=====APPENDIXA===== USEFUL INTERNET ADDRESSES S ix years ago, Walter Gilbert urged that scientists "hook our individual computers into the worldwide network that gives us access to daily changes in the databases and also makes immediate our communications with each other:'l The Internet expands constantly and with it the wealth of information; today's scientists can hardly do without it. New and addi- tional data come up every day-not to speak of the daily communication processes over the net. Many data found in the present book were retrieved from various www addresses (see below) and subsequently collected in order to offer a specific and comprehensive compila- tion of data relating to the structure and function of MHC molecules. As the present data will continuously be updated, we have listed below some helpful addresses which we think may serve the molecular biologist's and immunologist's interests. WWW Entrez: http://www.ncbi.nlm.nih.gov This network browser is provided by the National Center for Biotechnology Information and allows searching and browsing of protein and nucleic acid databases, as well as related references from MEDLINE. DBGET: http://www.genome.ad.jp/dbget/: This is a database retrieval system and allows retrieval of related entries in different data- bases such as GenBank, EMBL, SWISS-PROT, PIR etc. Pedro's Biomolecular Research Tools: http://www.public.iastate.edu/-pedro/research_tools.htmI.This is an outstanding collec- tion ofWWW links to services useful for molecular biologists. It comprises a list of molecu- lar biology database search and analysis facilities, and bibliographies. SEQUENCE DATABASES EMBL: http://www.ebi.ac.ukIebLdocs/embCdb/ebi/topembl.html GENBANK: http://www.ncbi.nlm.nih.gov/Genbankiindex.html GSDB:http://www.ncgr.org/gsdb/gsdb.html PIR:http://www.gdb.org/Dan/proteins/pir.html SWISS-PROT: http://www.ebi.ac.uk!ebLdocs/swiss-proCdb/swisshome.html MHC RESOURCES http://www.uni-tuebingen.de/unilkxi/: Our own homepage provides access to MHC ligands and peptide motifs. http://www.icnet.ukIaxp/tiaiindex.html: This page provides links to resources available from the Tissue Antigen Laboratory at the Imperial Cancer Research Fund. Included are HLA sequence data, HLA nomenclature in- cluding monthly updates.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
=====APPENDIXA=====
USEFUL INTERNET ADDRESSES
Six years ago, Walter Gilbert urged that scientists "hook our individual computers into the worldwide network that gives us access to daily changes in the databases and also makes
immediate our communications with each other:'l The Internet expands constantly and with it the wealth of information; today's scientists can hardly do without it. New and additional data come up every day-not to speak of the daily communication processes over the net. Many data found in the present book were retrieved from various www addresses (see below) and subsequently collected in order to offer a specific and comprehensive compilation of data relating to the structure and function of MHC molecules. As the present data will continuously be updated, we have listed below some helpful addresses which we think may serve the molecular biologist's and immunologist's interests.
WWW Entrez: http://www.ncbi.nlm.nih.gov This network browser is provided by the National Center for Biotechnology Information and allows searching and browsing of protein and nucleic acid databases, as well as related references from MEDLINE.
DBGET: http://www.genome.ad.jp/dbget/: This is a database retrieval system and allows retrieval of related entries in different databases such as GenBank, EMBL, SWISS-PROT, PIR etc.
Pedro's Biomolecular Research Tools: http://www.public.iastate.edu/-pedro/research_tools.htmI.This is an outstanding collection ofWWW links to services useful for molecular biologists. It comprises a list of molecular biology database search and analysis facilities, and bibliographies.
http://www.uni-tuebingen.de/unilkxi/: Our own homepage provides access to MHC ligands and peptide motifs.
http://www.icnet.ukIaxp/tiaiindex.html: This page provides links to resources available from the Tissue Antigen Laboratory at the
Imperial Cancer Research Fund. Included are HLA sequence data, HLA nomenclature including monthly updates.
450 MHC Ligands and Peptide Motifs
http://histo.cryst.bbk.ac. uk: Histo is dedicated to the investigation of the relationship between sequence, structure
and function of the proteins of the MHC. There are also collections of mouse class II sequences and non human and non mouse sequences.
http://www.hgmp.mrc.ac.uk: This is a database of the human MHC and contains eDNA sequences of all current
alleles as well as physical maps.2
http://wehi.wehi.edu.au/mhcpep/ : Database of Major Histocompatibility Complex binding pep tides at the Walter and Eliza
Hall Institute-Melbourne, Australia.
http://www3.ncbi.nlm.nih.gov: This access is provided by the National Center for Biotechnology Information and offers
gene maps of the human genome as well as human/mouse homology map.
http://www.swmed.edu/home_pages/ASHIIashi.htm: This is organized by the American Society for Histocompatibility and Immunogenetics
and offers access to HLA sequence alignments.
http://hiv-web.lanl.gov/immuno: HIV Molecular Immunology Database. Offers T cell epitope maps on HIV proteins,
alignments, and annotation, as well as a summary and map of linear B cell epitopes and monoclonal antibodies.
