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Garutti, Claudio (2009) Prediction of Protein-Ligand and Protein-Protein Interactions based on Local Surface Similarity. [Tesi di dottorato]

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Abstract (inglese)

The three-dimensional structure of a protein determines its function. This thesis describes a suite of methods for the problem of protein binding site recognition, based on a spin-images representation of the molecular surface. A procedure for cavity detection is coupled with a procedure for the recog- nition of similar regions in two proteins, and applied to the comparison of two protein's cavities, the all-to-all pairwise comparison of a set of cavities, and the recognition of multiple binding sites in one cavity. All the presented methods can be used to screen large collections of proteins.

Abstract (italiano)

La struttura tridimensionale di una proteina determina la sua funzione. Questa tesi descrive una suite di metodi per il problema del riconoscimento di siti di legame di proteine, basati su una rappresentazione a spin-images della supercie molecolare. Una procedura per l'identicazione di cavita' integrata con una procedura per il riconoscimento di regioni simili in due proteine, e applicata al confronto delle cavita' di due proteine, il confronto all-to-all pairwise di un insieme di cavita', e il riconoscimento di siti di legame multipli in una cavita'. I metodi presentato possono essere usati per analizzare vaste collezioni di proteine.

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Tipo di EPrint:Tesi di dottorato
Relatore:Guerra, Concettina - Toffolo, Gianna
Dottorato (corsi e scuole):Ciclo 21 > Scuole per il 21simo ciclo > INGEGNERIA DELL'INFORMAZIONE > BIOINGEGNERIA
Data di deposito della tesi:31 Gennaio 2009
Anno di Pubblicazione:2009
Parole chiave (italiano / inglese):bioinformatics, protein interactions, binding sites
Settori scientifico-disciplinari MIUR:Area 09 - Ingegneria industriale e dell'informazione > ING-INF/06 Bioingegneria elettronica e informatica
Struttura di riferimento:Dipartimenti > Dipartimento di Ingegneria dell'Informazione
Codice ID:1820
Depositato il:31 Gen 2009
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Le url contenute in alcuni riferimenti sono raggiungibili cliccando sul link alla fine della citazione (Vai!) e tramite Google (Ricerca con Google). Il risultato dipende dalla formattazione della citazione.

[1] R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, Cerca con Google

S. Ferro, E. Gasteiger, H. Huang, R. Lopez, and M. Magrane. UniProt: Cerca con Google

the Universal Protein knowledgebase. Nucleic Acids Research, 32:D115, Cerca con Google

2004. 45 Cerca con Google

[2] W.P. Arend. Interleukin-1 receptor antagonist. Advances in Immunology, Cerca con Google

54:167227, 1993. 2 Cerca con Google

[3] J.A. Barker and J.M. Thornton. An Algorithm for Constraint-Based Cerca con Google

Structural Template Matching: Application to 3D Templates with Sta- Cerca con Google

tistical Analysis. Bioinformatics, 19(13):1644{1649, 2003. 18, 37 Cerca con Google

[4] A. Ben-Shimon and M. Eisenstein. Looking at Enzymes from the Inside Cerca con Google

out: The Proximity of Catalytic Residues to the Molecular Centroid can Cerca con Google

be used for Detection of Active Sites and Enzyme{Ligand Interfaces. Cerca con Google

Journal of Molecular Biology, 351(2):309{326, 2005. 4, 60 Cerca con Google

[5] H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, Cerca con Google

H. Weissig, I.N. Shindyalov, and P.E. Bourne. The Protein Data Bank. Cerca con Google

Nucleic Acids Research, 28(1):235{242, Jan 1 2000. 25, 45 Cerca con Google

[6] T. A. Binkowski, A. Joachimiak, and J. Liang. Protein surface anal- Cerca con Google

ysis for function annotation in high-throughput structural genomics Cerca con Google

pipeline. Protein Science, 14(12):2972, 2005. 37 Cerca con Google

[7] T.A. Binkowski, L. Adamian, and J. Liang. Inferring functional rela- Cerca con Google

tionships of proteins from local sequence and spatial surface patterns. Cerca con Google

Journal of Molecular Biology, 332(2):505{526, Sep 12 2003. 37 Cerca con Google

67 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[8] M.E. Bock, G.M. Cortelazzo, C. Ferrari, and C. Guerra. Identifying Cerca con Google

