TITLE

Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

AUTHOR(S)
Hirose, Shuichi; Yokota, Kiyonobu; Kuroda, Yutaka; Wako, Hiroshi; Endo, Shigeru; Kanai, Satoru; Noguchi, Tamotsu
PUB. DATE
January 2010
SOURCE
BMC Structural Biology;2010, Vol. 10, p20
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. Results: In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naíve model and three published predictors. Conclusions: Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions.
ACCESSION #
53415417

 

Related Articles

  • A substrate channel in the nitrogenase MoFe protein. Barney, Brett M.; Yurth, Michael G.; Dos Santos, Patricia C.; Dean, Dennis R.; Seefeldt, Lance C. // Journal of Biological Inorganic Chemistry;Sep2009, Vol. 14 Issue 7, p1015 

    Nitrogenase catalyzes the six electron/six proton reduction of N2 to two ammonia molecules at a complex organometallocluster called �FeMo cofactor.� This cofactor is buried within the a-subunit of the MoFe protein, with no obvious access for substrates. Examination of high-resolution...

  • Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping. Ben-Shimon, Avraham; Niv, Masha Y. // PLoS Computational Biology;Nov2011, Vol. 7 Issue 11, Special section p1 

    Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phosphoaccepting residue in the substrate. Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important...

  • Crystallographic protein model-building on the web. Kreshna Gopal; Erik McKee; Tod Romo; Reetal Pai; Jacob Smith; James Sacchettini; Thomas Ioerger // Bioinformatics;Feb2007, Vol. 23 Issue 3, p375 

    Summary: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map....

  • Molecular Structure of the Amyloid-Forming Protein kappa I Bre1. Steinrauf, L.K.; Chiang, Michael Y.; Shiuan, David // Journal of Biochemistry;1999, Vol. 125 Issue 2, p422 

    The molecular structure of the amyloid-forming Bence-Jones protein kappa I Bre has been determined by X-ray crystallography at 2.0 Ã… resolution. The fragment from the kappa chain of immunoprotein contains 107 amino acid residues, and polymerizes in the crystal form into a giant helical...

  • Evolution of the arginase fold and functional diversity. Dowling, D. P.; Di Costanzo, L.; Gennadios, H. A.; Christianson, D. W. // Cellular & Molecular Life Sciences;Jul2008, Vol. 65 Issue 13, p2039 

    Novel structural superfamilies can be identified among the large number of protein structures deposited in the Protein Data Bank based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein Evolution, proteins with...

  • Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Eran Eyal; Chakra Chennubhotla; Lee-Wei Yang; Ivet Bahar // Bioinformatics;Jul2007, Vol. 23 Issue 13, pi175 

    Motivation: A common practice in X-ray crystallographic structure refinement has been to model atomic displacements or thermal fluctuations as isotropic motions. Recent high-resolution data reveal, however, significant departures from isotropy, described by anisotropic displacement parameters...

  • Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis. Kurgan, L.; Mizianty, M. J. // Natural Science;Sep2009, Vol. 1 Issue 2, p93 

    Structural genomics (SG) is an international effort that aims at solving three-dimensional shapes of important biological macro-molecules with primary focus on proteins. One of the main bottlenecks in SG is the ability to produce dif-fraction quality crystals for X-ray crystallography based...

  • Describing and Comparing Protein Structures Using Shape Strings. Nanjiang Shu; Hovmöller, Sven; Zhou, Tuping // Current Protein & Peptide Science;Aug2008, Vol. 9 Issue 4, p310 

    Different methods for describing and comparing the structures of the tens of thousands of proteins that have been determined by X-ray crystallography are reviewed. Such comparisons are important for understanding the structures and functions of proteins and facilitating structure prediction, as...

  • Medicinal Chemistry and Properties of 1,2,4-Thiadiazoles. Tam, Tim Fat; Leung-Toung, Regis; Li, Wanren; Spino, Michael; Karimian, Khashayar // Mini Reviews in Medicinal Chemistry;Apr2005, Vol. 5 Issue 4, p367 

    1,2,4-Thiadiazole is a distinctive class of small heterocyclic thiol trapping agents that serve as an interesting pharmacophore in the design of inhibitors targeting the cysteine residues of proteins. X-Ray crystal structures of enzyme-inhibitor complex indicate that the cysteine thiol reacts...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics