Protein evolution

Levels of protein structure
1. Primary
  1. Proteins with a similar primary structure have a similar tertiary structure
2. Secondary
  1. Supersecondary structure
    1. Helix-loop helix
    2. Coiled coil
    3. Helix bundle
    4. BaB unit
    5. Hairpin
    6. B meander
    7. Greek key
    8. B sandwich
3. Tertiary
  1. Domains
    1. Independent folding units
    2. Have specific functions
    3. Hydrophobic interactions are the major driving force for folding domains
    4. Building blocks of proteins
    5. Recombine with different partners to carry out different functions
    6. Important because
      1. They're basic evolutionary units
      2. Provide function
      3. Recombine with other proteins to perform different functions
    7. How to recognise domains?
      1. DNA sequence
        Pairs of closely related proteins have similar DNA sequences
        Useful for short evolutionary distances
      2. Amino acid sequence
        Domains have similar amino acid sequences
        Sequence pattern is lost as they diverge
      3. Protein structure
        Domains have the same fold
        Domains are independently folding units
    8. Folds
      1. Each domain has a specific topolgy/fold
      2. There are limited number of folds in nature
    9. Classification
      1. Taxonomy
      2. Evolution conserved structure because structure determines function
      3. Classification systems
        CATH
        Chop proteins into domains
        Use sequence and structural analysis programs to group domains into evolutionary and structural families
        Classes
        What is the major secondary structure
        Architecture
        Describes shape of fold
        Rossman fold
        An NAD binding domain
        NAD
        Cofactor that reversibly accepts a hydride ion
        Ion is lost or gained by substrate in redox reaction
        Consists of 2 nucleotides joined a phosphate group
        One nucleotide contains an adenine base and the other nicotinamide
        One of the most ubiquitous domains
        Rossman domain binds nicotinamide adenine dinucleotide (NAD+)
        Rossman domains have alpha/beta fold, central beta sheet with 5 alpha helices surrounding it
        Example
        Lactate dehydrogenase
        Metabolic enzyme
        Catalyses conversion of L-lactate to pyruvate
        Last step in anaerobic glycolysis
        N-terminal domain is NAD binding domain/Rossman fold
        C-terminal domain
        Catalytic domain
        For substrate specificity and precise reaction of enzyme
        Specific to lactate/malate dehydrogenases
        Malate dehydrogenase
        Catalyses conversion of malate to oxaloacetate
        N-terminal domain is NAD binding/Rossman fold
        C-terminal domain is catalytic domain
        LDH and MDH
        Structure is conserved more than sequence
        17% sequence identity
        Function of NAD binding domain conserved
        Change in sequence binding domain enables change of substrate specificity in catalytic domain
        Alcohol dehydrogenase
        Catalyses oxidation of ethanol to acetylaldehyde
        Topology
        Describes connectivity of fold
        Homologous superfamily
        Is there enough evidence to say the domains came from the same superfamily
        SCOP
        Structural Classification Of Proteins
        Class, fold, superfamily, species
        Structure based
        Pfam
        Protein family database
        Superfamily, clade
        Vary in domain definitions
4. Quaternary
Proteins are stabilised by non-bonded interactions
1. Electrostatic interactions
2. Hydrogen bonds
3. Hydrophobic interactions
4. Van der Waals
How can you tell if two proteins are similar?
1. Amino acid sequence
  1. Sequence identity = number of identical/number of residues aligned x 100
2. Measure protein structure directly
  1. Superposition of protein structures
    1. Proteins on an axis
      1. Superimpose one on the other
3. Scoring structural similarity
  1. Root mean square deviation (RMSD)
    1. Make an alignment- either using sequence or structural methods
      1. For each pair of aligned residues use C-alphas
        Calculate how far apart they are
        Sum this value for all residues
        Divide by number of residues
4. Reasons for structural similarity
  1. Divergent evolution from a common ancestor
    1. Structure is more highly conserved than sequence
  2. Convergent evolution
    1. Limited number of ways of packing helices and strands in 3D space
Homology
1. Implies evolutionary relationship
2. Genes (proteins) either are or aren't
3. Orthologs
  1. Common ancestor
  2. Speciation
  3. Different species
  4. Same or highly similar function
4. Paralogs
  1. Common ancestor
  2. Gene duplication
  3. Same or different species
  4. Different but related function
5. Identifying homologues
  1. Significant structural simialarity
  2. Significant sequence similarity
  3. Functional similarity
6. Example
  1. Cholera toxin and Heat labile enterotoxin
7. Analogous structures
  1. Structural similarity
  2. No sequence or functional similarity
  3. Example
    1. Heat labile enterotoxin and staphylococcal nuclease
Homologous domain superfamilies
1. Sequence diversity
  1. Different evolutionary constraints in different positions in the protein structure
  2. Core residues are more highly conserved
    1. Critical for folding and stability
  3. Functional residues highly conserved
    1. Residues for enzyme function or protein-protein interactions
  4. Surface residues are least conserved
    1. Can accommodate small insertions and deletions
2. Structural diversity
  1. Core is usually highly convserved
  2. Residue insertions occur in the loops connecting secondary structures
  3. Residue substitutions can cause shifts in the orientations of secondary structure
3. Functional diversity
  1. Dependent on fold
  2. Some folds can support a large variety of similar functions
  3. Some folds have a limited selection of functions
  4. 1 amino acid can change the function of a protein
  5. Proteins can share <10% sequence identity but have identical functions in different organisms
  6. What is function?
    1. Biochemical function
      1. Is chemistry conserved?
      2. Is substrate conserved?
      3. Is product conserved?
    2. Is cell localisation convserved?
    3. Several ideas have been developed to capture function
      1. Enzyme classification system
      2. GO terms
Methods for recognising domains uses CATH database
1. Algorithms for recognising domain boundaries
  1. Detective
    1. Each domain should have a recognisable hydrophobic core
  2. Domak
    1. Residues comprising a domain make more internal contacts than external ones
  3. PUU
    1. Computer program for protein folding units
    2. Finds what interacts most and least with domains
2. Sequence methods for detecting protein domain homologues
  1. Scan sequence against profiles if sequence identity <35%
3. Structural methods
  1. Distance matrices and contact maps
    1. Describes the points of contact between residues in a protein
4. Challenges in comparing protein structures
  1. Insertions or deletions of residues- usually not in secondary structures but in connecting loops
    1. Ignore variable loop regions and only compare secondary structures
    2. Use algorithms which can handle insertions/deletions
  2. Structures are highly conserved
  3. Structure is more conserved than sequence
    1. Considerable differences between structure outside the core
5. Use literature

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Protein evolution

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