Bioinformatic analysis of protein structure-function relationships: Case study of leukocyte elastase (ELA2) missense mutations

Human Mutation

Volumn 27, Issue 12, 2006, Pages 1230-1243

  Thusberg, Janita ^a   Vihinen, Mauno ^a,b  

^a UNIVERSITY OF TAMPERE   (Finland)

^b TAMPERE UNIVERSITY HOSPITAL   (Finland)

Author keywords

ELA2; Human neutrophil elastase; Immunogenetics; Immunology; Neutropenia; Structural basis of diseases; Structure function relationships

Indexed keywords

HUMAN NEUTROPHIL ELASTASE; LEUKOCYTE ELASTASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOINFORMATICS; ELA2 GENE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME MECHANISM; ENZYME STABILITY; ENZYME STRUCTURE; GENE; GENE MUTATION; GENETIC ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; HUMAN; IMMUNE DEFICIENCY; IMMUNE SYSTEM; LIGAND BINDING; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NEUTROPENIA; NEUTROPHIL COUNT; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN FUNCTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; SURFACE CHARGE; WEB BROWSER;

ANTIGENS, SURFACE; CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, GENETIC; ELECTROSTATICS; ENZYME STABILITY; HUMANS; LEUKOCYTE ELASTASE; MEMBRANE POTENTIALS; MODELS, MOLECULAR; MUTATION, MISSENSE; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 33750971454     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20407     Document Type: Article

References (106)

