Document Detail


Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes.
MedLine Citation:
PMID:  23320673     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
A generalized method, termed Fast-SAXS-pro, for computing small angle x-ray scattering (SAXS) profiles of proteins, nucleic acids, and their complexes is presented. First, effective coarse-grained structure factors of DNA nucleotides are derived using a simplified two-particle-per-nucleotide representation. Second, SAXS data of a 18-bp double-stranded DNA are measured and used for the calibration of the scattering contribution from excess electron density in the DNA solvation layer. Additional test on a 25-bp DNA duplex validates this SAXS computational method and suggests that DNA has a different contribution from its hydration surface to the total scattering compared to RNA and protein. To account for such a difference, a sigmoidal function is implemented for the treatment of non-uniform electron density across the surface of a protein/nucleic-acid complex. This treatment allows differential scattering from the solvation layer surrounding protein/nucleic-acid complexes. Finally, the applications of this Fast-SAXS-pro method are demonstrated for protein/DNA and protein/RNA complexes.
Authors:
Krishnakumar M Ravikumar; Wei Huang; Sichun Yang
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  138     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-16     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  024112     Citation Subset:  IM    
Affiliation:
Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4988, USA.
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