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Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Organization

Protein Organization

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Protein-Protein Interfaces

Protein-Protein Interfaces

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Protein and Protein Structures

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

The Framework of Computational Protein Design.

Ilan Samish^1,2,3

¹Department of Plants and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel. ilan.samish@weizmann.ac.il.

Methods in Molecular Biology (Clifton, N.J.)

|December 4, 2016

Summary

Computational protein design (CPD) enables creating novel proteins with tailored functions, from enhanced stability to specific binding and enzymatic activity. This framework outlines the CPD cycle, covering goals, methods, and optimization tools for sequence and structure design.

Keywords:

Computational biophysics Computational protein design Negative design Protein structure prediction Structural bioinformatics Synthetic biology

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Area of Science:

Biochemistry
Computational Biology
Protein Engineering

Background:

Computational protein design (CPD) is a rapidly advancing field with significant implications for both fundamental science and practical applications.
CPD involves designing proteins computationally, from individual amino acids to entire functional complexes.
Current applications range from enhancing protein stability to engineering specific functions like binding, enzymatic activity, and nanotechnology.

Purpose of the Study:

To provide a comprehensive overview of the computational protein design framework.
To highlight the key elements and iterative cycle involved in CPD.
To introduce the diverse goals, methodologies, and optimization strategies within CPD.

Main Methods:

Defining the scope and objectives of computational protein design.
Detailing the components of a typical CPD protocol.
Exploring methods for searching sequence and structure space.
Discussing the role of scoring functions in evaluating designed proteins.
Integrating CPD with other optimization tools.

Main Results:

The study outlines the fundamental framework of computational protein design.
Key elements of the CPD iterative cycle are identified and explained.
A range of design targets and approaches, from local modifications to complete protein redesign, are presented.

Conclusions:

Computational protein design offers a powerful approach to engineering proteins with specific functions and properties.
Understanding the CPD framework, including its goals and methods, is crucial for advancing the field.
The iterative nature of CPD, combined with various optimization tools, facilitates the creation of novel protein functionalities.