CSE182-L6

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CSE182-L6

• Protein structure basics
• Protein sequencing

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Announcements

• Midterm 1 Nov 1, in class.
• Assignment 2 Online, due October 20.

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Distinguishing between families
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Distinguishing between families
Assignment 2
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Profiles

• Start with an alignment of strings of length m,
  over an alphabet A,
• Build an A X m matrix F(fki)
• Each entry fki represents the frequency of symbol
  k in position i

0.71
0.14
0.28
0.14
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Scoring Profiles
Scoring Matrix
i
k
fki
s
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Psi-BLAST idea

• Multiple alignments are important for capturing
  remote homology.
• Profile based scores are a natural way to handle
  this.
• Q What if the query is a single sequence.
• A Iterate
• Find homologs using Blast on query
• Discard very similar homologs
• Align, make a profile, search with profile.

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Psi-BLAST speed

• Two time consuming steps.
• Multiple alignment of homologs
• Searching with Profiles.
• Does the keyword search idea work?

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Protein Domains

• An important realization (in the last decade) is
  that proteins have a modular architecture of
  domains/folds.
• Example The zinc finger domain is a DNA-binding
  domain.
• What is a domain?
• Part of a sequence that can fold independently,
  and is present in other sequences as well

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Domain review

• What is a domain?
• How are domains expressed
• Motifs (Regular expression others)
• Multiple alignments
• Profiles
• Profile HMMs

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Domain databases
Can you speed up HMM search?
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A structural view of proteins
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CS view of a protein

• gtspP00974BPT1_BOVIN Pancreatic trypsin
  inhibitor precursor (Basic protease inhibitor)
  (BPI) (BPTI) (Aprotinin) - Bos taurus (Bovine).
• MKMSRLCLSVALLVLLGTLAASTPGCDTSNQAKAQRPDFCLEPPYTGPCK
  ARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGAIGPWENL

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Protein structure basics
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Side chains determine amino-acid type

• The residues may have different properties.
• Aspartic acid (D), and Glutamic Acid (E) are
  acidic residues

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Bond angles form structural constraints
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Various constraints determine 3d structure

• Constraints
• Structural constraints due to physiochemical
  properties
• Constraints due to bond angles
• H-bond formation
• Surprisingly, a few conformations are seen over
  and over again.

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Alpha-helix

• 3.6 residues per turn
• H-bonds between 1st and 4th residue stabilize the
  structure.
• First discovered by Linus Pauling

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Beta-sheet

• Each strand by itself has 2 residues per turn,
  and is not stable.
• Adjacent strands hydrogen-bond to form stable
  beta-sheets, parallel or anti-parallel.
• Beta sheets have long range interactions that
  stabilize the structure, while alpha-helices have
  local interactions.

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Domains

• The basic structures (helix, strand, loop)
  combine to form complex 3D structures.
• Certain combinations are popular. Many sequences,
  but only a few folds

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3D structure

• Predicting tertiary structure is an important
  problem in Bioinformatics.
• Premise Clues to structure can be found in the
  sequence.
• While de novo tertiary structure prediction is
  hard, there are many intermediate, and tractable
  goals.
• The PDB database is a compendium of structures

PDB
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Searching structure databases

• Threading, and other 3d Alignments can be used to
  align structures.
• Database filtering is possible through geometric
  hashing.

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Trivia Quiz

• What research won the Nobel prize in Chemistry in
  2004?
• In 2002?

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How are Proteins Sequenced? Mass Spec 101
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Nobel Citation 2002
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Nobel Citation, 2002
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Mass Spectrometry
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Sample Preparation
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Single Stage MS
Mass Spectrometry
LC-MS 1 MS spectrum / second
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Tandem MS
Secondary Fragmentation
Ionized parent peptide