REFERENCES I. Gilbert W. Towards a paradigm shift in biology. Nature 1991; 349:99. 2. Newell WR, Trowsdale 1, Beck S. MHCDB: database of the human MHC (release 2). Im
munogenetics 1996; 45:6-8.
===== APPENDIX B=====
COMPUTER PROGRAMS ARE AVAILABLE FROM THE FOLLOWING SOURCES:
Joe D'Amaro Department of Immunohematology and Blood Bank University Hospital Leiden PO Box 9600 2300 RD Leiden The Netherlands
Miles Davenport Molecular Immunology Group Institute of Molecular Medicine Nuffield Department of Medicine University of Oxford John Radcliffe Hospital Headington, OX3 9DU United Kingdom
Burkhard Fleckenstein NMI (Naturwissenschaftliches und Medizinisches Institut an der Universitat Tiibingen in Reutlingen) Eberhardstr. 29 72762 Reutlingen Germany
Jiirgen Hammer Roche Milano Ricerche Via Olgettina 58 20132 Milano Italy
=====APPENDIX C=====
ABBREVIATIONS
4F2 AA ACh Ag APC B. polymyxa ~2m BAGE Bf ~-gal BHRF BIP BLAST-l BSA BST-2 BZLFI C. cAg CArG CD CDK4wt CKS-2 CKShsl CLIP cM c-myc COl CRE CRY CSFV CSP CYP21 Derp E. coli EI-E7 EBNA EBV
lymphocyte activation antigen 4F2 amino acids acetylcholine antigen adenomatous polyposis coli protein Bacillus polymyxa ~2-micro globulin tumor antigen factor B ~-galactosidase Epstein-Barr virus bel-2 homologue bone inducing protein B-lymphocyte activation marker bovine serum albumin bone marrow stromal cell membrane protein Epstein-Barr virus trans-activator protein Caenorhabditis spec. core antigen mouse CArG-binding factor A cluster of differentiation cyeline dependent kinase cylcine dependent kinase subunit 2 cyeline-dependent kinases regulatory subunit 1 class II associated invariant chain peptide centiMorgans proto-oncogene cytochrome c oxidase polypeptide I cAMP response element Cryptomeria japonica major allergen classical swine fever virus circumsporozoite protein steroid 21-hydroxylase Dermatophagoides pteronyssinus Escherichia coli immediate early protein Epstein-Barr virus nuclear antigen Epstein-Barr-virus
454
elFC env EqMb ER ER60 ERP72 Fc FLU Fr GAD gag GAGE GBLP gp gplOO GPIX HA HBBCP HCV HEL HER-2 HER-2/neu HFPS HGNBP HIV HLA hnRNP HPV HSI HSC HSHM HSP HSrn HSV HTLV ICAM ICP-27 ICS IDDM IE IEF IFN Ig IgVH Ig-SF Ii IL Int-6
IP IRBP
protein translation factor envelope equine myoglobin endoplasmic reticulum
MHC Ligands and Peptide Motifs
endoplasmic reticulum resident protein endoplasmic reticulum resident protein fragment cystallizable Influenza fraction glutamic acid decarboxylase group-specific antigen tumor antigen guanine nucleotide binding protein ~ subunit-like protein gylcoprotein ->pmel platelet glycoprotein IX (syn.: CD42A) hemagglutimin human cytomegalovirus Hepatitis B virus hen egg lysozyme proto-oncogene ->HER-2 human fasyl pyrophosphate synthetase human nucleotide binding protein human immunodeficiency virus human lymphocyte antigen heterogenous ribonucleoprotein human papilloma virus hematopoietic lineage cell specific protein heat shock protein constitutive human expressed sequence tag heat shock protein human C6.1A protein (proto-oncogene) Herpes simplex virus Human T-lymphotrophic virus intercellular adhesion molecule HSV infected cell protein (transciptional regulator IE63) IFN consensus sequence insulin dependent diabetes mellitus immediate early human retinoblastoma binding protein P48 interferon immunoglobulin immunoglobulin variable region of heavy chain immunoglobulin super family invariant chain interleukin a highly conserved, widely expressed gene, which is mutated by mouse mammary tumor virus in mammary preneoplasia prostacyclin receptor gene interphotoreceptor retinoid-binding protein
Appendix C
IRS JAK1 JHMV kb kD K-ras L. LAR LCMV LDH LDL lemA LIF LLO Imp-1 Imp-2 ImrA Lol P LSA-1 Ly M. MAGE MART-1 MBP Mbp MCC MCMV mdm Melan/MART -1 MET MHV MIF miHAg MMTV MOG MoHb MoMb MP MuLV MUM-1 MUT MV nef NK NKAT NP NRE NS OGDH ORF OVA
