Accurate Random Coil Chemical Shifts from an Analysis of Loop Regions in Native States of Proteins

被引：74

作者：

De Simone, Alfonso ^{[1
]}

Cavalli, Andrea ^{[1
]}

Hsu, Shang-Te Danny ^{[1
]}

Vranken, Wim ^{[2
]}

Vendruscolo, Michele ^{[1
]}

机构：

[1] Univ Cambridge, Dept Chem, Cambridge CB2 1EW, England

[2] European Bioinformat Inst, Cambridge CB10 1SD, England

来源：

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY | 2009年 / 131卷 / 45期

关键词：

GELATION FACTOR ABP-120; DICTYOSTELIUM-DISCOIDEUM; SECONDARY STRUCTURE; DENATURED STATES; ALPHA; DYNAMICS; DOMAIN; SERVER; MODEL; N-15;

D O I：

10.1021/ja904937a

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We present a method for calculating accurate random coil chemical shift values of proteins. These values are obtained by analyzing the relationship between the amino acid sequences in flexible loop regions of native states and the corresponding experimentally measured chemical shifts. We estimate the errors in the random coil chemical shift scales to be 0.31 ppm for C-13(a), 0.37 ppm for C-13(B), 0.31 ppm for (CO)-C-13, 0.68 ppm for N-15, 0.09 ppm for H-1, and 0.04 ppm for H-1(a).

引用

页码：16332 / +

页数：4

共 19 条

[1] The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts [J].

Berjanskii, Mark V. ;

Wishart, David S. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W531-W537

[2] A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering [J].

Bernadó, P ;

Blanchard, L ;

Timmins, P ;

Marion, D ;

Ruigrok, RWH ;

Blackledge, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (47) :17002-17007

[3] SEQUENCE-CORRECTED N-15 RANDOM COIL CHEMICAL-SHIFTS [J].

BRAUN, D ;

WIDER, G ;

WUTHRICH, K .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (19) :8466-8469

[4] Protein misfolding, functional amyloid, and human disease [J].

Chiti, Fabrizio ;

Dobson, Christopher M. .

ANNUAL REVIEW OF BIOCHEMISTRY, 2006, 75 :333-366

[5] Pockets of short-range transient order and restricted topological heterogeneity in the guanidine-denatured state ensemble of GED of dynamin [J].

Chugh, Jeetender ;

Sharma, Shilpy ;

Hosur, Ramakrishna V. .

BIOCHEMISTRY, 2007, 46 (42) :11819-11832

[6] Comparison of NMR structural and dynamics features of the urea and guanidine-denatured states of GED [J].

Chugh, Jeetender ;

Sharma, Shilpy ;

Hosur, Ramakrishna V. .

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 2009, 481 (02) :169-176

[7] Intrinsically unstructured proteins and their functions [J].

Dyson, HJ ;

Wright, PE .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2005, 6 (03) :197-208

[8] STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins [J].

Heinig, M ;

Frishman, D .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W500-W502

[9] Structure, Dynamics and Folding of an Immunoglobulin Domain of the Gelation Factor (ABP-120) from Dictyostelium discoideum [J].

Hsu, Shang-Te Danny ;

Cabrita, Lisa D. ;

Fucini, Paola ;

Dobson, Christopher M. ;

Christodoulou, John .

JOURNAL OF MOLECULAR BIOLOGY, 2009, 388 (04) :865-879

[10] 1H, 15N and 13C assignments of domain 5 of Dictyostelium discoideum gelation factor (ABP-120) in its native and 8M urea-denatured states [J].

Hsu, Shang-Te Danny ;

Cabrita, Lisa D. ;

Christodoulou, John ;

Dobson, Christopher M. .

BIOMOLECULAR NMR ASSIGNMENTS, 2009, 3 (01) :29-31

← 1 2 →