Similar Surface Patches on Proteins using a Spin-Image Surface Repre- Cerca con Google

sentation. Proceedings CPM, pages 417{428, 2005. 18 Cerca con Google

[9] M.E. Bock, C. Garutti, and C. Guerra. Discovery of Similar Regions Cerca con Google

on Protein Surfaces. Journal of Computational Biology, 14(3):285{299, 2007. Cerca con Google

1, 36, 51 Cerca con Google

[10] M.E. Bock, C. Garutti, and C. Guerra. Eective Labeling of Molecular Cerca con Google

Surface Points for Cavity Detection and Location of Putative Binding Cerca con Google

Sites. Computational Systems Bioinformatics Conference, pages 263{274, 2007. 1 Cerca con Google

[11] M.E. Bock, C. Garutti, and C. Guerra. Cavity Detection and Matching Cerca con Google

for Binding Site Recognition. Theoretical Computer Science, 408:151{162, Cerca con Google

2008. 1 Cerca con Google

[12] G.P. Brady and P.F.W. Stouten. Fast prediction and visualization of Cerca con Google

protein binding pockets with PASS. Journal of computer-aided molecular Cerca con Google

design, 14(4):383{401, 2000. 37 Cerca con Google

[13] A. Brakoulias and R.M. Jackson. Towards a structural classication of Cerca con Google

phosphate binding sites in protein-nucleotide complexes: an automated Cerca con Google

all-against-all structural comparison using geometric matching. Proteins, Cerca con Google

56(2):250{260, Aug 1 2004. 37, 38 Cerca con Google

[14] J.M. Carsi, H.H. Valentine, and L.T. Potter. m2-Toxin: A Selective Cerca con Google

Ligand for M2 Muscarinic Receptors. Molecular Pharmacology, 56(5):933{ Cerca con Google

937, 1999. 2 Cerca con Google

[15] B.Y. Chen, D.H. Bryant, V.Y. Fofanov, D.M. Kristensen, A.E. Cruess, Cerca con Google

M. Kimmel, O. Lichtarge, and L.E. Kavraki. Cavity-Aware Motifs Re- Cerca con Google

duce False Positives in Protein Function Prediction. Computational Sys- Cerca con Google

tems Bioinformatics Conference, pages 311{323, 2006. 18, 38 Cerca con Google

[16] M. Comin, C. Guerra, and G. Zanotti. PROuST: A Comparison Cerca con Google

Method of Three-Dimensional Structures of Proteins Using Indexing Cerca con Google

Techniques. Journal of Computational Biology, 11(6):1061{1072, 2004. 7 Cerca con Google

68 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[17] M. Comin, C. Guerra, and G. Zanotti. Proust: a Comparison Method Cerca con Google

of Three-Dimensional Structures of Proteins using Indexing Techniques. Cerca con Google

Journal of Computational Biology, 11(6):1061{1072, 2004. 29, 33 Cerca con Google

[18] M.L. Connolly. Analytical Molecular Surface Calculation. Journal of Cerca con Google

Applied Crystallography, 16(5):548{558, 1983. 25, 46 Cerca con Google

[19] L.L. Conte, C. Chothia, and J. Janin. The atomic structure of protein- Cerca con Google

protein recognition sites. Journal of Molecular Biology, 285(5):2177{2198, Cerca con Google

1999. 3 Cerca con Google

[20] K.D. Corbett and J.M. Berger. Structural basis for topoisomerase Cerca con Google

VI inhibition by the anti-Hsp90 drug radicicol. Nucleic Acids Research, Cerca con Google

34(15):4269, 2006. 4 Cerca con Google

[21] D.G. Covell and A. Wallqvist. Analysis of protein-protein interactions Cerca con Google

and the eects of amino acid mutations on their energetics. The impor- Cerca con Google

tance of water molecules in the binding epitope. Journal of Molecular Cerca con Google

Biology, 269(2):281{297, 1997. 4 Cerca con Google

[22] L.P. Ehrlich and R.C. Wade. Protein-Protein Docking. Reviews in Com- Cerca con Google

putational Chemistry, 17:61{98, 2001. 3 Cerca con Google

[23] M. Gerstein. A resolution-sensitive procedure for comparing protein Cerca con Google

surfaces and its application to the comparison of antigen-combining Cerca con Google

sites. Foundations of Crystallography, 48(3):271{276, 1992. 7 Cerca con Google

[24] F. Glaser, R.J. Morris, R.J. Najmanovich, R.A. Laskowski, and J.M. Cerca con Google

