AL-Base: A visual platform analysis tool for the study of amyloidogenic immunoglobulin light chain sequences

Amyloid

Volumn 16, Issue 1, 2009, Pages 1-8

  Bodi, Kip ^a,b   Prokaeva, Tatiana ^a   Spencer, Brian ^a   Eberhard, Maurya ^a   Connors, Lawreen H ^a   Seldin, David C ^a  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b School of Medicine ^*  (United States)

Author keywords

AL amyloidosis; Immunoglobulin light chain; Online database

Indexed keywords

IMMUNOGLOBULIN LIGHT CHAIN;

AMINO ACID SEQUENCE; AMYLOIDOSIS; ARTICLE; DATA BASE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SOMATIC HYPERMUTATION; ALGORITHM; CHEMISTRY; GENETIC DATABASE; GENETICS; HUMAN; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

ALGORITHMS; AMINO ACID SEQUENCE; AMYLOIDOSIS; BASE SEQUENCE; DATABASES, GENETIC; HUMANS; IMMUNOGLOBULIN LIGHT CHAINS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

EID: 65449142488     PISSN: 13506129     EISSN: 17442818     Source Type: Journal    
DOI: 10.1080/13506120802676781     Document Type: Article

References (33)

1. Westermark P, Benson MD, Buxbaum JN, Cohen AS, Frangione B, Ikeda S, Masters CL, Merlini G, Saraiva MJ, Sipe JD. A primer of amyloid nomenclature. Amyloid 2007;14:179-183.
2. Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 2003;424:805-808.
3. Dobson CM. Experimental investigation of protein folding and misfolding. Methods 2004;34:4-14.
4. Lefranc MP, Pommie C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piedade I, Rouard M, Foulquier E, Thouvenin V, Lefranc G. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 2005;29:185-203.
5. Lefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 2003;27:55-77.
6. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85: 2444-2448.
7. Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 1988;73:237-244.
8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
9. Chang B, Casali P. The CDR1 sequences of a major proportion of human germline Ig VH genes are inherently susceptible to amino acid replacement. Immunol Today 1994;15:367-373.
10. Lossos IS, Tibshirani R, Narasimhan B, Levy R. The inference of antigen selection on Ig genes. J Immunol 2000; 165:5122-5126.
11. Juretic D, Lucic B, Zucic D, Trinajstic N. Protein transmem-brane structure: recognition and prediction by using hydro-phobicity scales through preference functions. Theor Comput Chem 1998;5:405-445.
12. Bhaskaran R, Ponnuswamy PK. Positional flexibilities of amino acid residues in globular proteins. Int J Pept Protein Res 1988;32:241-255.
13. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996;264:121-136.
14. Janin J, Wodak S, Levitt M, Maigret B. Conformation of amino acid side-chains in proteins. J Mol Biol 1978;125:357-386.
15. Zimmerman JM, Eliezer N, Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 1968;21:170-201.
16. Beghin F, Dirkx J. Une methode statistique simple de prediction des conformations proteiques. Arch Int Physiol Biochim 1975;83:167-168.
17. Comenzo RL, Wally J, Kica G, Murray J, Ericsson T, Skinner M, Zhang Y. Clonal immunoglobulin light chain variable region germline gene use in AL amyloidosis: association with dominant amyloid-related organ involvement and survival after stem cell transplantation. Br J Haematol 1999;106:744-751.
18. Bellotti V, Merlini G, Bucciarelli E, Perfetti V, Quaglini S, Ascari E. Relevance of class, molecular weight and isoelectric point in predicting human light chain amyloidogenicity. Br J Haematol 1990;74:65-69.
19. Alexanian R, Fraschini G, Smith L. Amyloidosis in multiple myeloma or without apparent cause. Arch Intern Med 1984;144:2158-2160.
20. Solomon A, Frangione B, Franklin EC. Bence Jones proteins and light chains of immunoglobulins. Preferential association of the V lambda VI subgroup of human light chains with amyloidosis AL (lambda). J Clin Invest 1982;70:453-460.
21. Perfetti V, Casarini S, Palladini G, Vignarelli MC, Klersy C, Diegoli M, Ascari E, Merlini G. Analysis of V(lambda)-J(lambda) expression in plasma cells from primary (AL) amyloidosis and normal bone marrow identifies 3r (lambdaIII) as a new amyloid-associated germline gene segment. Blood 2002;100:948-953.
22. Pommie C, Levadoux S, Sabatier R, Lefranc G, Lefranc MP. IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J Mol Recognit 2004;17:17-32.
23. Kawashima S, Ogata H, Kanehisa M. AAindex: amino acid index database. Nucleic Acids Res 1999;27:368-369.
24. Ganapathiraju M, Manoharan V, Klein-Seetharaman J. BLMT: statistical sequence analysis using N-grams. Appl Bioinformatics 2004;3:193-200.
25. Gallo G, Picken M, Buxbaum J, Frangione B. The spectrum of monoclonal immunoglobulin deposition disease associated with immunocytic dyscrasias. Semin Hematol 1989;26:234-245.
26. Stone MJ, Frendel EP. The clinical spectrum of light chain myeloma. A study of 35 patients with special reference to the occurrence of amyloidosis. Am J Med 1975;58:601-619.
27. Bahat G, Erten N, Saka B, Uzun S, Onur I, Kalayoglu-Besisik S, Buyukbabani N. Immunoglobulin D lambda multiple myeloma and amyloidosis with predominant soft tissue involvement. Amyloid 2007;14:305-308.
28. Gu M, Wilton R, Stevens FJ. Diversity and diversification of light chains in myeloma: the specter of amyloidogenesis by proxy. Contrib Nephrol 2007;153:156-181.
29. Yu C, Zavaljevski N, Stevens FJ, Yackovich K, Reifman J. Classifying noisy protein sequence data: a case study of immunoglobulin light chains. Bioinformatics 2005;21 (Suppl 1):i495-i501.
30. Baden EM, Owen BA, Peterson FC, Volkman BF, Ramirez-Alvarado M, Thompson JR. Altered dimer interface decreases stability in an amyloidogenic protein. J Biol Chem 2008;283:15853-15860.
31. Stevens FJ, Argon Y. Pathogenic light chains and the B-cell repertoire. Immunol Today 1999;20:451-457.
32. Stevens FJ. Four structural risk factors identify most fibril-forming kappa light chains. Amyloid 2000;7:200-211.
33. Raffen R, Dieckman LJ, Szpunar M, Wunschl C, Pokkuluri PR, Dave P, Wilkins Stevens P, Cai X, Schiffer M, Stevens FJ. Physicochemical consequences of amino acid variations that contribute to fibril formation by immunoglobulin light chains. Protein Sci 1999;8:509-517.