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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 Folding

Protein Folding

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

Protein and Protein Structures

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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[Modeling of protein spatial structure using tritium planigraphy].

E N Bogacheva, A N Bogachev, I B Dmitriev

|January 28, 2012

Summary

Tritium planigraphy offers a novel method for protein spatial structure modeling, overcoming limitations of X-ray crystallography and NMR. This technique successfully generates accurate three-dimensional protein models consistent with experimental data.

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Area of Science:

Biophysics
Structural Biology
Computational Chemistry

Context:

Understanding macromolecular interactions is crucial for biological systems and technological applications.
Existing methods like X-ray crystallography and NMR spectroscopy have limitations (e.g., crystal requirement, molecular weight limits).
Novel approaches are needed for accurate protein spatial structure modeling.

Purpose:

To present the results of protein spatial structure modeling using the semiempirical tritium planigraphy technique.
To demonstrate the efficacy of tritium planigraphy as an alternative or complementary method for protein structure determination.
To validate the technique against established methods like X-ray analysis.

Summary:

The study introduces tritium planigraphy, a method combining tritium atom bombardment with computer simulation for protein structure modeling.
The technique successfully generated three-dimensional protein models consistent with X-ray crystallography data across diverse protein classes.
Optimal model accuracy is achieved by analyzing contacts between secondary structure elements and assembling them sequentially from N- to C-terminus.

Impact:

Provides a new computational tool for elucidating protein structures, particularly for systems challenging for traditional methods.
Enhances understanding of protein structure-function relationships, aiding drug discovery and biomaterial design.
Contributes to advancing structural biology by offering a complementary approach to existing techniques.