Summary
A fast dynamic programming algorithm for the spatial superposition of protein structure without prior knowledge of an initial alignment has been developed. The program was applied to serine proteases, hemoglobins, cytochromes C, small copper-binding proteins, and lysozymes. In most cases the existing structural homology could be detected in a completely unbiased way. The results of the method presented are in general agreement with other studies. Applying our method, the different alignment results obtained by other authors for serine proteases and cytochromes C can be classified in terms of different alignment parameters such as gap penalties or cut-off length. Limitations of the method are discussed.
Similar content being viewed by others
References
Abagyan RA, Maiorov VN (1989) An automatic search for similar spatial arrangements of α-helices and β-strands in globular proteins. J Biomol Struct & Dyn 6:1045–1060
Adman ET (1985) Structure and function of small blue copper proteins. In: Harrison PM (ed) Metalloproteins, part I, chapter I. Verlag Chemie, Weinheim, pp 1–42
Adman ET, Jensen LH (1981) Structural features of azurin at 2.7 Angstroms resolution. Isr J Chem 21:8–12
Adman ET, Canters GW, Hill HAO, Kitchen NA (1982) The effect of pH and temperature on the structure of the active site of azurin fromPseudomonas aeruginosa. FEBS Lett 143: 287–292
Argos P, Rossmann MG (1979) Structural comparison of heme binding proteins. Biochemistry 18:4951–4960
Artymiuk PJ, Blake CCF (1981) Refinement of human lysozyme at 1.5 Angstroms resolution. Analysis of non-bonded and hydrogen-bond interactions. J Mol Biol 152:737–762
Baker EN (1988) Structure of azurin fromAlcaligenes denitrificans. Refinement at 1.8 Angstroms resolution and comparison of the two crystallographically independent molecules. J Mol Biol 203:1071–1095
Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanovichi T, Tatsumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535–542.
Bhatia GE (1981) Refinement of the crystal structure of oxidizedRhodospirillum rubrum cytochrome C2. Thesis, University of California, San Diego
Blevins RA, Tulinsky A (1985) The refinement and the structure of the dimer of alpha-chymotrypsin at 1.67 angstroms resolution. J Biol Chem 260:4264–4275
Bode W, Schwager P, Huber R (1976) Structural studies on the pancreatic trypsin inhibitor-trypsin complex and its free components. Structure and function relationships in serine protease inhibition and catalysis. Miami Winter Symposium 11: 43–76
Bode W, Chen Z, Bartels K, Kutzbach C, Schmidt-Kastner G, Bartunik H (1983) Refined 2 Angstroms x-ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, structure and its comparison with bovine trypsin. J Mol Biol 164:237–282
Carter DC, Melis KA, Donnell SEO, Burgess BK, Furey WF Jr, Wang BC, Stout CD (1985) Crystal structure ofAzotobacter cytochrome C5 at 2.5 Angstroms resolution. J Mol Biol 184: 279–295
Chotia C, Lesk AM (1982) Evolution of proteins formed by β-sheets. J Mol Biol 160:309–323
Chotia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823–826
Church WB, Guss JM, Potter JJ, Freeman HC (1986) The crystal structure of mercury-substituted poplar plastocyanin at 1.9-Angstroms resolution. J Biol Chem 261:234–237
Cohen GH, Silverton EW, Davies DR (1981) Refined crystal structure of gamma-chymotrypsin at 1.9 Angstroms resolution. Comparison with other pancreatic proteases. J Mol Biol 148:449–479
Cohen TE, Sternberg MJE (1980) On the prediction of protein structure. J Mol Biol 138:321–333
Delbaere LTJ, Brayer GD (1985) The 1.8 Angstroms structure of the complex between chymostatin andStreptomyces griseus protease A. A model for serine protease catalytic tetrahedral intermediates. J Mol Biol 183:89–103
Diamond R (1974) Real-space refinement of the structure of hen egg-white lysozyme. J Mol Biol 82:371–391
Fermi G, Perutz MF, Shaanan B, Fourme R (1984) The crystal structure of human deoxyhaemoglobin at 1.74 Angstroms resolution. J Mol Biol 175:159–174