1. Adkinson AM, Raptis SZ, Kelley DG, Pham CT. 2002. Dipeptidyl peptidase I activates neutrophil-derived serine proreases and regulates the development of acute experimental arthritis. J Clin Invest 109:363-371.
2. Aghamohammadi A, Parvaneh N, Kanegana H, Moin M, Amirzargar AA, Farhoudi A, Pourpak Z, Movahedi M, Gharagozlou M, Rezaei N, Futatani T, Miyawaki T. 2004. Screening of the Bruton tyrosine kinase (BTK) gene mutations in 13 Iranian patients wirh presumed X-linked agammaglobulinemia. Iran J Allergy Asthma Immunol 3:175-179.
3. Ahola V, Uusipaikka E, Aittokallio T, Vihinen M. 2003. Efficient estimation of emission probabilities in profile hidden Markov models. Bioinformarics 19:2359-2368.
4. Ahola V, Aittokallio T, Vihinen M, Uusipaikka E. 2004. Statistical multiple comparison methods for identifying conserved residues in protein sequence alignment. Star Appl Genet Mol Biol 3:28.
5. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database scatch programs. Nucleic Acids Res 25:3389-3402.
6. Bach-Gansmo ET, Halvorsen S, Godal HC, Skjonsbcrg OH. 1996. D-dimers are degraded by human neutrophil elastase. Thromb Res 82:177-186.
7. Barrett AJ, Rawlings ND. 1995. Families and clans of serine proteases. Arch Biochcm Biophys 318:247-250.
8. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. 2004. The Pfam protein families database. Nucleic Acids Res 32:D138-D141.
9. Bates G. 2003. Huntingtin aggregation and toxicity in Huntington's disease. Lancet 361:1642-1644.
10. Belaaouaj A, Kim KS, Shapiro SD. 2000. Degradation of outer membrane protein A in Escherichia coli killing by neureophil elastase. Science 289:1185-1187.
11. Bellanné-Chantelot C, Clauin S, Leblanc T, Cassinat B, Rodrigues-Lima F, Beaufils S, Vaury C, Barkaouti M, Fenneteau O, Maier-Redelsperger M, Chomienne C, Donadieu J. 2004. Mutations in the ELA2 gene correlate with more severe expression of neutropenia: a study of 81 patients from the French Neutropenia Register. Blood 11:4119-4125.
12. Benson KF, Li F-Q, Person RE, Albani D, Duan Z, Wechsler J, Meade-White K, Williams K, Acland GM, Niemeyer G, Lothrop CD, Horwitz M. 2003. Mutations associated with neutropenia in dogs and humans disrupt intracellular transport of neutrophil elastase. Nat Genet 35:90-96.
13. Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N. 2004. ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20:1322-1324.
14. Bieth JG. 1998. Leukocyte clastase. In: Barrett AJ, Rawlings ND, Woessner JF, editors. Handbook of proteolytic enzymes. San Diego: Academic Press. p 54-60.
15. Bode W, Meyer E Jr, Powers JC. 1989. Human leukocyte and porcine pancreatic clastase: X-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitors. Biochemistry 28:1951-1963.
16. Bode W, Wei AZ, Huber R, Meyer E, Travis J, Neumann S. 1986. X-ray structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J 5:2453-2458.
17. Boxer LA, Morganroth ML. 1987. Neutrophil function disorders. Dis Mon 33:681-780.
18. Brinkmann V, Reichard U, Goosmann C, Fauler B, Uhlemann Y, Weiss DS, Weinrauch Y, Zychlinsky A. 2004. Neutrophil extracellular traps kill bacteria. Science 303:1532-1535.
19. Bross P, Corydon TJ, Andersen BS, Jørgensen MM, Bolund L, Gregersen N. 1999. Protein misfolding and degradation in genetic diseases. Hum Mutat 14:186-198.
20. Chasman D, Adams RM. 2001. Predicting the functional consequences of nonsynonymous single nucleoride polymorphisms: structure based assessment of amino acid variation. J Mol Biol 307:683-706.
21. Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. 2003. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424:805-808.
22. Dale DC, Hammond WPT. 1988. Cyclic neutropenia: a clinical review. Blood Rev 2:178-185.
23. Dale DC, Person RE, Bolyard AA, Aprikyan AG, Bos C, Bonilla MA, Boxer LA, Kannourakis G, Zeidler C, Welte K, Benson KF, Horwitz M. 2000. Mutations in the gene encoding neutrophil elastase in congenital and cyclic neutropenia. Blood 96:2317-2322.
24. DeLano WL. 2002. The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific. Available at: http://www.pymol.org. Last date accessed: August 1, 2006.