IFN response sequence Janus kinase JHM strain of mouse hepatitus virus kilo base pairs kilo-Dalton Kirsten -ras Listeria spec. leucocyte antigen related lymphocytic choriomeningitis virus lactate dehydrogenase low density lipoprotein putative regulator protein in L.monocytogenes leukemia inhibitory factor listeriolysin 0 latent membrane protein 1 latent membrane protein 2 lincomycin resistance protein from S. lincolnensis Lolium perenne liver-stage antigen-1 lymphocyte antigen Mycobacterium spec. melanoma associated antigen melanoma antigen myelin basic protein megabase pairs moth cytochrome c murine cytomegalovirus tumor antigen ->Mart-1 oncogene mouse hepatitis virus migration inhibitory factor minor histocompatibility antigen murine mammory tumor virus myelin oligodendrocyte glycoprotein mouse hemoglobin mouse myoglobin matrix protein murine leukemia virus tumor antigen tumor antigen measles virus negative factor natural killer natural killer associated transcript nucleoprotein negative response element nonstructural proteins oxoglutarate dehydrogenase open reading frame ovalbumin
455
456
P. PI-CDC2I p2CA PA2S PAI-I PBI PCC PGAL PGSG PKM-2 PLP pmel pol pp PR PRAI-SCS
pree. preS RAGE ras RBAP-2 rep RSV RT s. lincolnensis sAg SEC6I SFV SIV SLE SMCY
SNase SSP2 SSR STARP Substance P SV SWM SWMb T TAP tax TCR TCRV TF Tf TIMP-I TIMP-2 TIS
MHC Ligands and Peptide Motifs
Plasmodium spee. human CDC2I homolog (chromatin binding protein) murine alpha-ketoglutarate dehydrogenase homologue 20S proteasome regulator (syn.: lIS regulator) plasminogen activator inhibitor-I RNA-directed RNA polymerase subunit PI pigeon cytochrome c phosphoglyceraldehyde platelet proteolycan core protein pyruvate kinase MI (muscle) isoenzyme proteolipid protein melanoma antigen (syn.: gp 100) polymerase phosphoprotein Puerto Rico yeast phospho ribosyl aminomidazole
succinocarboxamide cynthase precursor Hepatitis B virus S antigen precursos tumor antigen proto-oncogene retinoblastoma associated protein 2 regulator of replication and gene expression respiratory syncytial virus reverse transcriptase Streptomyces lincolnensis soluble antigen endoplasmic reticulum peptide exporter Semliki Forest virus simian immunodeficiency virus systemic lupus erythematosus male-specific transplantation antigen (ubiquitously transcribed
teratricopeptide repeat gene on the Y chromosome) Staphylococcal nuclease sporozoite S protein 2 signal sequence receptor sporozoite threonine and asparagine rich protein neuropeptide Sendai virus ->SWMb sperm whale myoglobin T-antigen transporter associated with antigen processing HTLV-I derived trans-activator T cell receptor T cell-receptor variable segment transcription factor transferrin tissue inhibitor of metalloproteinase 1 tissue inhibitor of metalloproteinase 2 EGF-response factor 1
tumor necrosis factor thrombospondin related anonymous protein tyrosinase related protein ubiquitin conjugating enzyme unrelated chromatin HCMV gene encoding a class I heavy chain homologue adhesion receptor Yersinia outer membrane protein yeast protein (Saccharomyces cerevisiae) minor histocompatibility antigen viral gene locus
class I groove 5,30 class I ligand 3, 5, 6, 220, 229 class II 3-5,7-9,17-19,21-26,28-31,
143,217-219,221,222,227,231,232, 372,373,383
class II groove 8,232 class II molecules 3-9,17,21, 23-25, 30,
143,218,219,221,231,232,372,373 class II motifs 3, 4 class III 18,25,29-31 class III region 18, 25 classical HLA class I loci 18 CLIP 8,232 clonal anergy 382 clonal deletion 372, 382 co-stimulatory interactions 372 Collla2 30
141-143,217-232,371-375,379-383 MHC class I 3-7,9,17,19-21,24,28,30,
31,141, 217-223, 227, 229, 230,372, 375,383
MHC class I unrelated loci 20 MHC class II 4,5,7-9,17,23-25,30,31,
143,219,221,227,231,232 MHC class II transactivators 23 MHC function 2,3 MHC genes 1,2,5,17,20,21,31 MHC I assembly 231 MHC I molecules 141, 219, 225, 226,
230,231,373,381 MHC II peptide motifs 220,221 MHC molecules 2-4,6,7,9,17,19,21,
Nand C termini 5, 141 N-terminus 141, 142 natural killer cells 371 natural ligands 143,219,220,222-226,
381 natural MHC ligand 382 negative regulatory element 21 NK cell 27,37l NKATl 371 NKAT4371 nomenclature 18,22,449 nonamers 3,7,218,223,225,226,227 nonclassical HLA class I loci 19 number of alleles 19,22