Protein evolution

Protein evolution

1. Levels of protein structure

   • Primary
     • Proteins with a similar primary structure have a similar tertiary structure
   • Secondary
     • Supersecondary structure
       • Helix-loop helix
       • Coiled coil
       • Helix bundle
       • BaB unit
       • Hairpin
       • B meander
       • Greek key
       • B sandwich
   • Tertiary
     • Domains
       • Independent folding units
       • Have specific functions
       • Hydrophobic interactions are the major driving force for folding domains
       • Building blocks of proteins
       • Recombine with different partners to carry out different functions
       • Important because
         • They're basic evolutionary units
         • Provide function
         • Recombine with other proteins to perform different functions
       • How to recognise domains?
         • DNA sequence
           • Pairs of closely related proteins have similar DNA sequences
           • Useful for short evolutionary distances
         • Amino acid sequence
           • Domains have similar amino acid sequences
           • Sequence pattern is lost as they diverge
         • Protein structure
           • Domains have the same fold
           • Domains are independently folding units
       • Folds
         • Each domain has a specific topolgy/fold
         • There are limited number of folds in nature
       • Classification
         • Taxonomy
         • Evolution conserved structure because structure determines function
         • 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
   • Quaternary

2. Proteins are stabilised by non-bonded interactions

   • Electrostatic interactions
   • Hydrogen bonds
   • Hydrophobic interactions
   • Van der Waals

3. How can you tell if two proteins are similar?

   • Amino acid sequence
     • Sequence identity = number of identical/number of residues aligned x 100
   • Measure protein structure directly
     • Superposition of protein structures
       • Proteins on an axis
         • Superimpose one on the other
   • Scoring structural similarity
     • Root mean square deviation (RMSD)
       • Make an alignment- either using sequence or structural methods
         • 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
   • Reasons for structural similarity
     • Divergent evolution from a common ancestor
       • Structure is more highly conserved than sequence
     • Convergent evolution
       • Limited number of ways of packing helices and strands in 3D space

4. Homology

   • Implies evolutionary relationship
   • Genes (proteins) either are or aren't
   • Orthologs
     • Common ancestor
     • Speciation
     • Different species
     • Same or highly similar function
   • Paralogs
     • Common ancestor
     • Gene duplication
     • Same or different species
     • Different but related function
   • Identifying homologues
     • Significant structural simialarity
     • Significant sequence similarity
     • Functional similarity
   • Example
     • Cholera toxin and Heat labile enterotoxin
   • Analogous structures
     • Structural similarity
     • No sequence or functional similarity
     • Example
       • Heat labile enterotoxin and staphylococcal nuclease

5. Homologous domain superfamilies

   • Sequence diversity
     • Different evolutionary constraints in different positions in the protein structure
     • Core residues are more highly conserved
       • Critical for folding and stability
     • Functional residues highly conserved
       • Residues for enzyme function or protein-protein interactions
     • Surface residues are least conserved
       • Can accommodate small insertions and deletions
   • Structural diversity
     • Core is usually highly convserved
     • Residue insertions occur in the loops connecting secondary structures
     • Residue substitutions can cause shifts in the orientations of secondary structure
   • Functional diversity
     • Dependent on fold
     • Some folds can support a large variety of similar functions
     • Some folds have a limited selection of functions
     • 1 amino acid can change the function of a protein
     • Proteins can share <10% sequence identity but have identical functions in different organisms
     • What is function?
       • Biochemical function
         • Is chemistry conserved?
         • Is substrate conserved?
         • Is product conserved?
       • Is cell localisation convserved?
       • Several ideas have been developed to capture function
         • Enzyme classification system
         • GO terms

6. Methods for recognising domains uses CATH database

   • Algorithms for recognising domain boundaries
     • Detective
       • Each domain should have a recognisable hydrophobic core
     • Domak
       • Residues comprising a domain make more internal contacts than external ones
     • PUU
       • Computer program for protein folding units
       • Finds what interacts most and least with domains
   • Sequence methods for detecting protein domain homologues
     • Scan sequence against profiles if sequence identity <35%
   • Structural methods
     • Distance matrices and contact maps
       • Describes the points of contact between residues in a protein
   • Challenges in comparing protein structures
     • Insertions or deletions of residues- usually not in secondary structures but in connecting loops
       • Ignore variable loop regions and only compare secondary structures
       • Use algorithms which can handle insertions/deletions
     • Structures are highly conserved
     • Structure is more conserved than sequence
       • Considerable differences between structure outside the core
   • Use literature