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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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funtrp: identifying protein positions for variation driven functional tuning.

Maximilian Miller1, Daniel Vitale2, Peter C Kahn1

  • 1Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA.

Nucleic Acids Research
|October 5, 2019
PubMed
Summary
This summary is machine-generated.

A new computational method, funtrp, categorizes protein positions into Neutral, Rheostat, or Toggle types. This approach improves variant effect prediction by considering nuanced impacts beyond simple sequence conservation.

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Computational Biology
  • Protein Science

Background:

  • Evaluating genetic variants is crucial for understanding diseases and evolution.
  • Current variant effect predictors struggle with complex methods and often rely heavily on sequence conservation, potentially missing subtle impacts.

Purpose of the Study:

  • To introduce a novel computational method, funtrp, for categorizing protein positions based on their expected mutational impact range.
  • To assess if these new categories offer insights beyond traditional features like conservation.

Main Methods:

  • Developed the functionNeutral/Toggle/Rheostatpredictor (funtrp) computational method.
  • Categorized protein positions into Neutral, Rheostat, and Toggle types.
  • Analyzed correlations between position types and protein features (conservation, disorder) and across protein functions.

Main Results:

  • Position types (Neutral, Rheostat, Toggle) showed weak correlation with conservation and disorder.
  • The distribution of position types varied significantly across different protein functions.
  • Incorporating position types improved the performance of existing variant effect predictors.

Conclusions:

  • funtrp provides a new framework for understanding protein variation.
  • This categorization offers a higher resolution for evaluating variant effects, particularly for those with weaker impacts.
  • The method can enhance current variant effect prediction tools and guide future developments.