Lecture 5: Protein Sequence Analysis and Structure Visualization

the linear sequence of amino acids

Sources of Primary Structure

• National Biomedical Research Foundation (NBRF) • Functional annotation of protein data • Non-redundant, expertly annotated

Central hub of functional information on protein sequences

Databases of UniProtKB

defined as the local conformation of the protein backbone

sections of a polypeptide chain capable of INDEPENDENTLY maintaining a characteristic 3D structure apart from the bulky protein

shuffling of various domains across different proteins – form novel gene architectures/forms

short simple substructures identified within contiguous sequence

detect strongly conserved amino acid patterns that could represent an active site or important feature

These motifs allow proteins to bind to DNA and regulate gene expression.

Example of DNA binding Motifs

These motifs are found in enzymes and are involved in catalyzing specific chemical reactions.

Example of Catalytic Motifs

These motifs are involved in protein-protein interactions and can form coiled helical structures. They are often found in proteins that are part of larger protein complexes.

These motifs are involved in binding and hydrolyzing nucleotides like ATP or GTP and are common in nucleotide-binding proteins.

• groups of proteins that share a given domain • have similar biochemical function

arranges proteins by clans; related structure and function and significant similarity based on profile HMMs

lower sequence identity than families but share the same secondary structure in the same arrangement

Folding of secondary structural elements • gives a specific 3D shape of the polypeptide chain

Protein structure determination

Requires crystallizing the protein.

Used for identification and sequencing, increasingly used for structural insights

Refers to proteins that contain more than one polypeptide chain