Detection of trans–cis flips and peptide-plane flips in protein structures

A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip.

[1]  E. V. Makeyev,et al.  A mechanism for initiating RNA-dependent RNA polymerization , 2001, Nature.

[2]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[3]  D. Christianson,et al.  Inhibition of human arginase I by substrate and product analogues. , 2010, Archives of biochemistry and biophysics.

[4]  C. Janson,et al.  Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[5]  G. Langlet,et al.  International Tables for Crystallography , 2002 .

[6]  T. A. Jones,et al.  The Uppsala Electron-Density Server. , 2004, Acta crystallographica. Section D, Biological crystallography.

[7]  W. Cheng,et al.  Structures of Helicobacter pylori Shikimate Kinase Reveal a Selective Inhibitor-Induced-Fit Mechanism , 2012, PloS one.

[8]  James C. Sacchettini,et al.  Crystal structure of a plant catechol oxidase containing a dicopper center , 1998, Nature Structural Biology.

[9]  G. N. Ramachandran,et al.  An explanation for the rare occurrence of cis peptide units in proteins and polypeptides. , 1976, Journal of molecular biology.

[10]  Tristan Ian Croll,et al.  The rate of cis-trans conformation errors is increasing in low-resolution crystal structures. , 2015, Acta crystallographica. Section D, Biological crystallography.

[11]  Anastassis Perrakis,et al.  Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank , 2011, Bioinform..

[12]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[13]  B. Matthews,et al.  Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Dimitrios I. Fotiadis,et al.  Prediction of cis/trans isomerization using feature selection and support vector machines , 2009, J. Biomed. Informatics.

[15]  C Cambillau,et al.  Revisiting the Catalytic CuZ Cluster of Nitrous Oxide (N2O) Reductase , 2000, The Journal of Biological Chemistry.

[16]  J E Wampler,et al.  Occurrence and role of cis peptide bonds in protein structures. , 1990, Journal of molecular biology.

[17]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[18]  Yigong Shi,et al.  Mechanism of procaspase-8 activation by c-FLIPL , 2009, Proceedings of the National Academy of Sciences.

[19]  K. N. Trueblood,et al.  On the rigid-body motion of molecules in crystals , 1968 .

[20]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[21]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[22]  G. D. Markham,et al.  Crystal structure of human type II inosine monophosphate dehydrogenase: implications for ligand binding and drug design. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. McNicholas,et al.  Presenting your structures: the CCP4mg molecular-graphics software , 2011, Acta crystallographica. Section D, Biological crystallography.

[24]  A. Scheidig,et al.  High resolution crystal structures of human Rab4a in its active and inactive conformations , 2005, FEBS letters.

[25]  Gert Vriend,et al.  BDB: databank of PDB files with consistent B-factors. , 2014, Protein engineering, design & selection : PEDS.

[26]  Z. Zeng,et al.  Optical 2-benzyl-5-hydroxy-4-oxopentanoic acids against carboxypeptidase A: Synthesis, kinetic evaluation and X-ray crystallographic study , 2010 .

[27]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[28]  H. Scheraga,et al.  Stability of cis, trans, and nonplanar peptide groups. , 1976, Macromolecules.

[29]  S. Withers,et al.  Order and disorder: differential structural impacts of myricetin and ethyl caffeate on human amylase, an antidiabetic target. , 2012, Journal of medicinal chemistry.

[30]  M. Saraste,et al.  FEBS Lett , 2000 .

[31]  D. Schomburg,et al.  Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. , 2002, Biochemistry.

[32]  J. C. Evans,et al.  Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Chandrasekhar,et al.  Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers. , 1998, Journal of molecular biology.

[34]  Roland L. Dunbrack,et al.  Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites , 2011, Proceedings of the National Academy of Sciences.

[35]  Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis. , 2002, Biochemistry.

[36]  D. Pal,et al.  Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations. , 1999, Journal of molecular biology.

[37]  R. Stenkamp.  Anatomy of a trans-cis peptide transition during least-squares refinement of rubrerythrin. , 2005, Acta crystallographica. Section D, Biological crystallography.

[38]  Vincent Breton,et al.  PDB_REDO: automated re-refinement of X-ray structure models in the PDB , 2009, Journal of applied crystallography.

[39]  B. González,et al.  Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of β‐glucosidase A from Bacillus polymyxa , 1998, Proteins.

