Bioinformatics Lecture 8: Structural Bioinformatics

The linear sequence of amino acids in a protein is known as its primary structure. This structure encompasses all the covalent bonds between the amino acids.

The unique three-dimensional arrangement of amino acids in a protein, formed by interactions between the side chains (R groups) of the amino acids.

The protein's structure is organized into various levels, starting with the sequence of amino acids and progressing to the complex 3D arrangement formed by interactions among multiple polypeptide chains.

These are regular spatial arrangements of adjacent amino acids in a polypeptide chain. They are characterized by hydrogen bonds between the backbone atoms.

The peptide bond is the main covalent bond linking amino acids together in a protein chain. It forms through a condensation reaction, where water is released.

The protein sequence consists of 20 different amino acids, each containing a central alpha carbon (Cα) and a specific side chain (R group) that differentiates them.

The arrangement of multiple polypeptide chains, each with its own tertiary structure, in a functional protein complex.

Alpha (α) helices and beta (β) sheets are common secondary structures in proteins.

The specific arrangement of amino acids in a polypeptide chain, forming a linear sequence. It determines the unique identity of each protein.

The regular, recurring structural patterns within a polypeptide chain. These patterns arise from hydrogen bonding between backbone atoms. Two main types are α-helix and β-sheet.

The three-dimensional spatial arrangement of all atoms in a single polypeptide chain. It results from interactions between side chains (R groups) of amino acids.

The association of multiple polypeptide chains (subunits) to form a functional protein. It involves non-covalent interactions between these subunits.

The process of predicting the three-dimensional structure of a protein based on its amino acid sequence. It aims to achieve accuracy comparable to experimental methods.

A helical structure in proteins, characterized by a tightly coiled polypeptide backbone. The side chains (R groups) project outwards from the helix.

A sheet-like structure in proteins, composed of extended polypeptide strands linked by hydrogen bonds. The strands run parallel or antiparallel to each other.

The strongest type of bond in protein structures, formed between the carbonyl group of one amino acid and the amino group of another amino acid, typically within the polypeptide backbone.

The interactions between side chains (R groups) of amino acids that contribute to the tertiary structure of a protein. These include hydrophobic interactions, ionic bonds, disulfide bridges, and hydrogen bonds.

The interactions between polypeptide chains in the quaternary structure of a protein. These are similar to the interactions that stabilize the tertiary structure.

The prediction of a protein's 3D structure from its amino acid sequence.

It's when a protein's amino acid sequence is similar to another known protein's sequence, implying that their 3D structures will also be alike.

A method used to assess the accuracy of a predicted protein structure. It compares the predicted model to a known, experimentally determined structure.

The percentage of identical amino acids between two protein sequences.

A range of sequence identity in which two proteins will likely have very similar 3D structures. Typically between 30-50%.

A widely used database containing experimentally determined 3D protein structures.

A bioinformatics platform that provides tools for protein structure prediction, including homology modeling.

Proteins are essential for biological processes, and their functions depend on their 3D structure and dynamics.

Tools and techniques for analyzing and evaluating the quality of predicted protein structures, ensuring their accuracy and reliability.

The primary structure of a protein is the linear sequence of amino acids, and knowing this sequence is crucial for predicting its 3D structure.

A graphical representation of the possible phi (φ) and psi (ψ) angles of amino acid residues in a polypeptide chain, showing which combinations are allowed and disallowed due to steric hindrance.

A method used to assess the quality of protein structure predictions, providing a benchmark for comparing different prediction algorithms.

A server used for validating the quality of protein models generated through homology modeling, providing two key metrics: GMQE and QMEAN.

A metric used by the Swiss Model Validation Server to assess the global quality of a protein model. It's based on the target-template alignment and identification method.

A metric provided by the Swiss Model Validation Server that estimates the quality of a protein model based on its geometric properties. It offers both global and local scores.