Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction.
Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures. Protein structural flexibility is often characterized by fluctuations in the Cartesian coordinate space. On the other hand, the protein backbone can be mostly defined by two torsion angles ϕ and ψ only. We introduce a new flexibility descriptor, backbone torsion-angle fluctuation derived from the variation of backbone torsion angles from different NMR models. The torsion-angle fluctuations correlate with mean-squared spatial fluctuations derived from the same collection of NMR models. We developed a neural-network based real-value predictor based on sequence information only. The predictor achieved ten-fold cross-validated correlation coefficients of 0.59 and 0.60, and mean absolute errors of 22.7° and 24.3° for the angle fluctuation of ϕ and ψ, respectively. This predictor is expected to be useful for function prediction and protein structure prediction when predicted torsion angles are used as restraints. Both sequence- and structure-based prediction of torsion-angle fluctuation will be available at http://sparks.informatics.iupui.edu within the SPINE-X package.
Zhang
Tuo
T
School of Informatics, Indiana University Purdue University, Indianapolis, Indiana 46202, USA.
Faraggi
Eshel
E
Zhou
Yaoqi
Y
D000596:Amino Acids / Q000737:chemistry; D030562:Databases, Protein; D019906:Nuclear Magnetic Resonance, Biomolecular; D018583:Pliability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry; D054159:Torsion, Mechanical
D000596:Amino Acids; D011506:Proteins; D012997:Solvents
Proteins. 2005 Jul 1;60(1):139-47
15856480
Annu Rev Biophys Biomol Struct. 2003;32:69-92
12471064
J Mol Recognit. 2001 Jan-Feb;14(1):42-61
11180561
J Mol Biol. 2003 Aug 29;331(5):1157-70
12927549
Curr Opin Struct Biol. 2009 Apr;19(2):145-55
19327982
J Mol Biol. 2004 Mar 26;337(3):635-45
15019783
J Mol Biol. 1963 Jul;7:95-9
13990617
J Mol Biol. 1999 Oct 22;293(2):321-31
10550212
Protein Pept Lett. 2009;16(12):1447-54
20001907
Nucleic Acids Res. 1998 Sep 15;26(18):4280-90
9722650
Biopolymers. 1983 Dec;22(12):2577-637
6667333
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18908-13
16354836
Cell Mol Life Sci. 2006 Jan;63(2):207-19
16389462
Proteins. 2008 Apr;71(1):61-7
17932927
Proteins. 2003 Mar 1;50(4):629-35
12577269
Proteins. 2005 Oct 1;61(1):115-26
16080156
Proteins. 2005 Mar 1;58(4):905-12
15645415
Proteins. 2007 Mar 1;66(4):838-45
17177203
Structure. 2009 Nov 11;17(11):1515-27
19913486
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D296-301
16381870
Proteins. 2008 Aug;72(2):625-34
18247347
Proteins. 2009 Mar;74(4):847-56
18704931
J Mol Biol. 1991 Mar 20;218(2):397-412
2010917
Protein Sci. 1995 Oct;4(10):2118-22
8535248
Nature. 2005 Nov 3;438(7064):117-21
16267559
Proteins. 2005;61 Suppl 7:176-82
16187360
Proteins. 1999 Mar 1;34(4):453-63
10081958
Phys Rev Lett. 2010 Jun 4;104(22):228103
20867208
Protein Sci. 2005 Mar;14(3):633-43
15722444
Nat Biotechnol. 2001 Sep;19(9):805-6
11533628
Bioinformatics. 2005 Aug 15;21(16):3433-4
15955779
Protein Sci. 1997 Dec;6(12):2561-7
9416605
Proteins. 2004 May 1;55(2):368-82
15048828
Proteins. 2007 Jul 1;68(1):76-81
17397056
Proteins. 2009 Aug 15;76(3):617-36
19274736
CRC Crit Rev Biochem. 1981;9(4):293-349
7009056
Bioinformatics. 2003 Aug 12;19(12):1589-91
12912846
Proteins. 2008 Jul;72(1):427-33
18214956
J Mol Biol. 1999 Jan 29;285(4):1371-5
9917381
J Mol Biol. 1993 May 5;231(1):82-102
8496968
Structure. 1997 Jul 15;5(7):949-59
9261088
Mol Cell Proteomics. 2006 Jul;5(7):1212-23
16571897
Protein Eng. 2003 Feb;16(2):109-14
12676979
Proteins. 2008 Aug 15;72(3):929-35
18300253