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Related Concept Videos

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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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.
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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
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Protein Families02:47

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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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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Sameer Velankar1, Glen van Ginkel2, Younes Alhroub2

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The Protein Data Bank in Europe (PDBe) website redesign offers improved access to macromolecular structures. New features enhance data discovery and analysis for both expert and non-expert users.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Data Science

Background:

  • The Protein Data Bank in Europe (PDBe) is a crucial resource for macromolecular structure data.
  • Effective dissemination and access to this data are vital for scientific advancement.

Purpose of the Study:

  • To redesign the PDBe website for enhanced user experience and data accessibility.
  • To integrate value-added information and improve data querying capabilities.
  • To develop a RESTful API for unified access to structural data.

Main Methods:

  • Website redesign based on user requirements analysis.
  • Development of a new query system incorporating data-quality metrics.
  • Implementation of a RESTful API for data access.
  • Integration of citation data and open-access publication figures.

Main Results:

  • Intuitive website access to enriched macromolecular structure information.
  • Identification of 'best structures' using data-quality information.
  • Unified access to PDB and EMDB data via a new API.
  • Inclusion of literature references and publication figures linked to PDB entries.

Conclusions:

  • The redesigned PDBe website and new API facilitate intuitive access to structural data.
  • Enhanced data integration and querying support both novice and expert users.
  • Improved access to structural information and associated literature accelerates research.