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Related Concept Videos

Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

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.
Protein Folding01:22

Protein Folding

Overview
Protein and Protein Structure02:15

Protein and Protein Structure

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.
A protein's shape is critical to its function. For example, an enzyme can...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Related Experiment Video

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Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
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Gaussian mixture modeling of alpha-helix subclasses: structure and sequence variations.

Ashish V Tendulkar1, Babatunde Ogunnaike, Pramod P Wangikar

  • 1Kanwal Rekhi School of Information Technology, Indian Institute of Technology Bombay, Powai, Mumbai-400 076, India. ashish@it.iitb.ac.in

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|November 11, 2006
PubMed
Summary

This study classifies helical structures in proteins using geometric methods. It reveals distinct amino acid propensities, particularly for proline, in regular, kinked, and curved helices.

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Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure analysis

Background:

  • Classifying protein helical structures is crucial for accurate protein structure modeling.
  • Identifying sequence features specific to different helix classes can improve predictive models.

Purpose of the Study:

  • To develop a method for classifying helix-like local conformations.
  • To identify class-specific amino acid sequence features within different helical structures.

Main Methods:

  • Utilized a geometric invariant-based method to select helix-like local conformations.
  • Mapped conformations in principal component space and applied Gaussian mixture modeling.
  • Performed class-conditional, position-specific amino acid propensity analysis.

Main Results:

  • Successfully classified regular alpha-helices, kinked helices, and curved helices using Gaussian mixture modeling.
  • Demonstrated striking differences in amino acid propensities among the three helix classes.
  • Identified unique proline propensity patterns: significant at the start of regular helices, a sharp peak at the center of kinked helices, and a broad peak in the middle of curved helices.

Conclusions:

  • The geometric invariant and Gaussian mixture modeling approach effectively distinguishes different helical structures.
  • Amino acid propensities, especially proline, are highly class-specific and provide valuable sequence-structure relationship insights.
  • These findings contribute to a deeper understanding of protein helical structure variations and sequence determinants.