Analysis of Amino Acid Sequences

499 Pages·2000·5.22 MB·English

by  Peer Bork (Eds.)

ADVANCES IN PROTEIN CHEMISTRY
Volume 54
Analysis of Amino Acid Sequences
This Page Intentionally Left Blank
ADVANCES IN
PROTEIN CHEMISTRY
EDITED BY
FREDERIC M. RICHARDS DAVID S. EISENBERG
DepartmentofMolecularBiophysics DepartmentofChemistryandBiochemistry
andBiochemistry UniversityofCalifornia,LosAngeles
YaleUniversity LosAngeles,California
NewHaven,Connecticut
PETER S. KIM
DepartmentofBiology
MassachusettsInstituteofTechnology
WhiteheadInstituteforBiomedicalResearch
HowardHughesMedicalInstituteResearchLaboratories
Cambridge,Massachusetts
VOLUME 54
Analysis of Amino Acid Sequences
EDITED BY
PEER BORK
EuropeanMolecularBiologyLaboratory
Max-DelbrueckCenterforMolecularMedicine
Heidelberg,Germany
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CONTENTS
PREFACE . . . . . . . . . . . xi
Mass Spectrometric Analysis of Proteins
MATTHIASWILM
I. Introduction . . . . . . . . . 1
II. Ionization Techniques and Mass Spectrometers . . 2
III. Protein Identification and Sequencing with
Mass Spectrometry . . . . . . . . 7
IV. Characterization of Posttranslational Modifications with
Mass Spectrometry . . . . . . . . 17
V. Applications of Protein Characterization with Mass
Spectrometry: Proteomics . . . . . . 24
References . . . . . . . . . 28
Protein Sequence Databases
ROLFAPWEILER
I. Introduction . . . . . . . . . 31
II. Protein Information Resource. . . . . . 32
III. SWISS-PROT . . . . . . . . . 32
IV. TrEMBL . . . . . . . . . . 47
V. SWISS-PROT (cid:2) TrEMBL: A Complete and
Nonredundant View on Protein World . . . . 65
VI. Specialized Protein Sequence Databases . . . . 68
References . . . . . . . . . 70
v
vi CONTENTS
Amino Acid Substitution Matrices
STEVENHENIKOFFANDJORJAG.HENIKOFF
I. Introduction . . . . . . . . . 73
II. Scoring Basics . . . . . . . . . 74
III. Theory . . . . . . . . . . 77
IV. Models for Substitution Scores . . . . . 78
V. Special Substitution Scores . . . . . . 82
VI. Gap Scores . . . . . . . . . 83
VII. Evaluating Scoring Functions . . . . . . 87
VIII. Position-Specific Scores . . . . . . . 91
IX. Using Multiple Substitution Matrices . . . . 94
X. Conclusions . . . . . . . . . 95
References . . . . . . . . . 96
Amino Acid-Based Phylogeny and Alignment
DESMONDG.HIGGINS
I. Introduction . . . . . . . . . 99
II. Trees . . . . . . . . . . 102
III. Sequences . . . . . . . . . 109
IV. Multiple Alignment. . . . . . . . 115
V. Phylogenetic Reconstruction . . . . . . 120
References . . . . . . . . . 133
Searching Databases to Find Protein Domain Organization
ALEXBATEMANANDEWANBIRNEY
I. Introduction . . . . . . . . . 137
II. Protein Domains . . . . . . . . 138
III. Domain Databases . . . . . . . . 143
IV. Finding New Domains . . . . . . . 148
V. Profile Methods . . . . . . . . 149
References . . . . . . . . . 155
CONTENTS vii
Identifying Nature’s Protein Lego Set
SUDESHNADASANDTEMPLEF.SMITH
I. Introduction . . . . . . . . . 159
II. Background . . . . . . . . . 160
III. Methods . . . . . . . . . . 167
IV. Validation and Comparison . . . . . . 175
V. Sensitivity and Specificity. . . . . . . 177
VI. Domain Recognition . . . . . . . 180
VII. Conclusions . . . . . . . . . 180
References . . . . . . . . . 182
Evolution of Domain Families
CHRISP.PONTING,JO¨RGSCHULTZ,RICHARDR.COPLEY,
MIGUELA.ANDRADE,ANDPEERBORK
I. Introduction . . . . . . . . . 185
II. Domain Families in Archaea, Bacteria,
and Eukarya . . . . . . . . . 213
III. Domain Orginating Early in
Eukaryotic Lineage . . . . . . . . 222
IV. Domain Families in Multicellular Organisms . . . 232
V. Domains in Diverse Molecular Contexts . . . . 234
VI. Conclusions . . . . . . . . . 237
References . . . . . . . . . 237
Protein Fold Recognition Using Sequence Profiles and Its
Application in Structural Genomics
EUGENEV.KOONIN,YURII.WOLF,ANDL.ARAVIND
I. Introduction . . . . . . . . . 246
II. Detecting Nontrivial Structural and Evolutionary
Relationships between Proteins Using Position-Specific
Scoring Matrices . . . . . . . . 248
III. Application of PSSMs in Structural-Genomic Analysis 257
IV. Conclusions and Perspective . . . . . . 269
References . . . . . . . . . 270
viii CONTENTS
Protein Sorting Signals and Prediction of Subcellular Localization
KENTANAKAI
I. Introduction . . . . . . . . . 277
II. Sorting of Bacterial Proteins . . . . . . 278
III. Sorting of Eukaryotic Proteins. . . . . . 302
IV. Concluding Remarks . . . . . . . 330
References . . . . . . . . . 331
Gene and Context: Integrative Approaches to Genome Analysis
MARTIJNA.HUYNENANDBERENDSNEL
I. Introduction . . . . . . . . . 345
II. Measuring Genome Evolution. . . . . . 347
III. Gene and Function Prediction by Conservation of
Genomic Context . . . . . . . . 357
IV. Variation of Genomic Context . . . . . 369
V. Discussion . . . . . . . . . 375
References . . . . . . . . . 376
Pathway Databases and Higher Order Function
MINORUKANEHISA
I. Introduction . . . . . . . . . 381
II. KEGG Pathways and Ortholog Groups . . . . 383
III. Prediction of Higher Order Function . . . . 396
IV. Concluding Remarks . . . . . . . 406
References . . . . . . . . . 407
Individual Variation in Protein-Coding Sequences of Human Genome
SHAMILSUNYAEV,JENSHANKE,DAVIDBRETT,ATAKANAYDIN,INGAZASTROW,
WARRENLATHE,PEERBORK,ANDJENSREICH
I. Introduction . . . . . . . . . 409
II. Polymorphism versus Mutation—Neutral Drift
versus Selection . . . . . . . . 412
III. Population Dynamics of Sequence Variation . . . 412
CONTENTS ix
IV. Species Difference versus Intraspecies Variation . . 415
V. Studies on Single-Nucleotide Polymorphism . . . 415
VI. ESTs as Data Source . . . . . . . 418
VII. Conclusions . . . . . . . . . 432
VIII. References . . . . . . . . . 433
AUTHORINDEX . . . . . . . . . . 439
SUBJECTINDEX . . . . . . . . . . 467