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Proteins and Protein Function
Charles Yan
Spring 2006
Amino Acids
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General structure of an amino acid
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20 standard amino acids each with a different R group
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Amino Acids
Table 1. 20 standard amino acids
Amino Acid
3-letter code
1-letter code
Alanine
Ala
A
Arginine
Arg
R
Asparagine
Asn
N
Aspartate
Asp
D
Cysteine
Cys
C
Glutamine
Gln
Q
Glutamate
Glu
E
Glycine
Gly
G
Histidine
His
H
Isoleucine
Ile
I
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Amino Acids
Table 1. 20 standard amino acids (Cont.)
Amino Acid
3-letter code
1-letter code
Leucine
Leu
L
Lysine
Lys
K
Methionine
Met
M
Phenylalanine
Phe
F
Proline
Pro
P
Serine
Ser
S
Threonine
Thr
T
Tryptophan
Trp
W
Tyrosine
Tyr
Y
Valine
Val
V
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Amino Acids
Amino Acid
3-letter code
1-letter code
Asparagine (N) or aspartate (D)
Asx
B
Glutamine (Q) or glutamate (E)
Glx
Z
Any amino acid
Xaa
X
Amino Acid Abbreviations (IUPAC)
Authority
Reference
IUPAC-IUB Joint Commission on Biochemical Nomenclature.
IUPAC-IUB Joint Commission on Biochemical Nomenclature.
Nomenclature and Symbolism for Amino Acids and Peptides.
Eur. J. Biochem. 138:9-37(1984).
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Proteins
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Two separate amino acids can be linked together by a peptide
bond
A chain of amino acids linked by peptide bonds is called a
polypeptide.
A protein is made up of one or more polypeptide chains
For simplicity, in this course, a protein is a chain of amino acids
linked by peptide bonds, e.g.
VSQLLKQRVRYAPYLSKVRRAEELLPLFKHGQYIGWSGFTGVGAPKVI
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Protein Database
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UniProt (Universal Protein Resource) (http://www.pir.uniprot.org/) is
the world's most comprehensive catalog of information on proteins.
It is a collaboration between
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Swiss Institute of Bioinformatics (SIB)
Department of Bioinformatics and Structural Biology of the
Geneva University
European Bioinformatics Institute (EBI)
Georgetown University Medical Center's Protein Information
Resource (PIR)
It includes three components
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Protein Database
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UniProt Knowledgebase (UniProtKB): the central access point
for extensive curated protein information.
 UniProtKB/Swiss-Prot: a manually annotated protein sequence
database which provide a high level of annotation, a minimal level
of redundancy and high level of integration with other databases.
UniProtKB/Swiss-Prot Release 48.7 of 20-Dec-2005: 204,086
entries
 UniProtKB/TrEMBL: a computer-annotated supplement of
Swiss-Prot that contains all the translations of EMBL nucleotide
sequence entries not yet integrated in Swiss-Prot.
UniProtKB/TrEMBL Release 31.7 of 20-Dec-2005: 2,506,886
entries
UniProt Reference Clusters (UniRef): databases combine closely
related sequences into a single record to speed searches.
UniProt Archive (UniParc): a comprehensive repository, reflecting
the history of all protein sequences
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Protein Database
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Protein Database
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Protein Database
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Protein Database
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Protein Database
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Gene Ontology
Goal: find all the proteins
that are involved protein
synthesis
Protein
synthesis
Translation
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Gene Ontology
Volkswagen Golf
I like
golf.
Me
too!
Golf
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Gene Ontology

Ontology
n. the branch of metaphysics dealing with the nature of being.
(The New Oxford American Dictionary, Edited by Elizabeth J.
Jewell, Frank Abate, Oxford University Press, 2001,pp 1197.)

Metaphysics
n. the branch of philosophy that deals with the first principles of
things, including abstract concepts such as being, knowing,
substance, cause, identity, time, and space.
(The New Oxford American Dictionary, Edited by Elizabeth J.
Jewell, Frank Abate, Oxford University Press, 2001,pp 1074.)
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Gene Ontology

The Gene Ontology (GO) (http://www.geneontology.org/)
project is a collaborative effort to address the need for
consistent descriptions of gene products in different
databases. The project began as a collaboration between
three model organism databases: FlyBase (Drosophila),the
Saccharomyces Genome Database (SGD) and the Mouse
Genome Database (MGD) in 1998. Since then, the GO
Consortium has grown to include many databases,
including several of the world's major repositories for
plant, animal and microbial genomes.
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Gene Ontology
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Develop structured, controlled vocabularies (ontologies)
that describe gene products
Make associations between the ontologies and the genes
and gene products in the collaborating databases,
Develop tools that facilitate the creation, maintainence
and use of ontologies
The use of GO terms facilitates uniform queries across
databases
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Gene Ontology
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The three components of GO are molecular function,
biological process and cellular component
GO terms are organized in structures called directed
acyclic graphs (DAGs), which differ from hierarchies in
that a child, or more specialized, term can have many
parent, or less specialized, terms
monosaccharide biosynthesis
hexose metabolism
hexose biosynthesis
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Gene Ontology
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The controlled vocabularies are structured so that you
can query them at different levels
GO browser AmiGO (http://www.godatabase.org/cgibin/amigo/go.cgi)
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Protein function
Three steps to get a set of proteins that have a certain
function
 Search for the GO term
(http://www.godatabase.org/cgi-bin/amigo/go.cgi)
 Search for the proteins belong to a certain GO
(http://www.pir.uniprot.org/search/textSearch.shtml)
 Save the sequence in FASTA format
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Search for the GO
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Search for the proteins belong to a certain GO
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Save sequences in FASTA format
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