+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Addition of missing loops and domains to protein models by x-ray solution scattering



Addition of missing loops and domains to protein models by x-ray solution scattering



Biophysical Journal 83(6): 3113-3125



Inherent flexibility and conformational heterogeneity in proteins can often result in the absence of loops and even entire domains in structures determined by x-ray crystallographic or NMR methods. X-ray solution scattering offers the possibility of obtaining complementary information regarding the structures of these disordered protein regions. Methods are presented for adding missing loops or domains by fixing a known structure and building the unknown regions to fit the experimental scattering data obtained from the entire particle. Simulated annealing was used to minimize a scoring function containing the discrepancy between the experimental and calculated patterns and the relevant penalty terms. In low-resolution models where interface location between known and unknown parts is not available, a gas of dummy residues represents the missing domain. In high-resolution models where the interface is known, loops or domains are represented as interconnected chains (or ensembles of residues with spring forces between the C(alpha) atoms), attached to known position(s) in the available structure. Native-like folds of missing fragments can be obtained by imposing residue-specific constraints. After validation in simulated examples, the methods have been applied to add missing loops or domains to several proteins where partial structures were available.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 010128973

Download citation: RISBibTeXText

PMID: 12496082

DOI: 10.1016/s0006-3495(02)75315-0


Related references

Annular arrangement and collaborative actions of four domains of protein-disulfide isomerase: a small angle X-ray scattering study in solution. Journal of Biological Chemistry 281(10): 6581-6588, 2006

Generation of models of protein structure from solution scattering experiments. Journal of Theoretical Biology 97(3): 511-528, 1982

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations. Proteins 65(1): 164-179, 2006

Protein structural dynamics of photoactive yellow protein in solution revealed by pump-probe X-ray solution scattering. Journal of the American Chemical Society 134(6): 3145-3153, 2012

The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains?. Cellular & Molecular Biology Letters 6(1): 59-69, 2001

Use of dynamic light scattering and small-angle X-ray scattering to characterize new surfactants in solution conditions for membrane-protein crystallization. Acta Crystallographica. Section F Structural Biology Communications 71(Pt 7): 838-846, 2015

Solution of multiple trait animal models with missing data on some traits. Journal of Animal Breeding and Genetics 110(1-6): 81-92, 1993

A small-angle X-ray scattering study of alginate solution and its sol-gel transition by addition of divalent cations. Biopolymers. 35(2): 227-238, 1995

Structural change of troponin C molecule and its domains upon Ca2+ binding in the presence of Mg2+ ions measured by a solution X-ray scattering technique. Journal of Biochemistry 107(3): 343-351, 1990

Small-angle X-ray scattering study of the ATP modulation of the structural features of the nucleotide binding domains of the CFTR in solution. European Biophysics Journal 40(7): 811-824, 2011

Structural study of hNck2 SH3 domain protein in solution by circular dichroism and X-ray solution scattering. Biophysical Chemistry 175-176: 39-46, 2013

Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering. Biophysical Journal 92(10): 3633-3642, 2007

Superhelical DNA studied by solution scattering and computer models. Genetica 106(1-2): 49-55, 1999

Superhelical DNA studied by solution scattering and computer models. Genetica (Dordrecht) 106(1-2): 49-55, 1999