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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Related Experiment Video

Updated: Nov 4, 2025

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Multiscale Quantum Refinement Approaches for Metalloproteins.

Zeyin Yan1, Xin Li1, Lung Wa Chung1

  • 1Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China.

Journal of Chemical Theory and Computation
|May 25, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a novel multiscale quantum refinement method to accurately determine the structures of metalloproteins. The ONIOM3(QM/SE/MM) scheme offers an efficient approach for refining metal binding sites in metalloproteins.

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Area of Science:

  • Biochemistry and Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Metalloproteins are crucial biomolecules, but their structural determination is challenging due to complex electronic structures and metal ion bonding.
  • Accurate structural information is vital for understanding metalloprotein function and developing targeted therapeutics.
  • Existing methods struggle with the intricate nature of metal-containing biomolecules, necessitating advanced computational approaches.

Purpose of the Study:

  • To develop and evaluate a multiscale quantum refinement method for improving the structural accuracy of metalloproteins.
  • To assess the performance of various ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations for refining metal binding sites.
  • To investigate novel quantum embedding methods for high-level electronic structure calculations within the refinement framework.

Main Methods:

  • Development of a quantum refinement protocol integrating experimental X-ray diffraction data with multiscale computational schemes.
  • Application of ONIOM2(QM1/QM2), ONIOM2(QM/MM), and ONIOM3(QM1/QM2/MM) methods to refine structures of Cu- and Zn-containing metalloproteins.
  • Exploration of ONIOM3(QM/SE/MM) and wavefunction-in-density functional theory (WF-in-DFT) based ONIOM methods for enhanced accuracy and efficiency.

Main Results:

  • The ONIOM3(QM/SE/MM) scheme demonstrated good accuracy for refining metal binding sites with reduced computational cost.
  • A two-center ONIOM approach accelerated calculations for metalloproteins with multiple active sites.
  • Novel ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) methods successfully refined a Zn binding site at the coupled-cluster singles and doubles (CCSD) level.

Conclusions:

  • Multiscale quantum refinement is an effective strategy for enhancing the structural accuracy of metal binding sites in metalloproteins.
  • The ONIOM3(QM/SE/MM) approach presents a computationally efficient and reliable option for metalloprotein structure refinement.
  • Advanced quantum embedding techniques offer unprecedented accuracy for critical regions within metalloproteins.