25. Deleage G, Roux B. 1987. An algorithm for protein secondary structure prediction based on class prediction. Protein Eng 1:289-294.
26. Dewald B, Rindler-Ludwig R, Bretz U, Baggiolim M. 1975. Subcellular localization and heterogeneity of neutral proteases in neutrophilic polymorphonuclear leukocytes. J Exp Med 141:709-723.
27. Dobson CM. 2003. Protein folding and misfolding. Nature 426:884-890.
28. Dosztányi Z, Fiser A, Simon I. 1997. Stabilization centers in proteins: identification, characterization and predictions. J Mol Biol 272:597-612.
29. Dosztányi Z, Magyar C, Tusnády G, Simon I. 2003a. Seide: identification of stabilization centers in proteins. Bioinformarics 19:899-900.
30. Dosztányi Z, Magyar C, Tusnády GE, Cserzá M, Fiser A, Simon I. 2003b. Servers for sequence-structure relationship analysis and prediction. Nucleic Acids Res 31:3359-3363.
31. Dosztányi Z, Csizmók V, Tompa P, Simon I. 2005a. IUPred: web server for the prediction of intrinsically unstructured proteins. Bioinformatics 21:3433-3434.
32. Dosztányi Z, Csizmók V, Tompa P, Simon I. 2005b. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 347:827-839.
33. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. 2004. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nature Biotechnol 22:1240-1241.
34. Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X, Orozco M. 2005. PMut: a web based tool for the annotation of pathological mutations on proteins. Bioinformatics 21:3176-3178.
35. Forloni G, Terreni L, Bertani I, Fogliarino S, Invernizzi R, Assini A, Ribizzi G, Negro A, Calabrese E, Volonte MA, Mariani C, Franceschi M, Tabaton M, Bertoli A. 2002. Protein misfolding in Alzheimer's and Parkinson's disease: genetics and molecular mechanisms. Neurobiol Aging 23:957-976.
36. Gilis D, Rooman M. 2000. PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein Eng 13:849-856.
37. Gillis S, Furie BC, Furie B. 1997. Interactions of neutrophils and coagulation proteins. Semin Hematol 34:336-342.
38. Gilson M, Honig B. 1988. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins Struct Funct Genet 4:7-18.
39. Gilson M, Sharp K, Honig B. 1988. Calculating electrostatic interactions in biomolecules: methods and ertor assessment. J Comput Chem 9:327-335.
40. Glaser F, Pupko T, Paz I, Bell RE, Bechot-Shental D, Martz E, Ben-Tal N. 2003. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinfotmatics 19:163-164.
41. Grateau G, Verine J, Delpech M, Ries M. 2005. Amyloidosis: a model of misfolded protein disorder. Med Sci 21:627-633.
42. Gromiha MM, Pujadas G, Magyat C, Selvataj S, Simon I. 2004. Locating the stabilizing residues in α/β barrel proteins based on hydrophobity, long-range interactions, and sequence conservation. Proteins 55:316-329.
43. Gullberg U, Lindmark A, Lindgren G, Persson AM, Nilsson E, Olsson I. 1995. Carboxyl-terminal prodomain-deleted human leukocyte elastase and cathepsin G are targeted to granules and enzymatically activated in the rat basophilic/mast cell line RBL. J Biol Chem 270:12912-12918.
44. Haurie C, Dale DC, Mackey MC. 1998. Cyclical neutropenia and other periodic haematological disorders: a review of mechanisms and mathematical models. Blood 92:2629-2640.
45. Horwitz M, Benson KF, Person RE, Aprikyan AG, Dale DC. 1999. Mutations in ELA2, encoding neutrophil elastase, define a 21-day biological clock in cyclic hematopoiesis. Nat Genet 23:433-436.
46. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
47. Kaplan B, Ratner V, Haas E. 2003. α-Synuclein: Its biological function and role in neurodegenerative diseases. J Mol Neurosci 20:83-92.
48. Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. 1986. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino acid modification. Proteins Struct Funct Genet 1:47-59.
49. Kraut J. 1977. Serine proteases: structure and mechanism of catalysis. Ann Rev Biochem 46:331-358.
50. Kwasigroch JM, Gilis D, Dehouck Y, Rooman M. 2002. PoPMuSiC, rationally designing point mutations in protein structures. Bioinformatics 18:1701-1702.
51. Lacroix E, Viguera AR, Serrano L. 1998. Elucidating the folding problem of α-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 284:173-191.
