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Local interactions in bends of proteins

S. S. Zimmerman, H. A. Scheraga
1977 Proceedings of the National Academy of Sciences of the United States of America  
Agreement between the calculated and observed fraction of bends was found for 26 dipeptides, suggesting that, for those particular dipeptide sequences, local interactions dominate over long-range interactions  ...  The analysis of dipeptide sequences in the twenty globular proteins also indicated that the 4 -1 hydrogen bond is not a dominant factor in stabilizing bends in proteins, and that most dipeptide sequences  ...  Zimmerman for assistance in preparing the manuscript.  ... 
doi:10.1073/pnas.74.10.4126 pmid:270658 pmcid:PMC431888 fatcat:toxkqorr5fb27kk43w6og6o7fu

Quantifying randomness in protein–protein interaction networks of different species: A random matrix approach

Ankit Agrawal, Camellia Sarkar, Sanjiv K. Dwivedi, Nitesh Dhasmana, Sarika Jalan
2014 Physica A: Statistical Mechanics and its Applications  
We demonstrate that spectral rigidity, which quantifies long range correlations in eigenvalues, for all protein-protein interaction networks follow random matrix prediction up to certain ranges indicating  ...  randomness in interactions.  ...  Long range correlation (∆ 3 statistics) ensues GOE statistics up to length L ∼ 13.  ... 
doi:10.1016/j.physa.2013.12.005 fatcat:cozlheul3zhwfdqqqvpokj7asa

Orientational potentials extracted from protein structures improve native fold recognition

N.-V. Buchete
2004 Protein Science  
We develop coarse-grained, distance-and orientation-dependent statistical potentials from the growing protein structural databases.  ...  By taking into account the importance of backbone interactions with a virtual backbone interaction center as the 21st anisotropic site, we construct a 21 × 21 interaction scheme.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1110/ps.03488704 pmid:15044723 pmcid:PMC2280067 fatcat:bvpm3lvybrht7f2ija5wlkmgr4

The role of long-range interactions in defining the secondary structure of proteins is overestimated

András Fiser, Zsuzsanna Dosztányi, István Simon
1997 Bioinformatics  
Therefore, non-local, long-range interactions seem to be a significant cause of this limitation.  ...  on this separate subset to assess the effect of long-range interactions on the prediction efficiencies.  ...  Acknowledgements We thank Drs Miklos Cserzb, Peter Tompa and Gabor Tusnady for critical review of the manuscript. The authors are grateful to Dr Finkelstein for providing the ALB prediction program.  ... 
doi:10.1093/bioinformatics/13.3.297 fatcat:xtwip4evdvgixcx7anir27kypi

Unique for human centromeric regions of interphase chromatin homing (CENTRICH) govern dynamic features of chromatin fractal globules

Gennadi Glinsky
2012 Nature Precedings  
of long-range physical interactions (Centromeric Regions of Interphase Chromatin Homing, CENTRICH).  ...  Here we report the results of the external point of contact analysis of chromatin fractal globules based on a genome-wide alignment of inter-and intra-chromosomal chromatin interactions within the context  ...  , plotted results of the analysis and look for regions that manifest statistically higher frequencies of long-range interactions.  ... 
doi:10.1038/npre.2012.6756.1 fatcat:7zc5ssddpjdqjfd6ulholltzsu

On the dominance of short-range interactions in polypeptides and proteins

H. A. Scheraga
1973 Pure and Applied Chemistry  
The development of the concept of the dominance of short-range interactions in polvpeptides and proteins is traced.  ...  These ideas are being applied in conformational energy calculations to try to determine the native conformations of proteins. 1 PAC 36 1 II  ...  Finkelstein and Ptitsyn4 also made a statistical analysis of the conformations of amino acid residues in proteins of known structure, and came to similar conclusions, viz, that short-range interactions  ... 
doi:10.1351/pac197336010001 fatcat:6vztpsdmr5azdgwemmvgcpppca

Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins

Yunjie Zhao, Yiren Jian, Zhichao Liu, Hang Liu, Qin Liu, Chanyou Chen, Zhangyong Li, Lu Wang, H. Howie Huang, Chen Zeng
2017 Scientific Reports  
Second, there happen to be abundant single-domain and double-domain lectins in plant genomes for us to distinguish these critical residues in terms of whether they are for short-range or long-range recognitions  ...  In contrast to the dimer complex of two single-domain lectins formed via protein-protein interactions, the double-domain lectin fuses two single-domain proteins into one protein with a short linker and  ...  The GLU91-MET5 pair is coevolved to maintain the interaction for long-range recognition in single-domain.  ... 
doi:10.1038/s41598-017-03003-5 pmid:28588265 pmcid:PMC5460271 fatcat:bxuhvjrvdvckhnq5shbsmvuz2i

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Ivan Juric, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Ming Hu (+1 others)
2019 PLoS Computational Biology  
Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions.  ...  significant chromatin interactions anchored at genomic regions bound by the protein of interest.  ...  statistically significant long-range chromatin interactions.  ... 
doi:10.1371/journal.pcbi.1006982 fatcat:3iqcq7mjmrdrnpqtx6pulxzt6e

