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Related Concept Videos

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.
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Rapid model building of beta-sheets in electron-density maps.

Thomas C Terwilliger1

  • 1Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

Acta Crystallographica. Section D, Biological Crystallography
|February 25, 2010
PubMed
Summary

This study presents a new method for quickly building beta-sheets in electron-density maps. The approach accurately models protein structures from experimental data.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Electron-density maps are crucial for determining protein structures.
  • Building secondary structure elements like beta-sheets can be labor-intensive.

Purpose of the Study:

  • To develop and validate a rapid method for constructing beta-sheet regions within electron-density maps.
  • To automate the process of building atomic models of beta-sheets.

Main Methods:

  • Identifying beta-strands as parallel density tubes in electron-density maps.
  • Analyzing patterns of high density corresponding to specific atoms (carbonyl, C-beta) to determine strand alignment and direction.
  • Assembling identified beta-strands into a complete atomic model of beta-sheet regions.

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Main Results:

  • The method successfully built beta-sheet regions in 42 experimental electron-density maps (1.5-3.8 A resolution).
  • High completion rates were achieved, with exceptions in lower-resolution maps.
  • The average root-mean-square deviation (r.m.s.d.) of main-chain atoms was 1.5 A compared to refined models.

Conclusions:

  • The presented method offers a rapid and effective way to build beta-sheets into electron-density maps.
  • This technique can significantly accelerate the process of protein structure determination.
  • The accuracy of the built models is comparable to refined structures, especially at higher resolutions.