid:19468340 pmcid:PMC2680648 fatcat:2v3hoy2upzfvfhb7cafok6qmwe

Topological determinants of protein folding

N. V. Dokholyan, L. Li, F. Ding, E. I. Shakhnovich
2002 Proceedings of the National Academy of Sciences of the United States of America  
We use a macroscopic measure of the protein contact network topology, the average graph connectivity, by constructing graphs that are based on the geometry of protein conformations.  ...  Using two small, well characterized proteins, CI2 and C-Src SH3, we show how topological properties of protein conformations determine their kinetic ability to fold.  ...  Further studies are necessary to shed light on the relation of protein graph properties to the formation of a specific nucleus.  ... 
doi:10.1073/pnas.122076099 pmid:12084924 pmcid:PMC124342 fatcat:p5zs4a7ucneb7ed6qqd3jsq6a4

Percolation-like phase transitions in network models of protein dynamics

Jeffrey K. Weber, Vijay S. Pande
2015 Journal of Chemical Physics  
We analyze the general and critical properties of these phase transitions in seven protein systems and discuss how closely dynamics on protein folding landscapes relate to percolation on random lattices  ...  As rare fluctuations are systematically repressed (or reintroduced), we observe percolation-like phase transitions in protein folding networks: whole sets of conformational states switch from nearly complete  ...  R01-GM062868) for their support of this work. J.K.W. was supported by the Fannie and John Hertz Foundation on the endowed Professor Yaser S. Abu-Mostafa Fellowship.  ... 
doi:10.1063/1.4921989 pmid:26049529 pmcid:PMC4457657 fatcat:m5glybz7ircfhktar2e54fuhqe

Folding Network of Villin Headpiece Subdomain

Hongxing Lei, Yao Su, Lian Jin, Yong Duan
2010 Biophysical Journal  
Analyses based on transition networks have become an alternative approach that has the potential to reveal detailed features of protein folding dynamics.  ...  The folding network revealed more complexity than the traditional two-dimensional map and demonstrated a variety of conformations in the unfolded state, intermediate states, and the native state.  ...  HP35 is one of the most studied proteins in the field of protein folding. We have reviewed some of the notable studies in our previous works (6, 8) .  ... 
doi:10.1016/j.bpj.2010.08.081 pmid:21081086 pmcid:PMC2980750 fatcat:djehih3vdjepjjzq52nk2qnelq

The protein folding network [article]

Francesco Rao, Amedeo Caflisch
2004 arXiv   pre-print
Conformations are nodes of the network, and the transitions between them are links.  ...  The network topology is used to identify conformations in the folding transition state ensemble, and provides a basis for understanding the heterogeneity of the transition state and denaturated state ensemble  ...  RESULTS AND DISCUSSION To study the conformation space network of polypeptides we concentrate on the analysis of topology, i.e., on the study of the connectivity between different conformations, leaving  ... 
arXiv:q-bio/0403034v1 fatcat:lyujwo3d5bat7ex3i5go3cl5am

Nonalgorithmicity and algorithmicity of protein science

Qinyi Zhao
2011 Advances in Bioscience and Biotechnology  
The metaphysical features of the mechanism for the integration of the information underlying protein folding were studied by applying principles of system logic theory.  ...  We conclude that it is not possible to predict all protein three-dimensional structures from protein sequences by one program only.  ...  property of "functional modules", or protein network, biosignal network, consisting of numerous macromolecules that interact with the given protein [41] .  ... 
doi:10.4236/abb.2011.25050 fatcat:cptwzxapmrgrhn7nggwu26g63m

The Protein Folding Network

Francesco Rao, Amedeo Caflisch
2004 Journal of Molecular Biology  
The network topology is used to identify conformations in the folding transition state (TS) ensemble, and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as  ...  The conformation space of a 20 residue antiparallel b-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network.  ...  The molecular dynamics simulations were performed on the Matterhorn Beowulf cluster at the Informatikdienste of the University of Zurich. We thank C. Bollinger and Dr A.  ... 
doi:10.1016/j.jmb.2004.06.063 pmid:15313625 fatcat:b6ypf4vnuneozhkf7vh6c3pcua

