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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....

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Updated: May 6, 2026

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

Using the RosettaSurface algorithm to predict protein structure at mineral surfaces.

Michael S Pacella¹, Da Chen Emily Koo, Robin A Thottungal

¹Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

Methods in Enzymology

|November 6, 2013

Summary

This summary is machine-generated.

Understanding protein structure on mineral surfaces is key for biomineralization research. RosettaSurface computational methods aid in predicting these structures, advancing disease treatment and material design.

Keywords:

Biased sampling Biomineralization Experimental constraints Hydroxyapatite Monte Carlo docking Osteocalcin Protein–surface interactions RosettaSurface Statherin

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Biomineralization
Structural Biology
Computational Chemistry

Background:

Determining protein structure on mineral surfaces is crucial for understanding biomineralization processes.
Limited atomic-resolution experimental data hinders progress in this field.
Molecular simulation offers a complementary approach to experimental methods.

Purpose of the Study:

To review RosettaSurface, a computational algorithm for predicting protein structures on mineral surfaces.
To summarize its computational approaches, applications, and recent updates.
To provide a practical protocol and case study using osteocalcin.

Main Methods:

RosettaSurface algorithm for broad conformational space sampling.
Computational structure prediction.
Review of published applications and code releases within the Rosetta 3 framework.
Demonstration using osteocalcin, a mineralization protein.

Main Results:

RosettaSurface effectively samples conformational space to identify low-energy protein structures on mineral surfaces.
The review details computational strategies and successful applications.
A practical protocol and analysis of osteocalcin structure prediction are provided.

Conclusions:

Computational methods like RosettaSurface are vital for studying proteins on mineral surfaces.
Challenges remain in energy function optimization and conformational searching.
Integrating experimental and computational approaches is essential for future advancements in biomineralization research.