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Related Concept Videos

Protein Organization01:24

Protein Organization

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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....
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Protein and Protein Structures02:15

Protein and Protein Structures

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Protein and Protein Structure02:15

Protein and Protein Structure

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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.
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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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Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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PSSKB: A Web Application to Study Protein Structures.

Denis V Petrovskiy1, Kirill S Nikolsky1, Liudmila I Kulikova1

  • 1Laboratory of Structural Proteomics, Institute of Biomedical Chemistry, Pogodinskaya, Moscow, Russia.

Journal of Computational Chemistry
|January 29, 2025
PubMed
Summary
This summary is machine-generated.

PSSKB is a new platform for modeling protein post-translational modifications (PTMs) and amino acid substitutions (AASs). It provides 3D structural analysis and similarity searches to understand protein function and alterations.

Keywords:
3D structurePSSKB platformPTM modelingamino acid substitution servicesbioinformatics

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Area of Science:

  • Structural biology
  • Biophysics
  • Bioinformatics
  • Computational biology

Background:

  • Cell cycle proteins are crucial for cell function and signaling.
  • Understanding protein structure changes from post-translational modifications (PTMs) and amino acid substitutions (AASs) is vital for comprehending protein function, stability, and localization.
  • Existing tools often lack integrated capabilities for comprehensive PTM and AAS analysis.

Purpose of the Study:

  • To introduce the Protein Structure and Stability Knowledge Base (PSSKB), an integrated platform for modeling and analyzing protein modifications.
  • To provide tools for visualizing and evaluating the impact of PTMs and AASs on protein structure and performance.
  • To offer protein structure similarity search functionalities.

Main Methods:

  • PSSKB integrates tools for modeling five common natural PTMs and all canonical AASs.
  • Users can input protein data via UniProt ID or PDB ID.
  • The platform performs energy minimization for intact and modified structures to analyze performance changes.
  • Structural motif similarity searches are conducted using previously developed software (SaFoldNet).

Main Results:

  • PSSKB generates 3D representations of modified protein structures.
  • It provides quantitative analysis of how AASs and PTMs affect protein characteristics.
  • The platform facilitates searching, aligning, and overlaying protein structure fragments, returning statistically ranked similar motifs.
  • The platform is publicly accessible without registration.

Conclusions:

  • PSSKB offers a comprehensive, user-friendly solution for studying the structural and functional consequences of PTMs and AASs in proteins.
  • The platform aids researchers in evaluating protein behavior and utilizing 3D models for further investigation.
  • PSSKB enhances protein structure analysis and discovery through integrated modeling and search tools.