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Related Concept Videos

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.
Applications Of NMR In Biology01:25

Applications Of NMR In Biology

Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics  for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
The...
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.
¹H NMR: Pople Notation01:09

¹H NMR: Pople Notation

The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Proteomics01:33

Proteomics

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 proteomics...

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Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

Journal of bioinformatics and computational biology·2015
Same author

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

The computer journal·2015
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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A tabu search approach for the NMR protein structure-based assignment problem.

Gizem Cavuşlar1, Bülent Çatay, Mehmet Serkan Apaydın

  • 1University of Wisconsin-Madison, 1513 University Avenue, Madison, WI 53706, USA. cavuslar@wisc.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|December 11, 2012
PubMed
Summary

We developed NVR-TS, a novel tabu search algorithm, to efficiently solve the protein nuclear magnetic resonance (NMR) assignment problem. This method proves NP-hard and outperforms previous approaches on large protein datasets.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy studies proteins in solution by exploiting nuclear magnetic properties.
  • A major challenge in NMR is the assignment problem: mapping NMR peaks to specific nuclei.
  • Structure-Based Assignment (SBA) uses homologous structures to computationally address this challenge.

Purpose of the Study:

  • To prove the NP-hard nature of the Structure-Based Assignment problem modeled as a binary integer programming problem (NVR-BIP).
  • To propose an efficient algorithm, NVR-TS, to solve the NVR-BIP problem.
  • To evaluate the performance of NVR-TS on protein datasets.

Main Methods:

  • Formulating the Structure-Based Assignment problem as a binary integer programming problem (NVR-BIP).
  • Proving the NP-hard complexity of NVR-BIP.
  • Developing a tabu search (TS) algorithm (NVR-TS) with a guided perturbation mechanism.
  • Utilizing a quadratic penalty relaxation of NVR-BIP, penalizing Nuclear Overhauser Effect constraint violations.

Main Results:

  • The NVR-TS algorithm successfully finds optimal solutions for NVR-BIP on a dataset of seven proteins (31-126 residues).
  • NVR-TS achieves high assignment accuracies on larger proteins (MBP: 348 residues, EIN: 243 residues), which were intractable for NVR-BIP.
  • The algorithm demonstrates superior efficiency and accuracy in solving the protein NMR assignment problem.

Conclusions:

  • The Structure-Based Assignment problem, as modeled by NVR-BIP, is NP-hard.
  • NVR-TS provides an efficient and effective computational solution for the protein NMR assignment problem.
  • NVR-TS advances the capabilities of NMR spectroscopy for studying protein structures in solution.