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Atomic displacement parameters in structural biology - Amino Acids

  • ️Carugo, Oliviero
  • ️Fri May 11 2018
  • Alber T, Petsko GA, Tsernoglou D (1976) Crystal structure of elastase-substrate complex at—55 degrees C. Nature 263:297–300

    Article  PubMed  CAS  Google Scholar 

  • Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 3:173–181

    Article  Google Scholar 

  • Bahar I, Rana Atilgan A, Demirel MC, Erman B (1998) Vibrational Dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett 80:2733–2736

    Article  CAS  Google Scholar 

  • ben-Avraham D, Tirion MM (1998) Normal modes analyses of macromolecules. Physica A. 249:415–423

    Article  Google Scholar 

  • Benkert P, Tosatto SC, Schomburg D (2008) QMEAN: a comprehensive scoring function for model quality assessment. Proteins. 71:261–277

    Article  PubMed  CAS  Google Scholar 

  • Bhaskaran R, Ponnuswamy PK (1988) Positional flexibilities of amino acid residues in globular proteins. Chem Biol Drug Des 32:241–255

    CAS  Google Scholar 

  • Bolognesi M, Rosano C, Losso R, Borassi A, Rizzi M, Wittenberg JB, Boffi A, Ascenzi P (1999) Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an X-ray crystallographic study. Biophys J 77:1093–1099

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bury CS, Carmichael I, Garman EF (2017) OH cleavage from tyrosine: debunking a myth. J Synchrotron Radiat 24:7–18

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Carugo O, Argos P (1997) Protein-protein crystal-packing contacts. Protein Sci 6:2261–2263

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Carugo O, Argos P (1999) Reliability of atomic displacement parameters in protein crystal structures. Acta Crystallogr D Biol Crystallogr 55(Pt 2):473–478

    Article  PubMed  CAS  Google Scholar 

  • Carugo O, Djinovic-Carugo K (2005) When X-rays modify the protein structure: radiation damage at work. Trends Biochem Sci 30:213–219

    Article  PubMed  CAS  Google Scholar 

  • Cruickshank DWJ (1999) Remarks about protein structure precision. Acta Cryst. D55:583–593

    CAS  Google Scholar 

  • Dauter Z, Lamzin VS, Wilson KS (1997) The benefits of atomic resolution. Curr Opin Struct Biol 7:681–688

    Article  PubMed  CAS  Google Scholar 

  • Declercq JP, Evrard C, Lamzin V, Parello J (1999) Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core. Protein Sci 8:2194–2204

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Djinovic-Carugo K, Carugo O (2015) Missing strings of residues in protein crystal structures. Intrinsically Disord Proteins 3(1):1–7

    Article  Google Scholar 

  • Duarte J, Srebniak A, Scharer M, Capitani G (2012) Protein interface classification by evolutionary analysis. BMC Bioinform 13:334

    Article  Google Scholar 

  • Dunitz JD, Maverick EF, Trueblood KN (1988a) Atomic motions in molecular crystals from diffraction measurements. Angew Chem Int Ed Eng 27:880–895

    Article  Google Scholar 

  • Dunitz JD, Shomaker V, Trueblood KN (1988b) Interpretation of atomic displacement parameters from diffraction studies of crystals. J Phys Chem 92:856–867

    Article  CAS  Google Scholar 

  • Elgavish S, Shaanan B (1998) Structures of the Erythrina corallodendron lectin and of its complexes with mono- and disaccharides. J Mol Biol 277:817–932

    Article  Google Scholar 

  • Erman B (2016) Universal features of fluctuations in globular proteins. Proteins. 84:721–725

    Article  PubMed  CAS  Google Scholar 

  • Fenwick RB, van den Bedem H, Fraser JS, Wright PE (2014) Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proc Natl Acad Sci USA 111:E445–E454

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fraser JS, van den Bedem H, Samelson AJ, Lang T, Holton JM, Echols N, Albera T (2011a) Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci USA 108:16247–16252

    Article  PubMed  PubMed Central  Google Scholar 

  • Fraser JS, van den Bedemb HE, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T (2011b) Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci USA 108:16247–16252

    Article  PubMed  PubMed Central  Google Scholar 

  • Frauenfelder H, Petsko GA (1980) Structural dynamics of liganded myoglobin. Biophys J 32:465–483