Fetrow JS, Zehfus MH, Rose GD (1988) Protein folding: new twists. Bio/Technology 6:167–171
Fujinaga M, James MNG (1987) Rat submaxillary gland serine protease, tonin. Structure solution and refinement at 1.8 Angstroms resolution. J Mol Biol 195:373–396
Fujinaga M, Delbaere LTJ, Brayer GD, James MNG (1985) Refined structure of alpha-lytic protease at 1.7 Angstroms resolution. Analysis of hydrogen bonding and solvent structure. J Mol Biol 184:479–502
Golub GH, Reinsch C (1971) Singular value decomposition and least squares solution. In: Handbook for automatic computations II: linear Algebra. Springer, Berlin, pp 134–151
Guss JM, Freeman HC (1983) Structure of oxidized poplar plastocyanin at 1.6 Angstroms resolution. J Mol Biol 169: 521–563
Hogle J (1978) The structure of the monoclinic crystal form of hen egg white lysozyme at 2.5 Angstroms resolution. Comparison of a protein structure in several crystalline environments. Thesis, University of Wisconsin-Madison
Honzatko RB, Hendrickson WA, Love WE (1985) Refinement of a molecular model for lamprey hemoglobin fromPetromyzon marinus. J Mol Biol 184:147–164
Hubbard TJ, Blundell TL (1987) Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng 1:159–171
James MNG, Sielecki AR, Brayer GD, Delbaere LTJ, Bauer CA (1980) Structures of product and inhibitor complexes ofStreptomyces griseus protease A at 1.8 Angstroms resolution. A model for serine protease catalysis. J Mol Biol 144:43–88
Johnson MS, Šali A, Blundell TL (1990a) Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol 183:670–690
Johnson MS, Sutcliffe MJ, Blundell TL (1990b) Molecular anatomy: phylogenetic relationships derived from three-dimensional structures of proteins. J Mol Evol 30:43–59
Kabsch W (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr sect A 32:922–923
Kernighan BW, Ritchie DM (1973) The C programming language. Prentice-Hall, Englewoods Cliffs NJ
Kurachi K, Sieker LC, Jensen LH (1976) Structures of triclinic mono- and di-N-acetylglucosamine: lysozyme complexes—a crystallographic study. J Mol Biol 101:11–24
Ladner RC, Heidner EG, Perutz MF (1977) The structure of horse methaemoglobin at 2.0 Angstroms resolution. J Mol Biol 114:385–414
Liebman MN (1981) Correlation of structure and function in biologically active small molecules and macromolecules by distance matrix partitioning. In: Griffin, Duax (eds) Molecular structure and biological activity. Elsevier, North Holland, pp 193–212
Liebman MN (1985) Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity. Biopolymers 24:1721–1758
Liebman MN (1986) Structural organization in the serine proteases. Enzyme 36:115–140
Louie AH, Somorjai RL (1982) Differential geometry of proteins: a structural and dynamical representation of patterns. J Theor Biol 98:189–209
Louie AH, Somorjai RL (1983) Differential geometry of proteins: helical approximations. J Mol Biol 168:143–162
Matsuura Y, Takano T, Dickerson RE (1982) Structure of cytochrome C551 fromPseudomonas aeruginosa. Refined at 1.6 Angstroms resolution and comparison of the two redox forms. J Mol Biol 156:389–409
McLachlan AD (1979) Gene duplication in structural evolution of chymotrypsin. J Mol Biol 128:49–79
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 48:443–453
Ochi H, Hata Y, Tanaka N, Kakudo M, Sakurai T, Aihara S, Morita Y (1983) Structure of rice ferricytochrome c at 2.0 Angstroms resolution. J Mol Biol 166:407–418
Phillips DE (1970) The development of crystallographic enzymology. In: British biochemistry, past and present. Biochemical Society Symposium, vol. 31. Academic Press, London, pp. 11–28
Rackovsky S, Goldstein DA (1988) Protein comparison and classification: a differential geometric approach. Proc Natl Acad Sci USA 85:777–781
Rackovsky S, Scheraga HA (1980) Differential geometry and polymer conformation. 2. Development of a conformational distance function. Macromolecules 13:1440–1453
