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Related Concept Videos

Protein-protein Interfaces02:04

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 polypeptide...
Protein-Protein Interfaces02:04

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 polypeptide...
Proteins: From Genes to Degradation02:11

Proteins: From Genes to Degradation

Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
Transcription is the synthesis of RNA molecules by RNA...
Proteins: From Genes to Degradation02:11

Proteins: From Genes to Degradation

Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
Transcription is the synthesis of RNA molecules by RNA...
Improving Translational Accuracy02:07

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...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Protein misinteraction avoidance causes highly expressed proteins to evolve slowly.

Jian-Rong Yang1, Ben-Yang Liao, Shi-Mei Zhuang

  • 1Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

Proceedings of the National Academy of Sciences of the United States of America
|March 15, 2012
PubMed
Summary

Protein evolution rates are linked to expression levels, but misfolding avoidance isn't the whole story. Natural selection against harmful protein-protein misinteractions also drives this pattern, especially for surface residues.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Genomics

Background:

  • The relationship between protein expression levels and evolutionary rates (E-R anticorrelation) is a key area of study.
  • The protein misfolding avoidance hypothesis currently explains this E-R anticorrelation.
  • This hypothesis, however, does not fully account for the evolution of protein surface residues.

Purpose of the Study:

  • To investigate the limitations of the protein misfolding avoidance hypothesis.
  • To propose and test an alternative hypothesis for the E-R anticorrelation.
  • To explore the role of protein-protein misinteractions in constraining protein evolution.

Main Methods:

  • Molecular-level evolutionary simulations were conducted.
  • Genomic analysis of yeast proteomes was performed.
  • Predictions derived from the proposed hypothesis were tested.

Main Results:

  • The protein misfolding avoidance hypothesis was found insufficient to explain the E-R anticorrelation, particularly for surface residues.
  • Natural selection against protein-protein misinteractions was identified as a significant factor.
  • Highly expressed proteins face stronger selection against misinteractions, leading to E-R anticorrelation in surface residues.

Conclusions:

  • The E-R anticorrelation has multiple contributing factors (pluralistic origin).
  • Protein-protein misinteraction plays a crucial role in constraining protein sequence evolution.
  • Cellular complexity and inherent properties like misinteraction are key evolutionary constraints.