Thornton. A Method for Localizing Ligand Binding Pockets in Protein Cerca con Google

Structures. Proteins, 62(2):479{488, Feb 1 2006. 18, 36, 37, 39, 45 Cerca con Google

[25] F. Glaser, Y. Rosenberg, A. Kessel, T. Pupko, and N. Ben-Tal. The Cerca con Google

ConSurf-HSSP database: The mapping of evolutionary conservation Cerca con Google

among homologs onto PDB structures. Proteins, 58(3):610{617, 2005. 4, 36, Cerca con Google

61 Cerca con Google

69 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[26] M. Hao, S. Rackovsky, A. Liwo, M.R. Pincus, and H.A. Scheraga. Ef- Cerca con Google

fects of Compact Volume and Chain Stiness on the Conformations of Cerca con Google

Native Proteins. Proceedings of the National Academy of Sciences, 89(14):6614{ Cerca con Google

6618, 1992. 61 Cerca con Google

[27] L. Holm and C. Sander. Protein Structure Comparison by Alignment Cerca con Google

of Distance Matrices. Journal of Molecular Biology, 233:123{123, 1993. 7 Cerca con Google

[28] B. Huang and M. Schroeder. LIGSITEcsc: predicting ligand binding Cerca con Google

sites using the Connolly surface and degree of conservation. BMC Struc- Cerca con Google

tural Biology, 6:19, Sep 24 2006. 37 Cerca con Google

[29] A.E. Johnson. Spin-Images: A Representation for 3-D Surface Matching. PhD Cerca con Google

thesis, Carnegie Mellon University, Pittsburgh, August 1997. 10, 12, 13 Cerca con Google

[30] A.E. Johnson and M. Hebert. Using Spin Images for Ecient Object Cerca con Google

Recognition in Cluttered 3D Scenes. IEEE Transactions on Pattern Analysis Cerca con Google

and Machine Intelligence, 21(5):433{449, 1999. 9, 22 Cerca con Google

[31] K. Kinoshita, J. Furui, and H. Nakamura. Identication of Protein Cerca con Google

Functions from a Molecular Surface Database, eF-site. Journal of Struc- Cerca con Google

tural and Functional Genomics, 2(1):9{22, 2002. 18, 37 Cerca con Google

[32] G.J. Kleywegt. Recognition of Spatial Motifs in Protein Structures. Cerca con Google

Journal of Molecular Biology, 285(4):1887{1897, Jan 29 1999. 18, 37 Cerca con Google

[33] N. Kobayashi and N. Go. A Method to Search for Similar Protein Lo- Cerca con Google

cal Structures at Ligand-Binding Sites and its Application to Adenine Cerca con Google

Recognition. European Biophysics Journal, 26(2):135{144, 1997. 7, 18, 37 Cerca con Google

[34] R. Kolodny, P. Koehl, and M. Levitt. Comprehensive Evaluation of Cerca con Google

Protein Structure Alignment Methods: Scoring by Geometric Mea- Cerca con Google

sures. Journal of Molecular Biology, 346(4):1173{1188, 2005. 5 Cerca con Google

[35] I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge, and T.E. Ferrin. Cerca con Google

A geometric approach to macromolecule-ligand interactions. Journal of Cerca con Google

Molecular Biology, 161(2):269{288, 1982. 37 Cerca con Google

70 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[36] Y.Y. Kuttner, V. Sobolev, A. Raskind, and M. Edelman. A Consensus- Cerca con Google

Binding Structure for Adenine at the Atomic Level Permits Searching Cerca con Google

for the Ligand Site in a Wide Spectrum of Adenine-Containing Com- Cerca con Google

plexes. Proteins Structure Function and Genetics, 52(3):400{411, 2003. 25, 37 Cerca con Google

[37] R.A. Laskowski. SURFNET: a program for visualizing molecular sur- Cerca con Google

faces, cavities, and intermolecular interactions. Journal of Molecular Graph- Cerca con Google

ics, 13(5):323{30, 307{8, Oct 1995. 36, 37 Cerca con Google

[38] R.A. Laskowski. PDBsum: summaries and analyses of PDB structures. Cerca con Google

