Structural Bioinformatics

These flashcards cover essential concepts related to the structural bioinformatics lecture, focusing on key definitions, principles, and applications in the field.

What was the goal of the Structural Genomics effort?

To systematically obtain the 3D structures of all proteins encoded in the genome.

What is Structural Bioinformatics?

An interdisciplinary field that deals with the three-dimensional structures of biomolecules.

What principle does the protein structure/function paradigm emphasize?

The function of a macromolecule is dictated by its 3D structure.

What is the focus of the Protein Structure Initiative?

To determine the exact 3D structure of all proteins in the genomes using experimental and computational methods.

What does the lock-and-key model in molecular recognition refer to?

The structural complementarity between interacting molecules.

How do molecular motions contribute to protein function?

They allow biomolecules to interact and adapt to other biomolecules, affecting biochemical functions.

What is the induced-fit theory?

It suggests that protein and ligand mutually adapt by conformational changes to achieve an optimal fit during the recognition process.

What are Van der Waals forces?

Weak forces between atoms due to temporary atomic induced polarization.

What do electrostatic interactions involve?

Strong forces acting between charged particles that can be attractive or repulsive.

Why is hydrogen bonding significant in biology?

It plays a crucial role in stabilizing the structures of macromolecules including DNA and proteins.

What does molecular docking aim to predict?

The association of two molecular surfaces.

What role does molecular dynamics play in structural bioinformatics?

It simulates the dynamic behavior of biomolecules to understand their interactions and functions.

What is the function of the Structural Genomics Consortium?

To solve the three-dimensional structures of medically relevant proteins.

What are the major components of molecular recognition?

Approach, desolvation, penetration, orientation, adaptation, and anchorage.

How does evolution help in understanding protein functions?

By providing insights into homologous proteins with significant sequence similarity and related functions.

What is the significance of protein flexibility?

It allows for induced-fit motions and adaptations crucial to protein function.

What are computational tools developed by Structural Bioinformatics used for?

Encoding and visualizing biomolecules, predicting 3D structures, and analyzing structural data.

What was one of the first examples of 3D knowledge leading to a better understanding of life processes?

The Watson and Crick DNA double helix model.

What is the main application of structural bioinformatics?

The discovery of novel therapeutic agents through rational drug design.

What is the purpose of normal mode analyses (NMA) in studying proteins?

To analyze vibrational modes and study protein conformational changes.