[40]  R. Huber,et al.  Crystal structure of 12-oxophytodienoate reductase 3 from tomato: Self-inhibition by dimerization , 2006, Proceedings of the National Academy of Sciences.

[41]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[42]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[43]  Shmuel Pietrokovski,et al.  Breaking up is hard to do , 1998, Nature Structural Biology.

[44]  T. Hahn.  International tables for crystallography , 2002 .

[45]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[46]  S. Withers,et al.  Mechanistic and Structural Analysis of a Family 31 α-Glycosidase and Its Glycosyl-enzyme Intermediate* , 2005, Journal of Biological Chemistry.

[47]  M-L Wang,et al.  Support vector machines for prediction of peptidyl prolyl cis/trans isomerization. , 2008, The journal of peptide research : official journal of the American Peptide Society.

[48]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[49]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[50]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[51]  Ian J. Tickle,et al.  Statistical quality indicators for electron-density maps , 2012, Acta crystallographica. Section D, Biological crystallography.

[52]  A. Jabs,et al.  Non-proline cis peptide bonds in proteins. , 1999, Journal of molecular biology.

[53]  R J Fletterick,et al.  Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex. , 1997, Biochemistry.

[54]  Characterization of alpha-nitromethyl ketone as a new zinc-binding group based on structural analysis of its complex with carboxypeptidase A. , 2009, Bioorganic & medicinal chemistry letters.

[55]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[56]  Dirk Labudde,et al.  COPS - Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information , 2005, Bioinform..

[57]  M. Weiss,et al.  A method to detect nonproline cis peptide bonds in proteins. , 1999, Biopolymers.

[58]  David G. Myszka,et al.  Covalent inhibition revealed by the crystal structure of the caspase-8/p35 complex , 2001, Nature.

[59]  S. Cottaz,et al.  The glucosinolate-myrosinase system. New insights into enzyme-substrate interactions by use of simplified inhibitors. , 2005, Organic & biomolecular chemistry.

[60]  A. Jabs,et al.  Peptide bonds revisited , 1998, Nature Structural &Molecular Biology.

[61]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[62]  Mark von Itzstein,et al.  Sialic Acid Recognition by Vibrio cholerae Neuraminidase* , 2004, Journal of Biological Chemistry.

[63]  H. Moriyama,et al.  Structure of human translin at 2.2 A resolution. , 2004, Acta crystallographica. Section D, Biological crystallography.

[64]  BMC Bioinformatics , 2005 .

[65]  S. Paik,et al.  Crystal Structure of the TLR1-TLR2 Heterodimer Induced by Binding of a Tri-Acylated Lipopeptide , 2007, Cell.

[66]  Robert Preissner,et al.  Prediction of prolyl residues in cis‐conformation in protein structures on the basis of the amino acid sequence , 1990, FEBS letters.

[67]  B. Matthews.  Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.

[68]  Gert Vriend,et al.  PDB Improvement Starts with Data Deposition , 2007, Science.

[69]  Robert Huber,et al.  Structure quality and target parameters , 2006 .

[70]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[71]  Bradley S Moore,et al.  Binding of Two Flaviolin Substrate Molecules, Oxidative Coupling, and Crystal Structure of Streptomyces coelicolor A3(2) Cytochrome P450 158A2* , 2005, Journal of Biological Chemistry.

[72]  W. Steigemann,et al.  Two cis‐prolines in the Bence‐Jones protein Rei and the cis‐pro‐bend , 1974, FEBS letters.

[73]  M Vijayan,et al.  Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex. , 1996, Journal of molecular biology.

[74]  Krista Joosten,et al.  PDB_REDO: constructive validation, more than just looking for errors , 2012, Acta crystallographica. Section D, Biological crystallography.

[75]  J. Hermoso,et al.  Crystal structure of beta-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases. , 1998, Journal of molecular biology.

[76]  S. Hayward,et al.  Peptide‐plane flipping in proteins , 2001, Protein science : a publication of the Protein Society.

[77]  Jiangning Song,et al.  Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information , 2006, BMC Bioinformatics.

[78]  J. Thornton,et al.  Influence of proline residues on protein conformation. , 1991, Journal of molecular biology.

[79]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[80]  T. Ramya,et al.  Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure. , 2004, Acta crystallographica. Section D, Biological crystallography.