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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.

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.
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Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Conservation of Protein Domains

Conservation of Protein Domains

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 form...

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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

Effect of using suboptimal alignments in template-based protein structure prediction.

Hao Chen¹, Daisuke Kihara

¹Department of Biological Sciences, College of Science, Purdue University, West Lafayette, Indiana 47907, USA.

|November 9, 2010

Summary

Suboptimal alignments improve template-based protein structure prediction. These alignments, often more accurate than optimal ones, enhance contact prediction and threading programs like SUPRB for better protein structure modeling.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Template-based protein structure prediction is increasingly important due to growing structural genomics data.
Effective methods are needed to utilize solved structures as templates, especially for remotely related proteins.
Current methods often rely solely on optimal alignments, potentially missing valuable information.

Purpose of the Study:

To investigate the impact of using suboptimal sequence alignments in template-based protein structure prediction.
To assess whether suboptimal alignments can improve the accuracy of protein structure modeling.
To develop and evaluate a novel threading approach incorporating suboptimal alignments.

Main Methods:

Examined the accuracy of suboptimal sequence alignments compared to optimal alignments.
Analyzed the presence of correct amino acid residue contacts within suboptimal alignments.
Integrated suboptimal alignments into the Modeller software for template-based modeling.
Developed and tested the SUPRB threading program using a probabilistic contact potential with suboptimal alignments.

Main Results:

Suboptimal alignments were found to be frequently more accurate than optimal alignments, even at low ranks.
Suboptimal alignments contain a significant number of correct residue contacts.
Using suboptimal alignments as input improved template-based models generated by Modeller.
The probabilistic contacts strategy in SUPRB, utilizing suboptimal alignments, outperformed existing methods.

Conclusions:

Suboptimal alignments offer a valuable resource for enhancing template-based protein structure prediction.
The SUPRB program, employing suboptimal alignments and a probabilistic contact potential, demonstrates competitive and superior performance in template recognition.
This approach provides a more effective way to exploit structural genomics data for protein structure prediction.