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Frauenfelder H, Petsko GA, Tsernoglou D (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280:558–563

    Article  PubMed  CAS  Google Scholar 

  • Frauenfelder H, Hartmann H, Karplus M, Kuntz IDJ, Kuriyan J, Parak F, Petsko GA, Ringe D, Tilton RFJ, Connolly ML et al (1987) Thermal expansion of a protein. Biochemistry 26:254–261

    Article  PubMed  CAS  Google Scholar 

  • Gao J, Zhang T, Zhang H, Shen S, Ruan J, Kurgan L (2010) Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility. Proteins. 78:2114–2130

    PubMed  CAS  Google Scholar 

  • Garman E (2003) ‘Cool’ crystals: macromolecular cryocrystallography and radiation damage. Curr Opin Struct Biol. 13:545–551

    Article  PubMed  CAS  Google Scholar 

  • Garman EF, Owen RL (2006) Cryocooling and radiation damage in macromolecular crystallography. Acta Crystallogr. D62:32–47

    CAS  Google Scholar 

  • Giacovazzo C, Monaco HL, Artioli G, Viterbo D, Ferraris G, Gilli G, Zanotti G, Catti M (2002) Fundamentals of crystallography. Oxford University Press, Oxford

    Google Scholar 

  • Gianese G, Bossa F, Pascarella S (2002) Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes. Proteins 47:236–249

    Article  PubMed  CAS  Google Scholar 

  • Gohlke H, Kuhn LA, Case DA (2004) Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 56:322–327

    Article  PubMed  CAS  Google Scholar 

  • Gourinath S, Himmel DM, Brown JH, Reshetnikova L, Szent-Györgyi AG, Cohen C (2003) Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head. Structure. 11:1621–1627

    Article  PubMed  CAS  Google Scholar 

  • Haliloglu T, Bahar I (1999) Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins. 37:654–667

    Article  PubMed  CAS  Google Scholar 

  • Halle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci USA 99:1274–1279

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Halle B (2004) Biomolecular cryocrystallography: structural changes during flash-cooling. Proc Natl Acad Sci USA 101:4793–4798

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hartmann H, Parak F, Steigemann W, Petsko GA, Ponzi DR, Frauenfelder H (1982) Conformational substates in a protein: structure and dynamics of metmyoglobin at 80 K. Proc Natl Acad Sci USA 79:4967–4971

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Higo J, Umeyama H (1997) Protein dynamics determined by backbone conformation and atom packing. Prot Eng. 10:373–380

    Article  CAS  Google Scholar 

  • Hinsen K, Kneller G (1999) A simplified force field for describing vibrational protein dynamics over the whole frequency range. J Chem Phys. 111:10766–10769

    Article  CAS  Google Scholar 

  • Holton JM (2009) A beginner’s guide to radiation damage. J Synchrotron Radiat 16:133–142

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huang YJ, Acton TB, Montelione GT (2014) DisMeta: a meta server for construct design and optimization. Methods Mol Biol 1091:3–16

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huang J, Xie DF, Feng Y (2017) Engineering thermostable (R)-selective amine transaminase from Aspergillus terreus through in silico design employing B-factor and folding free energy calculations. Biochem Biophys Res Commun 483:397–402

    Article  PubMed  CAS  Google Scholar 

  • Ishida T, Kinoshita K (2008) Prediction of disordered regions in proteins based on the meta approach. Bioinformatics 24:1344–1348

    Article  PubMed  CAS  Google Scholar 

  • Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins. 44:150–165

    Article  PubMed  CAS  Google Scholar 

  • Janin J, Rodier F (1995) Protein-protein interaction at crystal contacts. Proteins. 23:580–587

    Article  PubMed  CAS  Google Scholar 

  • Jiao X, Ranganathan S (2017) Prediction of interface residue based on the features of residue interaction network. J Theor Biol 432:49–54

    Article  PubMed  CAS  Google Scholar 

  • Joosten RP, Long F, Murshudov GN, Perrakis A (2014) The PDB_REDO server for macromolecular structure model optimization. IUCrJ. 1:213–220

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Juers DH, Matthews BW (2001) Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J Mol Biol 311:851–862

