PMID- 29510047
OWN - NLM
STAT- MEDLINE
DCOM- 20190307
LR  - 20191228
IS  - 1520-5207 (Electronic)
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 122
IP  - 21
DP  - 2018 May 31
TI  - Computational Signaling Protein Dynamics and Geometric Mass Relations in 
      Biomolecular Diffusion.
PG  - 5599-5609
LID - 10.1021/acs.jpcb.7b11846 [doi]
AB  - We present an atomistic level computational investigation of the dynamics of a 
      signaling protein, monocyte chemoattractant protein-1 (MCP-1), that explores how 
      simulation geometry and solution ionic strength affect the calculated diffusion 
      coefficient. Using a simple extension of noncubic finite size diffusion 
      correction expressions, it is possible to calculate experimentally comparable 
      diffusion coefficients that are fully consistent with those determined from cubic 
      box simulations. Additionally, increasing the concentration of salt in the 
      solvent environment leads to changes in protein dynamics that are not explainable 
      through changes in solvent viscosity alone. This work in accurate computational 
      determination of protein diffusion coefficients led us to investigate 
      molecular-weight-based predictors for biomolecular diffusion. By introducing 
      protein volume- and protein surface-area-based extensions of traditional 
      statistical relations connecting particle molecular weight to diffusion, we find 
      that protein solvent-excluded surface area rather than volume works as a better 
      geometric property for estimating biomolecule Stokes radii. This work highlights 
      the considerations necessary for accurate computational determination of 
      biomolecule diffusivity and presents insight into molecular weight relations for 
      diffusion that could lead to new routes for estimating protein diffusion beyond 
      the traditional approaches.
FAU - Fennell, Christopher J
AU  - Fennell CJ
AUID- ORCID: 0000-0001-8963-4103
FAU - Ghousifam, Neda
AU  - Ghousifam N
FAU - Haseleu, Jennifer M
AU  - Haseleu JM
AD  - Department of Chemistry , Saint Vincent College , Latrobe , Pennsylvania 15650 , 
      United States.
FAU - Gappa-Fahlenkamp, Heather
AU  - Gappa-Fahlenkamp H
LA  - eng
GR  - R01 GM063592/GM/NIGMS NIH HHS/United States
GR  - R15 EB009527/EB/NIBIB NIH HHS/United States
GR  - R56 GM063592/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20180314
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Chemokine CCL2)
RN  - 0 (Solvents)
RN  - 451W47IQ8X (Sodium Chloride)
SB  - IM
MH  - Chemokine CCL2/*chemistry/metabolism
MH  - Diffusion
MH  - Molecular Dynamics Simulation
MH  - Osmolar Concentration
MH  - Sodium Chloride/chemistry
MH  - Solvents/chemistry
MH  - Temperature
MH  - Viscosity
PMC - PMC5985777
COIS- The authors declare no competing financial interest.
EDAT- 2018/03/07 06:00
MHDA- 2019/03/08 06:00
PMCR- 2019/03/06
CRDT- 2018/03/07 06:00
PHST- 2018/03/07 06:00 [pubmed]
PHST- 2019/03/08 06:00 [medline]
PHST- 2018/03/07 06:00 [entrez]
PHST- 2019/03/06 00:00 [pmc-release]
AID - 10.1021/acs.jpcb.7b11846 [doi]
PST - ppublish
SO  - J Phys Chem B. 2018 May 31;122(21):5599-5609. doi: 10.1021/acs.jpcb.7b11846. Epub 
      2018 Mar 14.