Document Detail

Modeling the dynamics of the solvated SL1 domain of HIV-1 genomic RNA.
MedLine Citation:
PMID:  12717718     Owner:  NLM     Status:  MEDLINE    
A mode-coupling solution of the Smoluchowski diffusion equation (MCD theory), designed to describe the dynamics of wobbling macromolecules in water, is applied to a macromolecular bead model including water beads in the nearest layers. The necessary statistical averages are evaluated by time averaging along a molecular dynamics (MD) trajectory where both solute and water are introduced as atomistic models. The cross peaks in (1)H nuclear Overhauser effect spectroscopy (NOESY) NMR spectra that are routinely measured to determine biological structures are here calculated for the mutated 23 nucleotides stem-loop fragment of the SL1 domain in the HIV-1(Lai) genomic RNA. The calculations are in acceptable agreement with experiments without requiring any screening of the hydrodynamic interactions. The screening of hydrodynamics was necessary in previous MCD calculations obtained by using the same full atomistic MD trajectory, but a nonsolvated frictional model.
G La Penna; D Genest; A Perico
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Biopolymers     Volume:  69     ISSN:  0006-3525     ISO Abbreviation:  Biopolymers     Publication Date:  2003 May 
Date Detail:
Created Date:  2003-04-28     Completed Date:  2003-07-02     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  0372525     Medline TA:  Biopolymers     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1-14     Citation Subset:  IM    
Copyright Information:
Copyright 2003 Wiley Periodicals, Inc. Biopolymers 69: 1-14, 2003
Istituto di Studi Chimico-Fisici di Macromolecole Sintetiche e Naturali, CNR, Genova, Italy.
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MeSH Terms
Base Sequence
Genome, Viral*
HIV-1 / genetics*
Magnetic Resonance Spectroscopy
Nucleic Acid Conformation
Oligoribonucleotides / chemistry
RNA, Viral / chemistry*,  genetics
Surface Properties
Reg. No./Substance:
0/Oligoribonucleotides; 0/RNA, Viral; 0/Solutions; 0/Solvents

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