    Article  PubMed  CAS  Google Scholar 

  • Karplus PA, Schulz GE (1985) Preiction of chain flexibility in proteins. Natuwissenschaften. 72:212–213

    Article  CAS  Google Scholar 

  • Kozlowski LP, Bujnicki JM (2012) MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinform 13:111

    Article  Google Scholar 

  • Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797

    Article  PubMed  CAS  Google Scholar 

  • Kundu S, Melton JS, Sorensen DC, Phillips GN Jr (2002) Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 83:723–732

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kuzmanic A, Pannu NS, Zagrovic B (2014) X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals. Nat Commun 5:3220

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Läuger P (1985) Ionic channels with conformational substates. Biophys J 47:581–590

    Article  PubMed  PubMed Central  Google Scholar 

  • Levitt M, Sander C, Stern PS (1985) Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 181:423–447

    Article  PubMed  CAS  Google Scholar 

  • Lieutaud P, Canard B, Longhi S (2008) MeDor: a metaserver for predicting protein disorder. BMC Genomics 9(Suppl 2):S25

    Article  PubMed  PubMed Central  Google Scholar 

  • Lieutaud P, Ferron F, Longhi S (2016) Predicting conformational disorder. Methods Mol Biol 1415:265–299

    Article  PubMed  CAS  Google Scholar 

  • Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB (2003) Protein disorder prediction: implications for structural proteomics. Structure (Camb). 11(11):1453–1459

    Article  CAS  Google Scholar 

  • Liu Q, Kwoh CK, Li J (2010) Identifying protein-protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area. Amino Acids 38:263–270

    Article  PubMed  CAS  Google Scholar 

  • Liu Q, Kwoh CK, Li J (2013) Binding affinity prediction for protein-ligand complexes based on β contacts and B factor. J Chem Inf Model 53:3076–3085

    Article  PubMed  CAS  Google Scholar 

  • Liu Q, Li Z, Li J (2014) Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts. BMC Bioinform 15:S3

    Google Scholar 

  • MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 102:3586–3616

    Article  PubMed  CAS  Google Scholar 

  • Maguid S, Fernández-Alberti S, Parisi G, Echave J (2006) Evolutionary conservation of protein backbone flexibility. J Mol Evol 63:448–457

    Article  PubMed  CAS  Google Scholar 

  • Necci M, Piovesan D, Dosztányi Z, Tosatto SCE (2017) MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. Bioinformatics 33:1402–1404

    PubMed  Google Scholar 

  • Nguyen DD, Xia K, Wei GW (2016) Generalized flexibility-rigidity index. J Chem Phys. 144:234106

    Article  PubMed  CAS  Google Scholar 

  • Pan XY, Shen HB (2009) Robust prediction of B-factor profile from sequence using two-stage SVR based on random forest feature selection. Protein Pept Lett 16:1447–1454

    Article  PubMed  CAS  Google Scholar 

  • Pang YP (2016) Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins. Heliyon. 2:e00161

    Article  PubMed  PubMed Central  Google Scholar 

  • Parthasarathy S, Murthy MRN (1997) Analysis of temperature factor distribution in high-resolution protein structures. Protein Sci 6:2561–2567

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Parthasarathy S, Murthy MRN (1999) On the correlation between the main-chain and side-chain atomic displacement parameters (B values) in high-resolution protein structures. Acta Crystallogr. D55:173–180

    CAS  Google Scholar 

  • Parthasarathy S, Murthy MR (2000) Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng 13:9–13

    Article  PubMed  CAS  Google Scholar 

  • Potenza E, Domenico TD, Walsh I, Tosatto SC (2015) MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic Acids Res. 43:D315–D320

    Article  PubMed  CAS  Google Scholar 

  • Ragone R, Facchiano F, Facchiano A, Facchiano AM, Colonna G (1989) Plexibility plot of proteins. Prot Eng. 2:497–504

    Article  CAS  Google Scholar 

  • Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357:423–424

    Article  PubMed  CAS  Google Scholar 

  • Rathi PC, Fulton A, Jaeger K-E, Gohlke H (2016) Application oft he rigidity theory tot he thermostabilization of Lipase A from Bacillus subtilis. PLoS Comput Biol 12:e1004754

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reetz MT, Carballeira JD, Vogel A (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Eng. 45:7745–7751

