Mars - robust automatic backbone assignment of proteins

被引:225
作者
Jung, YS [1 ]
Zweckstetter, M [1 ]
机构
[1] Max Planck Inst Biophys Chem, D-37077 Gottingen, Germany
关键词
automated assignment; NMR; software; structural genomics; triple resonance; unfolded protein;
D O I
10.1023/B:JNMR.0000042954.99056.ad
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
MARS a program for robust automatic backbone assignment of C-13/N-15 labeled proteins is presented. MARS does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds and it can work with a wide variety of NMR experiments. Using only C-13(alpha)/C-13(beta) connectivity information, MARS allows automatic, error-free assignment of 96% of the 370-residue maltose-binding protein. MARS can successfully be used when data are missing for a substantial portion of residues or for proteins with very high chemical shift degeneracy such as partially or fully unfolded proteins. Other sources of information, such as residue specific information or known assignments from a homologues protein, can be included into the assignment process. MARS exports its result in SPARKY format. This allows visual validation and integration of automated and manual assignment.
引用
收藏
页码:11 / 23
页数:13
相关论文
共 44 条
[31]  
OLSON JB, 1994, J BIOMOL NMR, V4, P385
[32]   Efficient identification of amino acid types for fast protein backbone assignments [J].
Ou, HD ;
Lai, HC ;
Serber, Z ;
Dötsch, V .
JOURNAL OF BIOMOLECULAR NMR, 2001, 21 (03) :269-273
[33]   Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules [J].
Riek, R ;
Wider, G ;
Pervushin, K ;
Wüthrich, K .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (09) :4918-4923
[34]   MUSIC in triple-resonance experiments:: Amino acid type-selective 1H-15N correlations [J].
Schubert, M ;
Smalla, M ;
Schmieder, P ;
Oschkinat, H .
JOURNAL OF MAGNETIC RESONANCE, 1999, 141 (01) :34-43
[35]   NMR investigation of the multidrug transporter EmrE, an integral membrane protein [J].
Schwaiger, M ;
Lebendiker, M ;
Yerushalmi, H ;
Coles, M ;
Gröger, A ;
Schwarz, C ;
Schuldiner, S ;
Kessler, H .
EUROPEAN JOURNAL OF BIOCHEMISTRY, 1998, 254 (03) :610-619
[36]   High-resolution solution NMR structure of the Z domain of staphylococcal protein A [J].
Tashiro, M ;
Tejero, R ;
Zimmerman, DE ;
Celda, B ;
Nilsson, B ;
Montelione, GT .
JOURNAL OF MOLECULAR BIOLOGY, 1997, 272 (04) :573-590
[37]   Four-dimensional NMR spectroscopy of a 723-residue protein: Chemical shift assignments and secondary structure of malate synthase G [J].
Tugarinov, V ;
Muhandiram, R ;
Ayed, A ;
Kay, LE .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2002, 124 (34) :10025-10035
[38]   Assignment of the backbone resonances of oxidized Fe-superoxide dismutase, a 42 kDa paramagnet-containing enzyme [J].
Vathyam, S ;
Byrd, RA ;
Miller, AF .
JOURNAL OF BIOMOLECULAR NMR, 1999, 14 (03) :293-294
[39]   Characterizing the use of perdeuteration in NMR studies of large proteins C-13, N-15 and H-1 assignments of human carbonic anhydrase II [J].
Venters, RA ;
Farmer, BT ;
Fierke, CA ;
Spicer, LD .
JOURNAL OF MOLECULAR BIOLOGY, 1996, 264 (05) :1101-1116
[40]  
WANG AC, 1995, J BIOMOL NMR, V5, P376