D.S. Wishart and B.D. Sykes
Department of Biochemistry, University of Alberta, Edmonton, Canada.
Abstract: A simple technique for identifying protein secondary structures through the analysis of backbone 13C chemical shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647-1651] which was originally developed for the analysis of 1Ha chemical shifts. By extending the Chemical-Shift Index to include 13Ca, 13Cb and carbonyl 13C chemical shifts, it is now possible to use four independent chemical-shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C chemical-shift indices to produce a 'consensus' estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C chemical shifts, without recourse to NOE measurements.
J Biomol NMR 1994 Mar;4(2):171-80
Below is the updated table of proteins from the BMRB database that comprise the 13C Chemical Shift Index
Protein | BMRB code: |
Interleukin-1beta | 1061 |
Ovomucoid third domain | 1375 |
Cytochrome c | 1404 |
Micrococcal nuclease | 1581 |
Tendamistat | 1642 |
Ribonuclease H | 1657 |
Ribonuclease T1 | 1658 |
Flavodoxin | 1673 |
Thioredoxin | 1812 |
Interleukin 4 | 2031 |
Phosphocarrier protein HPr | 2060 |
Cyclophilin | 2208 |
Phosphocarrier protein HPr | 2371 |
Lysozyme | 2542 |
Basic pancreatic trypsin inhibitor | 262 |
Thioredoxin | 283 |
Transcriptional regulator ner | 287 |
OB-fold sub-domain of staphylococcal nuclease' | 4010 |
Plastocyanin | 4019 |
Human carbonic anhydrase I | 4022 |
RNA-binding Interface to the Multiple-RBD ProteinSex-Lethal | 4028 |
Bovine Pancreatic Ribonuclease A | 4031 |
Apokedarcidin | 4036 |
Component IV glycera dibranchiata monomerichemoglobin-CO | 4038 |
Calcium-free form of the first C2-domain ofsynaptotagmin I | 4039 |
Escherichia Coli Topoisomerase I | 4045 |
Drosophila Heat Shock Factor | 4046 |
Urokinase-type plasminogen activator | 4049 |
Rubredoxin | 4050 |
Coiled Coil domain of Chicken Cartilage MatrixProtein | 4055 |
Calmodulin W-7 complex | 4056 |
Myoglobin carbon monoxide complex | 4061 |
Human fibroblast collagenase | 4064 |
Turkey ovomucoid third domain | 4068 |
FimC | 4070 |
RNA-1_Modulator_Protein | 4072 |
Oxidized human ferredoxin | 4073 |
DnaB helicase | 4075 |
Outer Surface Protein A | 4076 |
Group II Phospholipase A2 | 4078 |
A-Domain of HMG1 | 4079 |
Interferon-alpha-2a | 4081 |
Human Profilin | 4082 |
RNA Binding Domain of Mammalian hnRNP A1 Protein | 4084 |
Tumor Suppressor p16ink4a | 4086 |
E2 | 4087 |
peptide deformylase | 4089 |
Basic fibroblast growth factor | 4091 |
Core binding factor b subunit | 4092 |
Human Interleukin 4 | 4094 |
SacY(1-55) | 4095 |
RNase H domain of HIV-1 RVT strain BH10 | 4097 |
Liver Fatty Acid-Binding Protein | 4098 |
S100B-Ca(2+)-p53_peptide_complex | 4099 |
Mrf-2 | 4100 |
Cutinase | 4101 |
Metallo-beta-lactamase | 4102 |
Rat CD2 domain 1 | 4109 |
IM9 E9-complex | 4115 |
Human Elongation Factor-1beta | 4117 |
Isl-1 homeodomain | 4121 |
Second PDZ domain from human phosphatase hPTP1E | 4123 |
hPTP1E-Fas receptor complex | 4124 |
Single chain three helix bundle' | 4126 |
Origin DNA-binding domain of SV40 T-antigen | 4127 |
Cyanobacterial metallothionein gene repressor | 4128 |
Human ubiquitin-conjugating enzyme | 4132 |
Den-LysN | 4134 |
EH1 domain of mouse Eps15 | 4140 |
Neural cell adhesion molecule module 2 | 4143 |