Nucleic Acids Research, 29(1):221{222, 2001. 45 Cerca con Google

[39] R.A. Laskowski, J.D. Watson, and J.M. Thornton. Protein Func- Cerca con Google

tion Prediction Using Local 3D Templates. Journal of Molecular Biology, Cerca con Google

351(3):614{626, 2005. 18 Cerca con Google

[40] A.T. Laurie and R.M. Jackson. Methods for the prediction of protein- Cerca con Google

ligand binding sites for structure-based drug design and virtual ligand Cerca con Google

screening. Current Protein & Peptide Science, 7(5):395{406, Oct 2006. 37 Cerca con Google

[41] B. Lee and F.M. Richards. The interpretation of protein structures: Cerca con Google

Estimation of static accessibility. Journal of Molecular Biology, 55:379{400, Cerca con Google

1971. 8 Cerca con Google

[42] D.G. Levitt and L.J. Banaszak. POCKET: a computer graphics method Cerca con Google

for identifying and displaying protein cavities and their surrounding Cerca con Google

amino acids. Journal of Molecular Graphics, 10(4):229{234, 1992. 37 Cerca con Google

[43] J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar, and S. Subramaniam. Cerca con Google

Analytical Shape Computation of Macromolecules: I. Molecular Area Cerca con Google

and Volume Through Alpha Shape. PROTEINS: Structure, Function, and Cerca con Google

Genetics, 33:1{17, 1998. 37 Cerca con Google

[44] J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar, and S. Subramaniam. Cerca con Google

Analytical shape computation of macromolecules: II. Inaccessible cav- Cerca con Google

ities in proteins. Proteins Structure Function and Genetics, 33(1):18{29, 1998. Cerca con Google

37 Cerca con Google

71 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[45] L. Lo Conte, C. Chothia, and J. Janin. The Atomic Structure Cerca con Google

of Protein-Protein Recognition Sites. Journal of Molecular Biology, Cerca con Google

285(5):2177{2198, 1999. 18, 37 Cerca con Google

[46] J.A. McCammon and S.C. Harvey. Dynamics of Proteins and Nucleic Acids. Cerca con Google

Cambridge University Press, 1987. 4 Cerca con Google

[47] K. Mehlhorn and S. Naher. LEDA: A Platform for Combinatorial and Geo- Cerca con Google

metric Computing. Cambridge University Press, 1999. 33 Cerca con Google

[48] R.J. Morris, R.J. Najmanovich, A. Kahraman, and J.M. Thornton. Real Cerca con Google

Spherical Harmonic Expansion Coecients as 3D Shape Descriptors Cerca con Google

for Protein Binding Pocket and Ligand Comparisons. Bioinformatics, Cerca con Google

21(10):2347{2355, 2005. 18, 32, 36, 37, 38, 52, 53 Cerca con Google

[49] R. Najmanovich, N. Kurbatova, and J. Thornton. Detection of 3D Cerca con Google

atomic similarities and their use in the discrimination of small molecule Cerca con Google

protein-binding sites. Bioinformatics, 24(16):i105, 2008. 7 Cerca con Google

[50] R. Najmanovich, N. Kurbatova, and J. Thornton. Detection of 3D Cerca con Google

atomic similarities and their use in the discrimination of small molecule Cerca con Google

protein-binding sites. Bioinformatics, 24(16):i105, 2008. 65 Cerca con Google

[51] R. J. Najmanovich, A. AllaliHassani, R. J. Morris, L. Dombrovsky, Cerca con Google

P. W. Pan, M. Vedadi, A. N. Plotnikov, A. Edwards, C. Arrowsmith, Cerca con Google

and J. M. Thornton. Analysis of binding site similarity, small-molecule Cerca con Google

similarity and experimental binding proles in the human cytosolic sul- Cerca con Google

fotransferase family. Bioinformatics, 23(2):e104, 2007. 37 Cerca con Google

[52] D.W. Ritchie. Recent Progress and Future Directions in Protein- Cerca con Google

Protein Docking. Current Protein and Peptide Science, 9(1):1{15, 2008. 4 Cerca con Google

[53] M. Rosen. Molecular Shape Comparisons in Searches for Active Cerca con Google

Sites and Functional Similarity. Protein Engineering Design and Selection, Cerca con Google

