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Related Concept Videos

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 Organization01:13

Protein Organization

Overview
Angle of Twist: Problem Solving01:13

Angle of Twist: Problem Solving

An electric motor applies a torque of 700 N·m to an aluminum shaft, triggering a stable rotation. Two pulleys, B and C, are subjected to torques of 300 N·m and 400 N·m, respectively. The modulus of rigidity is provided as 25 GPa. With the knowledge of the length and diameter of each segment, the twist angle between the two pulleys can be computed. First, a section cut is made between pulleys B and C, and the cut cross-section is analyzed using a free-body diagram. Given that the torque exerted...
Unsymmetric Bending - Angle of Neutral Axis01:15

Unsymmetric Bending - Angle of Neutral Axis

Unsymmetrical bending occurs when a structural member is subjected to bending moments in a plane that does not align with the member's principal axes. This scenario typically arises in beams and other structural components when loads are applied at non-ideal angles, introducing complexities in stress analysis.
When a bending moment is applied at an angle θ concerning the vertical axis of a symmetrical member, it can be resolved into components along the member's principal centroidal axes. The...
Angle of Twist - Elastic Range01:13

Angle of Twist - Elastic Range

Consider a cylindrical shaft with a length denoted by L and a consistent cross-sectional radius referred to as r. This shaft undergoes a torque at the free end. The highest shearing strain within the shaft is directly proportional to the twist angle and the radial distance from the shaft axis. When the shaft behaves elastically, this shearing strain can be articulated using variables such as the applied torque, radial distance, the polar moment of inertia, and the modulus of rigidity. By...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation

Tae-Rae Kim1, Joshua Sungwoo Yang, Seokmin Shin

  • 1Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.

Proteins
|February 15, 2013
PubMed
Summary

New statistical torsion angle potential energy functions were developed using protein X-ray data. These functions improve protein model quality and aid in structure prediction and design.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein structure modeling relies on accurate energy functions.
  • Knowledge-based potentials derived from experimental data are crucial.
  • Torsion angle potentials are fundamental components of these functions.

Purpose of the Study:

  • To introduce novel grid-based, knowledge-derived energy functions for key protein torsion angle combinations.
  • To address challenges like derivative discontinuity in periodic boundary conditions.
  • To evaluate the impact of these functions on protein model quality and explore potential biases.

Main Methods:

  • Development of grid-based statistical torsion angle potential energy functions for specific torsion angle pairs (ϕ-χ₁, ψ-χ₁, ϕ-ψ, χ₁-χ₂).
  • Assumption of Boltzmann distribution for torsion angle populations derived from protein X-ray crystallography data.
  • Implementation of a method to handle periodic boundary conditions by duplicating grid points, mitigating derivative discontinuity.

Main Results:

  • The newly devised functions significantly enhance the quality of protein model structures.
  • Investigation into potential biases within the developed functions was conducted.
  • The utility of incorporating secondary structure information was assessed.

Conclusions:

  • The statistical torsion angle potential energy functions offer a rapid improvement in protein model quality.
  • These functions are expected to be valuable tools for various protein structure modeling applications.
  • Further analysis confirmed their potential to aid protein structure prediction, design, and refinement.