Importance of Long-Range Interactions for Determining the Folding Rate and Transition State Structures of Two-state Proteins

Michael M. Gromiha, Samuel Selvaraj
2002 Genome Informatics Series  
Consequently, medium and long-range interactions play an active role in the folding and stability of proteins.  ...  Method and Results Concept of Long-Range Order We defined a novel parameter, long-range order (LRO) for a protein from the knowledge of long-range contacts in protein structure [1] .  ... 
doi:10.11234/gi1990.13.348 fatcat:w3xp5xknvfddpob7qkddwl3uky

Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis

N.-V. Buchete, J.E. Straub, D. Thirumalai
2004 Journal of Molecular Graphics and Modelling  
Coarse-grained, anisotropic potentials are constructed for short-, medium-, and long-range interactions using the Boltzmann method and a database of non-homologous protein structures.  ...  A new method is presented for extracting statistical potentials dependent on the relative side chain and backbone orientations in proteins.  ...  Acknowledgements This work was supported by the National Institutes of Health R01 NS41356-01 (JES and DT), the National Science Foundation CHE-9975494 (JES), and CHE-0209340 (DT).  ... 
doi:10.1016/j.jmgm.2003.12.010 pmid:15099839 fatcat:hp3vduztvrdwpphorqyqt2vsxi

Are there Still Surprises Buried Inside Statistical Analysis of Protein Structure?

Ravishankar Ramanathan, Abhinav Verma
2011 Journal of Biomolecular Structure and Dynamics  
The Protein Folding Problem has been a long standing challenge towards achieving a complete molecular understanding of life (1).  ...  Since the days of Anfinsen, scientists over the world have been trying to understand the basic laws governing protein folding and have come a long way.  ...  Acknowledgements RR and AV acknowledge the support of Marie Curie Actions through Marie Curie Excellence Grant MEXT-CT-2006-042334.  ... 
doi:10.1080/073911011010524981 pmid:21142253 fatcat:rghvrk65tvaqjgfd5mrdgqcyp4

Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases

N.-V. Buchete, J.E. Straub, D. Thirumalai
2004 Polymer  
The complexity of inter-residue interactions is reflected in a high degree of orientational anisotropy for the twenty amino acids.  ...  By including in this coarse-grained interaction model the possibility of quantifying the backbone -backbone and backbone-side chain interactions, important improvements are obtained in characterizing the  ...  Acknowledgements This work was supported by the National Institutes of Health R01 NS41356-01 (JES and DT), the National Science Foundation CHE-9975494 (JES), and CHE-0209340 (DT).  ... 
doi:10.1016/j.polymer.2003.10.093 fatcat:sc2afvlu6zejfiaqgiwcukyrj4

Integrative genomics analysis identifies pericentromeric regions of human chromosomes affecting patterns of inter-chromosomal interactions [article]

Gennadi V. Glinsky
2014 arXiv   pre-print
Genome-wide analysis of distributions of densities of long-range interactions of human chromosomes with each other, nucleoli, nuclear lamina, and binding sites of chromatin state regulatory proteins, CTCF  ...  Our analysis suggests that centromeric sequences and pericentromeric heterochromatin may play an important role in human cells beyond the critical functions in chromosome segregation.  ...  regions that manifest statistically higher densities of long-range interactions.  ... 
arXiv:1401.2238v1 fatcat:enmvnpk5iffolefmyi7peukahy

Short-Range Contact Preferences and Long-Range Indifference: Is Protein Folding Stoichiometry Driven?

Hue Sun Chan
2011 Journal of Biomolecular Structure and Dynamics  
They interpreted the results of this "neighborhood analysis" of theirs (1) as implying a lack of preferential interactions.  ...  By analyzing the spatial neighborhoods of amino acid residues in an extensive set of structures in the Protein Data Bank (PDB), the authors concluded that preferential interactions between amino acid residues  ...  Short-Range Contact Preferences and Long-Range Indifference: Is Protein Folding Stoichiometry Driven?  ... 
doi:10.1080/073911011010524960 pmid:21142231 fatcat:l3n7y76zkfgldcvtzeveqksf5y

Short-Range Contact Preferences and Long-Range Indifference: Is Protein Folding Stoichiometry Driven?

Hue Sun Chan
2011 Journal of Biomolecular Structure and Dynamics  
They interpreted the results of this "neighborhood analysis" of theirs (1) as implying a lack of preferential interactions.  ...  By analyzing the spatial neighborhoods of amino acid residues in an extensive set of structures in the Protein Data Bank (PDB), the authors concluded that preferential interactions between amino acid residues  ...  Short-Range Contact Preferences and Long-Range Indifference: Is Protein Folding Stoichiometry Driven?  ... 
doi:10.1080/07391102.2011.10524960 fatcat:hvbnx5yvqjcqnox43pzeyme5aq
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