Introduction to Bioinformatics and Protein Structures

The 3D structure of a protein is often more conserved during evolution than its amino acid sequence.

'+' signifies similar amino acids, sharing chemical and/or structural properties.

Homology analysis can help researchers understand evolutionary relationships between proteins, predict the function of unknown proteins, and build 3D protein models

Homologous proteins in different species that arose from speciation. Orthologs often have similar functions.

Homologous proteins within the same organism arising from gene duplication. Paralogs might have similar or different functions.

A protein variant very similar to others encoded by the same or related genes, caused by genetic differences. It's NOT a paralog.

A chain of molecular interactions that lead to a specific product or cellular change.

Bioinformatics uses computational tools to model and predict protein structure and function.

A database containing information about metabolic pathways and interactions within cells. It helps researchers understand biological processes and their connections.

A graphical representation of the hydrophobicity (water-loving vs. water-hating) of amino acids within a protein sequence. It helps predict transmembrane domains.

Techniques that allow modification of gene expression (overexpression or silencing) to study their effects on phenotypes.

A central repository for 3D structures of biomolecules like proteins, DNA, and RNA. It provides valuable insights into their structure and function, aiding in drug development and understanding biological processes at the atomic level.

A tool for predicting the topology (folding) of membrane proteins using only the amino acid sequence, considering its physical-chemical properties, such as hydrophobicity.

A region of a protein that spans a cell membrane. It is often composed of one or more transmembrane helices, which are highly hydrophobic and about 20-25 amino acids long.

A short sequence of amino acids at the beginning of a protein that signals its transport to the cell membrane or other compartments.

A visual explanation of how a protein folds across the cell membrane based on its hydrophobicity and the presence of transmembrane domains (TMDs) and signal sequences (SSs).

Bioinformatics is a field that combines biology, computer science, and statistics to analyze and interpret biological data. It uses tools to identify patterns in DNA and protein sequences, predict protein structures, determine gene and protein function, and study evolutionary relationships between organisms.

Bioinformatics databases are vast repositories of biological information, including DNA and protein sequences, 3D protein structures, pathway information, and more. Examples include Uniprot, KEGG, PDB, and NCBI BLAST.

The primary structure of a protein refers to the linear sequence of amino acids that makes up the polypeptide chain.

The secondary structure of a protein refers to the local folding patterns of the polypeptide chain, such as alpha-helices and beta-sheets.

The tertiary structure of a protein describes its three-dimensional shape, which is formed by the interactions between different parts of the polypeptide chain. This structure determines the protein's function.

The quaternary structure of a protein refers to the arrangement of multiple polypeptide chains (subunits) that come together to form a functional protein complex.

Proteins that share a common ancestor are considered homologous. Homologs can share a similar sequence and function. They are usually identified by having more than 100 amino acids with greater than 25% identity in their sequences or more than 100 nucleotides for DNA with greater than 70% identity.

Amino acid sequence, location in the cell, interactions with other molecules, post-translational modifications, and proteolytic cleavage can all influence a protein's function.