    Article  CAS  Google Scholar 

  • Ringe D, Petsko GA (1986) Study of protein dynamics by X-ray diffraction. Methods Enzymol 131:389–433

    Article  PubMed  CAS  Google Scholar 

  • Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H (2017) Conformational variation of proteins at room temperature is not dominated by radiation damage. J Synchrotron Radiat 24:73–82

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schmidt A, Lamzin VS (2010) Internal motion in protein crystal structures. Protein Sci 19:944–953

    PubMed  PubMed Central  CAS  Google Scholar 

  • Siglioccolo A, Gerace R, Pascarella S (2010) “Cold spots” in protein cold adaptation: insights from normalized atomic displacement parameters (B-factors). Biophys Chem 153:104–114

    Article  PubMed  CAS  Google Scholar 

  • Singh TP, Bode W, Huber R (1980) Low-temperature protein crystallography. Effect on flexibility, temperature factor, mosaic spread, extinction and diffuse scattering in two examples: bovine trypsinogen and Fc fragment. Acta Cryst. B36:621–627

    Article  CAS  Google Scholar 

  • Smith JL, Hendrickson WA, Honzatko RB, Sheriff S (1986) tructural heterogeneity in protein crystals. Biochemistry 25:5018–5027

    Article  PubMed  CAS  Google Scholar 

  • Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G (2003) Improved amino acid flexibility parameters. Protein Sci 12:1060–1072

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stein DL (1985) A model of protein conformational substates. Proc Natl Acad Sci USA 82:3670–3672

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tilton RFJ, Dewan JC, Petsko GA (1992) Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry 31:2469–2481

    Article  PubMed  CAS  Google Scholar 

  • Tirion MM (1996) Large amplitude elastic motions in proteins from a single-parameter. Atomic analysis. Phys Rev Lett. 77:1905–1908

    Article  PubMed  CAS  Google Scholar 

  • Trueblood KN, Bürgi H-B, Burzlaff H, Dunitz JC, Gramaccioli CM, Schulz HH, Shmueli U, Abrahams SC (1996) Atomic displacement parameter nomenclature. Report of a subcommittee on atomic displacement parameter nomenclature. Acta Cryst. A52:770–781

    Article  CAS  Google Scholar 

  • Vihinen M, Torkkila E, Riikonen P (1994) Accuracy of protein flexibility predictions. Proteins. 19:141–149

    Article  PubMed  CAS  Google Scholar 

  • Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L (2014) Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity. Acta Cryst. D70:2833–2839

    Google Scholar 

  • Warkentin M, Thorne RE (2009) Slow cooling of protein crystals. J Appl Cryst. 42:944–952

    Article  CAS  Google Scholar 

  • Warkentin M, Thorne RE (2010) Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements. Acta Cryst. D66:1092–1100

    Google Scholar 

  • Watson HC (1969) The stereochemistry of the protein myoglobin. Prog Stereochem 4(299–312):5

    Google Scholar 

  • Weiss MS (2007) On the interrelationship between atomic displacement parameters (ADPs) and coordinates in protein structures. Acta Crystallogr. D63:1235–1242

    Google Scholar 

  • Woldeyes RA, Sivak DA, Fraser JS (2014) E pluribus unum, no more: from one crystal, many conformations. Curr Opin Struct Biol 28:56–62

    Article  PubMed  CAS  Google Scholar 

  • Xia K, Opron K, Wei GW (2015) Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM). J Chem Phys. 143:204106

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yang J, Wang Y, Zhang Y (2016) ResQ: an Approach to unified estimation of B-factor and residue-specific error in protein structure prediction. J Mol Biol 428:693–701

    Article  PubMed  CAS  Google Scholar 

  • Yuan Z, Bailey TL, Teasdale RD (2005) Prediction of protein B-factor profiles. Proteins. 58:905–912

    Article  PubMed  CAS  Google Scholar 

  • Zanotti G (2002) Protein Crystallography. In: Giacovazzo C (ed) Fundamental of crystallography. Oxfor University Press, Oxford, pp 667–757

    Google Scholar 

  • Zhang XF, Yang GY, Zhang Y, Xie Y, Withers SG, Feng Y (2016) A general and efficient strategy for generating the stable enzymes. Sci Rep. 6:33797

    Article  PubMed  PubMed Central  CAS  Google Scholar