Probing Structural Properties of KCNE1 Membrane Protein: A Site-Directed Spin Labeling EPR Study

Megan M. Dunagan, Indra D. Sahu, Rongfu Zhang, Andrew Craig, Robert M. McCarrick, Gary A. Lorigan
2014 Biophysical Journal  
This study showed that the relative populations of the two distinct conformations change depending on the amount of cholesterol present in the lipid bilayer.  ...  Sitedirected spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy has emerged as a well-established method to study the structural properties of membrane proteins.  ...  The high unfolded state population makes DrkN SH3 a useful model system to study the physical polymeric properties of disordered protein states and to advance the understanding of the mechanism of protein  ... 
doi:10.1016/j.bpj.2013.11.355 fatcat:wk7pkry7cfgbdllg3zrfeektne

Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design [article]

Miklos A. Antal, Csaba Bode, Peter Csermely
2009 arXiv   pre-print
We also summarize available data on the application of percolation theory for the prediction of amino acid network- and interactome-dynamics.  ...  and in protein-protein interaction networks (interactomes).  ...  ACKNOWLEDGEMENTS Authors would like to thank members of the LINK-group (www.linkgroup.hu) for helpful suggestions.  ... 
arXiv:0802.2330v2 fatcat:p3ve4wp3wfg5nnpnflc7es5agq

Modeling Proteins as Residue Interaction Networks to Understand Structure-Function Relationship

Isha D. Mehta, Brian W. Beck
2014 Biophysical Journal  
This study showed that the relative populations of the two distinct conformations change depending on the amount of cholesterol present in the lipid bilayer.  ...  Sitedirected spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy has emerged as a well-established method to study the structural properties of membrane proteins.  ...  The high unfolded state population makes DrkN SH3 a useful model system to study the physical polymeric properties of disordered protein states and to advance the understanding of the mechanism of protein  ... 
doi:10.1016/j.bpj.2013.11.358 fatcat:widrvbzwdnctta7f4xpczjbcx4

The Conformations of the DrkN SH3 Domain Studied by Single Molecule Fluorescence Spectroscopy

Zhenfu Zhang, Amir Mazouchi, Andrew Chong, Julie Forman-Kay, Claudiu Gradinaru
2014 Biophysical Journal  
This study showed that the relative populations of the two distinct conformations change depending on the amount of cholesterol present in the lipid bilayer.  ...  Sitedirected spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy has emerged as a well-established method to study the structural properties of membrane proteins.  ...  The high unfolded state population makes DrkN SH3 a useful model system to study the physical polymeric properties of disordered protein states and to advance the understanding of the mechanism of protein  ... 
doi:10.1016/j.bpj.2013.11.356 fatcat:uz2k5yp6fjf4zkdozlfx7z65pq

The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets

Evandro Ferrada, Erich Bornberg-Bauer
2014 PLoS Computational Biology  
In this study, I explore the impact of the relative forces of the potential on the architecture of the sequencestructure map.  ...  I adopt a graph perspective and study the distribution of viable sequences and the structures they produce, as networks of sequences connected by point mutations.  ...  According to the thermodynamic hypothesis of protein folding, a sequence s folds onto a conformation c [ P, if and only if, s is nondegenerate on c (i.e. g c = 1).  ... 
doi:10.1371/journal.pcbi.1003946 pmid:25473967 pmcid:PMC4256021 fatcat:5wkf27p54jhxzgm27it3c3vaou

The Protein Translocase Activity of Anthrax Toxin Protective Antigen is Stereoselective

Debasis Das
2014 Biophysical Journal  
This study showed that the relative populations of the two distinct conformations change depending on the amount of cholesterol present in the lipid bilayer.  ...  Sitedirected spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy has emerged as a well-established method to study the structural properties of membrane proteins.  ...  The high unfolded state population makes DrkN SH3 a useful model system to study the physical polymeric properties of disordered protein states and to advance the understanding of the mechanism of protein  ... 
doi:10.1016/j.bpj.2013.11.360 fatcat:q7vaynuxgrbxlb2amf7eisa6n4
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