52. Lappalainen I, Giliani S, Franceschini R, Bonnefoy J-Y, Duckett C, NotarangeIo LD, Vihinen M. 2000. Structural basis for SH2D1A mutations in X-linked lymphoproliferative disease (XLP). Biochem Biophys Res Commun 269:124-130.
53. Lappalainen I, Vihinen M. 2002. Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B. Prot Eng 15:1005-1014.
54. Lehrer RI, Ganz T, Selsted ME, Babior BM, Curnutre JT. 1988. Neuttophils and host defense. Ann Intern Med 109:127-142.
55. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. 2003a. Protein disorder prediction: implications for structural proteomics. Structure 11:1453-1459.
56. Linding R, Russell RB, Neduva V, Gibson TJ. 2003b. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 31:3701-3708.
57. Linding R, Schymkovitz J, Rousseau F, Diella F, Serrano L. 2004. A comparative study of the relationship between protein structure and β-aggregation in globular and intrinsically disordered proteins. J Mol Biol 342:345-353.
58. Lovell SC, Word JM, Richardson JS, Richardson DC. 2000. The penultimate rotamer library. Proteins 40:389-408.
59. Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. 2003. Structure validation by Ca geometry: φ, ψ and cβ deviation. Proteins 50:437-450.
60. MacCallum RM. 2006. Order/disorder prediction with self organising maps. Available at: http://www.sbc.su.se/~maccallr/disorder. Last accessed: August 1, 2006.
61. Magyar C, Gromiha MM, Pujadas G, Tusnady GE, Simon I. 2005. Sride: a server for identifying stabilizing residues in proteins. Nucleic Acids Res 33:W303-W305.
62. Matthews BW. 1995. Studies on protein stability with T4 lysozyme. Adv Protein Chem 46:249-278.
63. Millet MP, Kumar S. 2001. Understanding human disease mutations through the use of interspecific genetic variation. Hum Mol Genet 10:2319-2328.
64. Mooney SD, Klein TE. 2002. The functional importance of disease-associated mutation. BMC Bioinformatics 3:24.
65. Muños V, Serrano L. 1994. Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol 1:399-409.
66. Neurath H. 1986. The versatility of proteolytic enzymes. J Cell Biochem 32:35-49.
67. Ng PC, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res 11:863-874.
68. Palmer SE, Stephens K, Dale DC. 1996. Genetics, phenotype and natural history of autosomal dominant cyclic hematopoiesis. Am J Med Genet 66:413-422.
69. Pei J, Grishin NV. 2001. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17:700-712.
70. Piirilä H, Vihinen M. 2006. Immunodeficiency mutation databases (IDbases). Hum Mutat 27:1200-1208.
71. Poussu E, Vihinen M, Paulin L, Savilahti H. 2004. Probing the α-complementing domain of E. coli β-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition. Proteins 54:681-692.
72. Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-3900.
73. Rony S-B, Väliaho J, Vihinen M. 2000. Structural basis of Bloom syndrome (BS) causing mutations in the BLM helicase domain. Mol Med 6:155-164.
74. Rong S-B, Vihinen M. 2000. Structural basis of Wiscott-Aldrich syndrome (WAS) causing mutations in the WH1 domain. J Mol Med 78:530-537.
75. Salvesen G, Enghild JJ. 1990. An unusual specificity in the activation of neutrophil serine proteinase zymogens. Biochemistry 29:5304-5308.
76. Sandberg WS, Schlunk PM, Zahm HB, Terwilliger TC. 1995. Relationship between in vivo activity and in vitro measures of function and stability of a protein. Biochemistry 34:11970-11978.
77. Saunders CT, Baker D. 2002. Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol 322:891-901.
78. Sanders CR, Myers JK. 2004. Disease-relared misassembly of membrane proteins. Annu Rev Biophys Biomol Struct 33:25-51.
79. Schweers O, Schönhrunn-Hanebcck E, Marx A, Mandelkow E. 1994. Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for β-structure. J Biol Chem 269:24290-24297.
80. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. 2005. The FoldX web server: an online force field. Nucleic Acids Res 33: W382-W388.
81. Shen B, Vihinen M. 2003. RankViaContact: ranking and visualization of amino acid contacts. Bioinformatics 19:2161-2162.
82. Shen B, Vihinen M. 2004. Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain. Protein Eng Des Sel 17:267-276.
