Literature DB >> 17959779

Structural motifs of biomolecules.

Jayanth R Banavar1, Trinh Xuan Hoang, John H Maddocks, Amos Maritan, Chiara Poletto, Andrzej Stasiak, Antonio Trovato.   

Abstract

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularity-free self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.

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Year:  2007        PMID: 17959779      PMCID: PMC2077247          DOI: 10.1073/pnas.0704594104

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  16 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Optimal shapes of compact strings.

Authors:  A Maritan; C Micheletti; A Trovato; J R Banavar
Journal:  Nature       Date:  2000-07-20       Impact factor: 49.962

3.  Mathematics. Best packing in proteins and DNA.

Authors:  A Stasiak; J H Maddocks
Journal:  Nature       Date:  2000-07-20       Impact factor: 49.962

4.  Weak pairwise correlations imply strongly correlated network states in a neural population.

Authors:  Elad Schneidman; Michael J Berry; Ronen Segev; William Bialek
Journal:  Nature       Date:  2006-04-09       Impact factor: 49.962

5.  Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets.

Authors:  L Pauling; R B Corey
Journal:  Proc Natl Acad Sci U S A       Date:  1951-11       Impact factor: 11.205

Review 6.  Protein misfolding, functional amyloid, and human disease.

Authors:  Fabrizio Chiti; Christopher M Dobson
Journal:  Annu Rev Biochem       Date:  2006       Impact factor: 23.643

7.  Solvation of proteins: linking thermodynamics to geometry.

Authors:  Hendrik Hansen-Goos; Roland Roth; Klaus Mecke; S Dietrich
Journal:  Phys Rev Lett       Date:  2007-09-17       Impact factor: 9.161

8.  The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.

Authors:  L PAULING; R B COREY; H R BRANSON
Journal:  Proc Natl Acad Sci U S A       Date:  1951-04       Impact factor: 11.205

9.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

10.  General structural motifs of amyloid protofilaments.

Authors:  Neil Ferguson; Johanna Becker; Henning Tidow; Sandra Tremmel; Timothy D Sharpe; Gerd Krause; Jeremy Flinders; Miriana Petrovich; John Berriman; Hartmut Oschkinat; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-23       Impact factor: 11.205

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  6 in total

1.  Symmetry, shape, and order.

Authors:  Antonio Trovato; Trinh Xuan Hoang; Jayanth R Banavar; Amos Maritan
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-21       Impact factor: 11.205

2.  Simulations of knotting in confined circular DNA.

Authors:  C Micheletti; D Marenduzzo; E Orlandini; D W Sumners
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

3.  Chiral symmetry breaking by spatial confinement in tactoidal droplets of lyotropic chromonic liquid crystals.

Authors:  Luana Tortora; Oleg D Lavrentovich
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-14       Impact factor: 11.205

4.  First-order coil-globule transition driven by vibrational entropy.

Authors:  Carlo Maffi; Marco Baiesi; Lapo Casetti; Francesco Piazza; Paolo De Los Rios
Journal:  Nat Commun       Date:  2012       Impact factor: 14.919

Review 5.  Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes.

Authors:  Kieran Finan; Peter R Cook; Davide Marenduzzo
Journal:  Chromosome Res       Date:  2011-01       Impact factor: 5.239

6.  Physical mechanism for biopolymers to aggregate and maintain in non-equilibrium states.

Authors:  Wen-Jong Ma; Chin-Kun Hu
Journal:  Sci Rep       Date:  2017-06-08       Impact factor: 4.379

  6 in total

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