Literature DB >> 23496746

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.

Yi He1, Maciej Maciejczyk, Stanisław Ołdziej, Harold A Scheraga, Adam Liwo.   

Abstract

A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and excluded-volume interactions, are sufficient to form double-helical structures of DNA and RNA molecules. Additionally, local interactions determine helix handedness and direction of strand packing. This result, and earlier research on reduced protein models, suggests that mean-field multipole-multipole interactions are the principal factors responsible for the formation of regular structure of biomolecules.

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Year:  2013        PMID: 23496746      PMCID: PMC3627500          DOI: 10.1103/PhysRevLett.110.098101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  23 in total

1.  Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.

Authors:  J D WATSON; F H CRICK
Journal:  Nature       Date:  1953-04-25       Impact factor: 49.962

2.  Bubble nucleation and cooperativity in DNA melting.

Authors:  Yan Zeng; Awrasa Montrichok; Giovanni Zocchi
Journal:  J Mol Biol       Date:  2004-05-21       Impact factor: 5.469

3.  Statistical mechanics of a nonlinear model for DNA denaturation.

Authors: 
Journal:  Phys Rev Lett       Date:  1989-06-05       Impact factor: 9.161

4.  Coarse-grained force field for the nucleosome from self-consistent multiscaling.

Authors:  Karine Voltz; Joanna Trylska; Valentina Tozzini; Vandana Kurkal-Siebert; Jörg Langowski; Jeremy Smith
Journal:  J Comput Chem       Date:  2008-07-15       Impact factor: 3.376

Review 5.  DNA nanomachines.

Authors:  Jonathan Bath; Andrew J Turberfield
Journal:  Nat Nanotechnol       Date:  2007-05       Impact factor: 39.213

Review 6.  Simulating DNA at low resolution.

Authors:  W K Olson
Journal:  Curr Opin Struct Biol       Date:  1996-04       Impact factor: 6.809

7.  Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide.

Authors:  A Liwo; M R Pincus; R J Wawak; S Rackovsky; H A Scheraga
Journal:  Protein Sci       Date:  1993-10       Impact factor: 6.725

8.  Coarse-grained model of nucleic acid bases.

Authors:  Maciej Maciejczyk; Aleksandar Spasic; Adam Liwo; Harold A Scheraga
Journal:  J Comput Chem       Date:  2010-06       Impact factor: 3.376

9.  Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

Authors:  Adam Liwo; Stanisław Ołdziej; Cezary Czaplewski; Dana S Kleinerman; Philip Blood; Harold A Scheraga
Journal:  J Chem Theory Comput       Date:  2010-03-09       Impact factor: 6.006

10.  Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

Authors:  Cezary Czaplewski; Sebastian Kalinowski; Adam Liwo; Harold A Scheraga
Journal:  J Chem Theory Comput       Date:  2009-03-10       Impact factor: 6.006

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  20 in total

1.  Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach.

Authors:  Yi He; Adam Liwo; Harold A Scheraga
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

2.  An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.

Authors:  Daniel M Hinckley; Gordon S Freeman; Jonathan K Whitmer; Juan J de Pablo
Journal:  J Chem Phys       Date:  2013-10-14       Impact factor: 3.488

3.  Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.

Authors:  Lei Jin; Ya-Zhou Shi; Chen-Jie Feng; Ya-Lan Tan; Zhi-Jie Tan
Journal:  Biophys J       Date:  2018-08-30       Impact factor: 4.033

Review 4.  Close encounters with DNA.

Authors:  C Maffeo; J Yoo; J Comer; D B Wells; B Luan; A Aksimentiev
Journal:  J Phys Condens Matter       Date:  2014-09-19       Impact factor: 2.333

Review 5.  My 65 years in protein chemistry.

Authors:  Harold A Scheraga
Journal:  Q Rev Biophys       Date:  2015-04-08       Impact factor: 5.318

Review 6.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

7.  Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions.

Authors:  Yanping Yin; Adam K Sieradzan; Adam Liwo; Yi He; Harold A Scheraga
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

Review 8.  Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.

Authors:  Li-Zhen Sun; Dong Zhang; Shi-Jie Chen
Journal:  Annu Rev Biophys       Date:  2017-03-15       Impact factor: 12.981

9.  A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.

Authors:  Adam K Sieradzan; Artur Giełdoń; Yanping Yin; Yi He; Harold A Scheraga; Adam Liwo
Journal:  J Comput Chem       Date:  2018-10-11       Impact factor: 3.376

Review 10.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Authors:  Fabio Sterpone; Simone Melchionna; Pierre Tuffery; Samuela Pasquali; Normand Mousseau; Tristan Cragnolini; Yassmine Chebaro; Jean-Francois St-Pierre; Maria Kalimeri; Alessandro Barducci; Yoann Laurin; Alex Tek; Marc Baaden; Phuong Hoang Nguyen; Philippe Derreumaux
Journal:  Chem Soc Rev       Date:  2014-04-23       Impact factor: 54.564

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