11(4):263{277, 1998. 18 Cerca con Google

72 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[54] S. Schmitt, D. Kuhn, and G. Klebe. A New Method to Detect Related Cerca con Google

Function Among Proteins Independent of Sequence and Fold Homology. Cerca con Google

Journal of Molecular Biology, 323(2):387{406, 2002. 63 Cerca con Google

[55] M. Shatsky, A. Shulman-Peleg, R. Nussinov, and H.J. Wolfson. The Cerca con Google

Multiple Common Point Set Problem and Its Application to Molecule Cerca con Google

Binding Pattern Detection. Journal of Computational Biology, 13(2):407{428, Cerca con Google

2006. 37 Cerca con Google

[56] I.N. Shindyalov. Protein structure alignment by incremental combina- Cerca con Google

torial extension (CE) of the optimal path. Protein Engineering Design and Cerca con Google

Selection, 11(9):739{747, 1998. 7 Cerca con Google

[57] I.N. Shindyalov and P.E. Bourne. Protein Structure Alignment by In- Cerca con Google

cremental Combinatorial Extension (CE) of the Optimal Path. Protein Cerca con Google

Engineering, 11(9):739{747, Sep 1998. 29, 33, 52 Cerca con Google

[58] A. Shulman-Peleg, R. Nussinov, and H.J. Wolfson. Recognition of Cerca con Google

Functional Sites in Protein Structures. Journal of Molecular Biology, Cerca con Google

339(3):607{633, Jun 4 2004. 18, 25, 27, 28, 37, 38, 51 Cerca con Google

[59] V. Sobolev. Automated Analysis of Interatomic Contacts in Proteins. Cerca con Google

Bioinformatics, 15(4):327{332, 1999. 28, 46 Cerca con Google

[60] I. Sommer, O. Muller, F.S. Domingues, O. Sander, J. Weickert, and Cerca con Google

T. Lengauer. Moment invariants as shape recognition technique for Cerca con Google

comparing protein binding sites. Bioinformatics, 23(23):3139, 2007. 37 Cerca con Google

[61] G. Steinkellner, R. Rader, G.G. Thallinger, C. Kratky, and K. Gruber Cerca con Google

. VASCo: computation and visualization of annotated protein sur- Cerca con Google

face contacts. BMC Bioinformatics, 10(32), 2009. 63 Cerca con Google

[62] G.R. Stockwell and J.M. Thornton. Conformational diversity of lig- Cerca con Google

ands bound to proteins. Journal of Molecular Biology, 356(4):928{944, Mar 3 Cerca con Google

2006. 2, 51 Cerca con Google

73 Cerca con Google

BIBLIOGRAPHY Cerca con Google

[63] S. Subbiah, D.V. Laurents, and M. Levitt. Structural similarity of Cerca con Google

DNA-binding domains of bacteriophage repressors and the globin core. Cerca con Google

CUrrent Biology, 3:141{141, 1993. 7 Cerca con Google

[64] A. Via, F. Ferre, B. Brannetti, and M. Helmer Citterich. Protein Cerca con Google

Surface Similarities: a Survey of Methods to Describe and Compare Cerca con Google

Protein Surfaces. Cellular and Molecular Life Sciences, 57(13):1970{1977, 2000. Cerca con Google

18, 37 Cerca con Google

[65] M. Weisel, E. Proschak, and G. Schneider. PocketPicker: analysis of Cerca con Google

ligand binding-sites with shape descriptors. Chemistry Central Journal, 1:7, Cerca con Google

2007. 37 Cerca con Google

[66] K.A. Xavier and R.C. Willson. Association and Dissociation Kinetics of Cerca con Google

Anti-Hen Egg Lysozyme Monoclonal Antibodies HyHEL-5 and HyHEL- Cerca con Google

10. Biophysical Journal, 74(4):2036{2045, 1998. 4 Cerca con Google

[67] H. Yao, D.M. Kristensen, I. Mihalek, M.E. Sowa, C. Shaw, M. Kimmel, Cerca con Google

L. Kavraki, and O. Lichtarge. An Accurate, Sensitive, and Scalable Cerca con Google

Method to Identify Functional Sites in Protein Structures. Journal of Cerca con Google

Molecular Biology, 326(1):255{261, 2003. 18, 37 Cerca con Google

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