83. Shortle D, Stites WE, Meeker AK. 1990. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 29:8033-8041.
84. Serrano E, Kellis JT Jr, Cann P, Matouschck A, Fersht AR. 1992. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J Mol Biol 224:783-804.
85. Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M. 1999. Automated analysis of interatomic contacts in proteins. Bioinformntics 15:327-332.
86. Steward RE, MacArthur MW, Easkowski RA, Thornton JM. 2003. Molecular basis of inherited diseases: a structural perspective. Trends Genet 19:505-513.
87. Strickler SS, Gribenko AV, Grinenko AV, Keiffer TR, Tomlinson J, Reihle T, Loladze VV, Makhatadze GI. 2006. Protein stability and surface electrostatics: a charged relationship? Biochemistry 45:2761-2766.
88. Sunyaev S, Ramensky V, Koch I, Lathe W, Kondrashov A, Bork P. 2001. Prediction of delererious human alleles. Hum Mol Gen 10:591-597.
89. Vihinen M, Nilsson L, Smith CIE. 1994a. Structural basis of SH2 domain mutations in X-linked agammaglobulinemia. Biochem Biophys Res Commun 205:1270-1277.
90. Vihinen M, Vetrie D, Maniar HS, Ochs HD, Zhu Q, Vořechovský I, Webster AD, Notarangelo LD, Nilsson L, Sowadski JM, Smith CIE. 1994b. Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease. Proc Natl Acad Sci USA 91:12803-12807.
91. Vihinen M, Kwan SP, Lester T, Ochs HD, Rosnick I, Väliaho J, Conley ME, Smith CIE. 1999. Mutations of the human BTK gene coding for bruton tytosine kinase in X-linked agammaglobulinemia. Hum Mutat 13:280-285.
92. Vihinen M, Zvelehil JJM, Zhu Q, Brooimans RA, Ochs HD, Zegers BJM, Nilsson E, Waterfield MD, Smith CIE. 1995. Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry 34:1475-1481.
93. Vitkup D, Sander C, Chutch CM. 2003. The amino-acid mutational spectrum ot human genetic disease. Genome Biol 4:R72.
94. Vogt G, Chapgiet A, Yang K, Chuzhanova N, Feinberg J, Fieschi C, Boisson-Dupuis S, Alcais A, Filipe-Santos O, Bustamante J, de Beaucourdey E, Al-Mohsen I, Al-Haijar S, Al-Ghonaium A, Adimi P, Mirsaeidi M, Khalilzadeh S, Rosenzweig S, de la Calle Martin O, Bauer TR, Puck JM, Ochs HD, Furthner D, Engelhorn C, Belohradsky B, Mansouri D, Holland SM, Schreiber RD, Abel E, Cooper DN, Soudais C, Casanova J-E. 2005. Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations. Nat Gen 37:692-700.
95. Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. 2004a. The DISOPRED server for the prediction of protein disorder. Bioinformatics 20:2138-2139.
96. Ward JJ, Sodhi JS, McGuffin EJ, Buxton BF, Jones DT 2004b. Prediction and functional analysis of native disorder in proteins from three kingdoms of life. J Mol Biol 337:635-645.
97. Weiss SJ. 1989. Tissue destruction by neutrophils. N Engl J Med 320:365-376.
98. Wang Z, Moult J. 2001. SNPs, protein structure, and disease. Hum Mutat 17:263-270.
99. Weinrauch Y, Drujan D, Shapiro SD, Weiss J, Zychlinsky Z. 2002. Neutrophil elastase targers virulence factors ot enterobacteria. Nature 417:91-94.
100. Wiedow O, Muhle K, Streit V, Kameyoshi Y. 1996. Human eosinophils lack human leukocyte elasrase. Biochim Biophys Acta 1315:185-187.
101. Wintroub BU, Coblyn JS, Kaempfer CE, Austen KF, 1980. Cleavage of fibrinogen by the human neutrophil neutral peptide-generating protease. Proc Natl Acad Sci USA 77:5448-5452.
102. Word JM, Lovell SC, La Bean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. 1999a. Visualizing and quantifying molecular goodness of fit: small probe conflict dors with explicit hydrogen atoms. J Mol Biol 285:1711-1733.
103. Word JM, Lovell SC, La Bean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. 1999b. Visualizing and quantifying molecular goodness of fit: small probe contact dots with explicit hydrogen atoms. J Mol Biol 285:1711-1733.
104. Word JM, Bateman RC Jr, Presley BK, Lovell SC, Richardson DC. 2000. Exploring sreric constraints on prorein mutations using MAGE/PROBE. Protein Sci 9:2251-2259.
105. Yang ZR, Thompson R, McMeil P, Esnouf RM. 2005. RONN: the bio-basis function neural network recbnique applied to the detection of natively disordered regions in proteins. Bioinformarics 21:3369-3376.
106. Zhou H, Zhou Y. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11:2714-2726.