F1Fo ATP Synthase Subunit c | 4146 |
Gallium putidaredoxin | 4149 |
Adenylate kinase from E. coli | 4152 |
Eotaxin | 4155 |
Protein Disulfide Isomerase | 4156 |
Tn916 integrase subunit 1 | 4160 |
Neural cell adhesion molecule module 1 | 4162 |
Tn916 integrase DNA complex | 4165 |
eps15 homology domain | 4184 |
CRABPII system | 4186 |
Adenylate kinase/AP5A complex | 4193 |
M13 major coat protein | 4197 |
N-terminal domain of syntaxin 1A | 4198 |
N-term linker Type III Antifreeze protein RD3 | 4199 |
Ets-1 Pointed | 4205 |
fibronectin | 4206 |
M13 major coat protein | 4209 |
TATA box binding protein associated factorII 230 | 4223 |
Glutaredoxin 3 system | 4225 |
Calcium binding subunit of troponin TnC monomer | 4232 |
Internal xylan binding domain from XYLD | 4241 |
Major Sperm Protein | 4242 |
Lymphoid enhancer-binding factor | 4248 |
Human NER factor XPA | 4249 |
Src homology domain 3 and 2 | 4251 |
Mbp1 | 4254 |
Mbp1(2-124) | 4256 |
RNAse-SA | 4259 |
Dihydrofolate reductase | 4262 |
PTB domain of Drosophila Numb protein/GPpY_peptidecomplex' | 4263 |
Ca2+/calmodulin - 26-residue peptide from ratCa2+/calmodulin dependent protein kinase | 4270 |
Methyl binding domain of MeCP2 | 4280 |
EDB | 4283 |
Calmodulin-Ca2+-Pump-Peptide Complex | 4284 |
DNase domain of colicin E9 | 4293 |
Titin type I domain | 4295 |
Major cold shock protein from E. coli | 4296 |
DnaB helicase N-terminal domain | 4297 |
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase | 4299 |
Pathogenesis-related Protein P14a | 4301 |
Cytokine receptor common beta chain domain4 | 4308 |
HasA | 4309 |
Bromodomain | 4312 |
Iron-containing superoxide dismutase | 4315 |
NS1(1-73) dimer | 4317 |
N-Terminal Domain of DNA Polymerase B | 4326 |
N-terminal inhibitory domain of human tissueinhibitor of metalloproteinases-1 | 4327 |
Streptomyces subtilisin inhibitor | 4331 |
ARID domain of dead-ringer protein | 4334 |
Methylamine loaded form of the Glycine CleavageSystem H-protein | 4336 |
Interleukin 1-beta | 4341 |
Iron-containing superoxide dismutase | 4342 |
Frataxin | 4344 |
CopZ | 4348 |
Nitrogen Regulatory protein C-C-term-3Ala | 4349 |
Inhibitor (Im9)-bound DNase domain of colicinE9 | 4352 |
E. coli maltose binding protein | 4354 |
Pbx1 homeodomain | 4357 |
S19 | 4369 |
Recombinant Onconase/P30 protein | 4371 |
VATN VCP-like ATPase of Thermoplasma N-domain | 4376 |
Human prion protein fragment 121-230 | 4379 |
Epithelial Cadherin | 4380 |
Capsid protein from Rous Sarcoma Virus | 4384 |
Translation initiation factor IF3 | 4394 |
Ribosomal protein L25 | 4395 |
Fractalkine | 4397 |
Skeletal N-troponin C | 4401 |
Human prion protein hPrP(23-230) | 4402 |
hnRNP K | 4405 |
GATA-1 N-terminal zinc finger | 4423 |
Ribonuclease HI | 4424 |
Methane monooxygenase regulatory protein B | 4431 |
Human prion protein fragment 90-230 | 4434 |
Merozoite Surface Protein 1 | 4437 |
Sea raven Type II antifreeze protein | 4452 |
CD58 adhesion domain, 1dCD58 | 4455 |
Hen Egg White Lysozyme | 4562 |
Ribosomal Protein S4 Delta 41 | 4577 |
Basic pancreatic trypsin inhibitor | 4661 |
Apoptotic protease activating factor 1 | 46 |
Basic pancreatic trypsin inhibitor | 485 |
Micrococcal nuclease | 497 |
Calmodulin | 547 |
T4 lysozyme | 915 |
Cytochrome c551 | 968 |