Rao ST, Rossmann MG (1973) Comparison of super-secondary structures in proteins. J Mol Biol 76:241–256
Read RJ, Fujinaga M, Sielecki AR, James MNG (1983) Structure of the complex ofStreptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8 Angstroms resolution. Biochemistry 22:4420–4433
Remington SJ, Matthews BW (1980) A systemtatic approach to the comparison of protein structures. J Mol Biol 140:77–99
Reynolds RA, Remington SJ, Weaver LH, Fisher RG, Anderson WF, Ammon HL, Matthews BW (1985) Structure of a serine protease from rat mast cells determined from twinned crystals by isomorphous and molecular replacement. Acta Crystallogr sect B 41:139–147
Richards FM, Kundrot CE (1988) Identification of structural motifs from protein coordinate data: secondary structure and first level supersecondary structure. Proteins 3:71–84
Rose GD, Gierasch LM, Smith JA (1985) Turns in peptides and proteins. Adv Protein Chem 37:1–109
Rossmann MG, Argos P (1976) Exploring structural homology of proteins. J Mol Biol 105:75–96
Rossmann MG, Argos P (1977) The taxonomy of protein structure. J Mol Biol 109:99–129
Salemme FR, Freer ST, Xuong NH, Alden RA, Kraut J (1973) The structure of oxidized cytochrome c2 ofRhodospirillum rubrum. J Biol Chem 248:3910–3921
Sarma R, Bott R (1976) Crystal structure of turkey egg-white lysozyme. Results of the molecular replacement method at 5 Angstroms resolution. J Mol Biol 106:1037–1046
Sawyer L, Shotton DM, Campbell JW, Wendell PL, Muirhead H, Watson HC, Diamond R, Ladner RC (1978) The atomic structure of crystalline porcine pancreatic elastase at 2.5 Angstroms resolution. Comparisons with the structure of alpha-chymotrypsin. J Mol Biol 118:137–208
Sipple MJ (1982) On the problem of comparing protein structures. J Mol Biol 156:359–388
Sklenar H, Etchebest C, Lavery R (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins Struct Funct Genet 6:46–60
Sutcliffe MJ, Haneef I, Carney D, Blundell TL (1987a) Knowledge based modelling of homologous proteins, part I: threedimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1:377–384
Sutcliffe MJ, Hayes FRF, Blundell TL (1987b) Knowledge based modelling of homologous proteins, part II: rules for the conformations of substituted sidechains. Protein Eng 1:385–392
Takano T (1977) Structure of myoglobin refined at 2.0 Angstroms resolution, II. Structure of deoxymyoglobin from sperm whale. J Mol Biol 110:569–584.
Takano T, Dickerson RE (1980) Redox conformation changes in refined tuna cytochrome C. Proc Natl Acad Sci USA 77: 6371–6375
Taylor WR, Orengo CO (1989) Protein structure alignment. J Mol Biol 208:1–22
Timkovich R, Dickerson RE (1976) The structure ofParacoccus denitrificans cytochrome c550. J Biol Chem 251:4033–4046
Vainshtein BK, Arutyunyan EG, Kuranova IP, Borisov VV, Sosfenov NI, Pavlovskii AG, Grebenko AI, Nekrasov YV (1978) X-ray diffraction study of leghemoglobin. Determination of the structure with 2.8 Angstroms resolution. Kristallografiya 23:517–527 [in Russian]
Walter J, Steigemann W, Singh TP, Bartunik H, Bode W, Huber R (1982) On the disordered activation domain in trypsinogen. Chemical labelling and low temperature crystallography. Acta Crystallogr sect B 38:1462–1472
Weaver LH, Grütter MG, Remington SJ, Gray TM, Isaacs NW, Matthews BW (1985) Comparison of goose-type, chickentype, and phage-type lysozymes illustrates the changes that occur in both amino acid sequence and three-dimensional structure during evolution. J Mol Evol 21:97–111
Weaver LH, Matthews BW (1987) Structure of bacteriophage T4 lysozyme refined at 1.7 Angstroms resolution. J Mol Biol 193:189–199
Zuker M, Somorjai RJ (1989) The alignment of protein structures in three dimensions. Bull Math Biol 51:55
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Rose, J., Eisenmenger, F. A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm. J Mol Evol 32, 340–354 (1991). https://doi.org/10.1007/BF02102193
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF02102193