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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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Structural Protein Function01:56

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Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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Three main types of fibers are secreted by fibroblasts: collagen fibers, elastic fibers, and reticular fibers. Collagen fiber is made from fibrous protein subunits linked together to form a long, straight fiber. Collagen fibers, while flexible, have great tensile strength, resist stretching, and give ligaments and tendons their characteristic resilience and strength. These fibers hold connective tissues together, even during the body's movement.
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Structure of Benzene: Kekulé Model01:07

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In 1865, August Kekule suggested the structure of benzene according to the structural theory of organic chemistry based on the three assertions—formula of benzene is C6H6, all the hydrogens of benzene are equivalent, and each carbon must have four bonds due to its tetravalency.
He proposed that benzene has a cyclic structure of six carbon atoms attached to one hydrogen atom each, with three alternating pi bonds.
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Related Experiment Video

Updated: Jan 25, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Methods for the Refinement of Protein Structure 3D Models.

Recep Adiyaman1, Liam James McGuffin2

  • 1School of Biological Sciences, University of Reading, Reading RG6 6AS, UK. r.adiyaman@pgr.reading.ac.uk.

International Journal of Molecular Sciences
|May 12, 2019
PubMed
Summary

Refining predicted 3D protein models is essential for computational studies. Current methods face challenges in accurately selecting the most native-like conformations from generated models.

Keywords:
Critical Assessment of techniques for Structure Prediction (CASP)energy functionsmodel quality estimatesmolecular dynamics simulationsprotein model refinementtertiary structure prediction

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Accurate 3D protein models are vital for downstream computational analyses.
  • Current refinement strategies struggle to consistently improve initial model accuracy.
  • Deviations from native structures can occur due to force-field limitations.

Purpose of the Study:

  • To enhance the accuracy of predicted 3D protein models.
  • To address challenges in distinguishing near-native conformations during refinement.
  • To improve the selection of the most biologically relevant protein structures.

Main Methods:

  • Utilizing Molecular Dynamics (MD)-based protocols for sampling improved 3D models.
  • Employing physics-based force fields and targeted restraint strategies to guide refinement.
  • Integrating energy functions and Model Quality Assessment Programs (MQAPs) for scoring and discrimination.

Main Results:

  • MD-based protocols with smart restraints show progress in consistent 3D model refinement.
  • Physics-based force fields aid in generating more accurate protein structures.
  • MQAPs assist in differentiating near-native from non-native conformations.

Conclusions:

  • Refining 3D protein models remains challenging due to subtle differences between conformations.
  • Accurate prediction of local errors and contacts can guide effective restraint strategies.
  • Identifying the most native-like conformations is a critical ongoing challenge in structural bioinformatics.