Proteins and Protein Function

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Proteins and Protein Function

• Charles Yan
• Spring 2006

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Amino Acids

• General structure of an amino acid
• 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       IUPAC-IUB Joint Commission on
Biochemical  Nomenclature. Reference     
IUPAC-IUB Joint Commission on Biochemical  
Nomenclature.    Nomenclature   and   
Symbolism   for   Amino   Acids   and  Peptides.
                Eur. J. Biochem.
1389-37(1984).
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Proteins

• 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.
• VSQLLKQRVRYAPYLSKVRRAEELLPLFKHGQYIGWSGFTGVGAPK
  VI

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Protein Database

• 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
• 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

• 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
Translation
Protein synthesis
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Gene Ontology

• Volkswagen Golf

Golf
I like golf.
Me too!
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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.or
  g/) 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

• 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

• 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

• The controlled vocabularies are structured so
  that you can query them at different levels
• GO browser AmiGO (http//www.godatabase.org/cgi-bi
  n/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.shtm
  l)
• 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