Literature DB >> 28943833

The contribution of electrostatic interactions to the collapse of oligoglycine in water.

D Karandur1, B M Pettitt1,2.   

Abstract

Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone, becomes more favorable with an increasing length, yet longer peptides collapse due to the formation of favorable intrapeptide interactions between CO dipoles, in some cases without hydrogen bonds. The strongly repulsive solvent cavity formation is balanced by van der Waals attractions and electrostatic contributions. In order to investigate the competition between solvent exclusion and charge interactions we simulate the collapse of a long oligoglycine comprised of 15 residues while scaling the charges on the peptide from zero to fully charged. We examine the effect this has on the conformational properties of the peptide. We also describe the approximate thermodynamic changes that occur during the scaling both in terms of intrapeptide potentials and peptide-water potentials, and estimate the electrostatic solvation free energy of the system.

Entities:  

Keywords:  hydration free energy; oligoglycine collapse

Year:  2016        PMID: 28943833      PMCID: PMC5607018          DOI: 10.5488/CMP.19.23802

Source DB:  PubMed          Journal:  Condens Matter Phys        ISSN: 1607-324X            Impact factor:   1.128


  33 in total

1.  Net charge per residue modulates conformational ensembles of intrinsically disordered proteins.

Authors:  Albert H Mao; Scott L Crick; Andreas Vitalis; Caitlin L Chicoine; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-19       Impact factor: 11.205

2.  Anatomy of energetic changes accompanying urea-induced protein denaturation.

Authors:  Matthew Auton; Luis Marcelo F Holthauzen; D Wayne Bolen
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-18       Impact factor: 11.205

Review 3.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

4.  Unified description of urea denaturation: backbone and side chains contribute equally in the transfer model.

Authors:  Beate Moeser; Dominik Horinek
Journal:  J Phys Chem B       Date:  2013-12-20       Impact factor: 2.991

5.  Abnormal solubility behavior of beta-lactoglobulin: salting-in by glycine and NaCl.

Authors:  T Arakawa; S N Timasheff
Journal:  Biochemistry       Date:  1987-08-11       Impact factor: 3.162

6.  Computer simulations of the diffusion of a substrate to an active site of an enzyme.

Authors:  K Sharp; R Fine; B Honig
Journal:  Science       Date:  1987-06-12       Impact factor: 47.728

7.  Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density using proximal Radial Distribution Functions.

Authors:  Bin Lin; Ka-Yiu Wong; Char Hu; Hironori Kokubo; B Montgomery Pettitt
Journal:  J Phys Chem Lett       Date:  2011-06       Impact factor: 6.475

8.  Backbone additivity in the transfer model of protein solvation.

Authors:  Char Y Hu; Hironori Kokubo; Gillian C Lynch; D Wayne Bolen; B Montgomery Pettitt
Journal:  Protein Sci       Date:  2010-05       Impact factor: 6.725

9.  Solvation free energies of alanine peptides: the effect of flexibility.

Authors:  Hironori Kokubo; Robert C Harris; Dilipkumar Asthagiri; B Montgomery Pettitt
Journal:  J Phys Chem B       Date:  2013-12-13       Impact factor: 2.991

10.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

View more
  1 in total

1.  Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15.

Authors:  D Asthagiri; Deepti Karandur; Dheeraj S Tomar; B Montgomery Pettitt
Journal:  J Phys Chem B       Date:  2017-08-21       Impact factor: 2.991

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.