PROTEIN SEQUENCE ANALYSIS

Course Code: MIC-403

By: Mahrukh Zakir
Email Address: [email protected]
PROTEIN SEQUENCE ANALYSIS

 Protein sequence analysis is a scientific method to study the sequence of amino acids in a protein, known
as its primary structure.
 The sequence contains crucial details about the protein's structure, function, and evolutionary history.
 Understanding the biological roles of proteins.
 Identifying interactions with other molecules.
 Exploring their significance in cellular processes.
Applications:
➢ Predicting protein function.
➢ Investigating evolutionary relationships.
➢ Understanding protein behavior in health and disease.
UNDERSTANDING PROTEIN STRUCTURE

 Proteins adopt specific three-dimensional structures that are essential for their function. Sequence analysis plays a
critical role in predicting the following structural levels:
• Secondary Structure: Predicts patterns such as alpha-helices and beta-sheets.
• Tertiary Structure: Provides insights into the overall 3D folding of the protein.
Common Tools for Structural Prediction:
 PSIPRED: Predicts secondary structures with high accuracy.
 AlphaFold: Utilizes AI to predict detailed 3D protein structures.
 SWISS-MODEL: Builds 3D models of proteins based on sequence homology.
PREDICTING PROTEIN FUNCTION

 Protein sequence analysis enables researchers to predict the potential function of a protein by leveraging similarity
with known proteins in databases.
• Comparative Analysis: Tools like BLAST and UniProt are used to compare sequences against existing
databases.
Functional Features Identified:
• Functional Domains: Regions associated with specific biological roles.
• Active Sites: Key areas involved in enzymatic activity.
• Binding Regions: Sites for interactions with other molecules (e.g., ligands, DNA, or proteins).
IDENTIFYING MOTIFS AND DOMAINS
 Protein motifs and domains are critical features that provide insights into a protein's structure, function,
and evolutionary relationships.
Motifs
Motifs are short, conserved sequences of amino acids that are often linked to specific biological functions.
• Example: Catalytic Motifs in enzymes or Binding Motifs for DNA, RNA, or ligands.
• Typically span 5–20 amino acids in length.
Functions:
• Enable enzymatic activity (e.g., ATP-binding motifs in kinases).
• Facilitate protein-protein or protein-ligand interactions.
• Often found in regulatory regions, signaling pathways, or as functional hotspots
CONT.
Domains
Domains are larger, structurally and functionally distinct units within proteins that are stable
and self-folding.
• Domains are often composed of one or more motifs.
• Example: SH2 domains mediate protein interactions, and Zinc Finger domains enable DNA
binding.
Function:
• Domains often define the overall function of a protein, such as DNA recognition, catalysis, or
cellular localization.
• Proteins can have multiple domains, each with a distinct role, enabling complex functions.
TOOLS FOR MOTIF AND DOMAIN IDENTIFICATION
EVOLUTIONARY RELATIONSHIPS
 The study of evolutionary relationships between proteins across species provides insights into their conservation,
functional significance, and evolutionary history.
Sequence Alignment for Evolutionary Conservation
• Sequence alignment is the process of comparing protein sequences from different species to identify similarities and
differences.
• Conserved Sequences: Sequences that remain unchanged across species, indicating their importance for
protein function or structure.
• Divergent Sequences: Variations that may reflect species-specific adaptations or evolutionary changes.
Significance:
• Highly Conserved Sequences: Often critical for maintaining protein function and structure (e.g., active sites,
binding regions).
• Less Conserved Regions: May evolve to accommodate specific biological functions or environmental
conditions in different species.
CONT.
Phylogenetic Analysis
Phylogenetic tools help construct evolutionary trees (phylogenetic trees) that visualize the relationships between
species or proteins based on sequence similarity.
• Goal: To trace the evolutionary origins and diversification of proteins across different organisms.
Key Tools for Phylogenetic Analysis:
• MEGA (Molecular Evolutionary Genetics Analysis):
• A comprehensive software for creating phylogenetic trees and analyzing evolutionary relationships based
on sequence data.
• It offers various alignment and tree-building methods, including maximum likelihood, neighbor-joining,
and bootstrapping for statistical validation.
• Clustal Omega:
• A tool for multiple sequence alignment and phylogenetic analysis.
STUDYING PROTEIN INTERACTIONS
 Protein interaction analysis is essential for understanding cellular processes such as signaling, metabolism, and
gene regulation.
 Sequence analysis plays a crucial role in identifying potential interaction sites and predicting how proteins interact
with other biomolecules.
Tools for Predicting Protein Interactions
Sequence-Based Predictions:
• InterPro: Identifies interaction motifs and functional domains in proteins.
• STRING: Predicts protein-protein interaction networks based on sequence similarity, functional annotations, and
experimental data.
• PSORT: Predicts the subcellular localization of proteins, which is useful in understanding their potential interactions with
other biomolecules.
• PredictProtein: Provides a comprehensive analysis of protein structure, function, and potential interaction sites.
STEPS IN PROTEIN SEQUENCE ANALYSIS
Sequence Alignment:
Sequence Retrieval: Database Searches: Tools
Alignments (e.g., pairwise
Protein sequences are like BLAST (Basic Local
or multiple sequence
Alignment Search Tool)
retrieved from databases alignments) are used to
compare sequences against
like UniProt, NCBI identify similarities or
large protein databases to
Protein, or PDB. differences between
identify homologs.
sequences.

Phylogenetic Analysis: Motif and Domain

Determine evolutionary Structure Prediction: Predict Identification: Analyze the
relationships to understand the the protein’s secondary and sequence for conserved
protein's origin and its tertiary structure to infer motifs or functional
conservation across different potential biological roles. domains using specialized
species. tools.
IMPORTANCE OF PROTEIN SEQUENCE ANALYSIS

 Drug Development: Identifying active sites in proteins helps design targeted drugs.
 Disease Research: Understanding mutations in protein sequences can reveal their
roles in diseases like cancer or genetic disorders.
 Synthetic Biology: Enables the design of novel proteins with desired functions.
 Agriculture: Helps improve traits in crops or livestock by studying stress-related
proteins.