Evidence map›Paper›PMID 32970192›Full record

ArticleJournal of molecular modeling2020

Critical assessment of the FeC and CO bond strength in carboxymyoglobin: a QM/MM local vibrational mode study.

Marek Freindorf, Elfi Kraka

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Article in Journal of molecular modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Uranium: The Nuclear Fuel Cycle and Beyond.International journal of molecular sciences · 2022
    Review
  6. Article
  7. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Marek FreindorfComputational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX, 75275-0314, USA.
Elfi KrakaComputational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX, 75275-0314, USA. ekraka@smu.edu.ORCID http://orcid.org/0000-0002-9658-5626

Funding

National Science Foundation (US) CHE 146490
6 · The paper itself

Abstract

The interplay between FeC and CO bonding in carboxymyoglobin (MbCO) and the role of potential hydrogen bonding between the CO moiety and the side chains of the surrounding protein amino acids have been the subject of numerous experimental and theoretical studies. In this work, we present a quantitative measure for the intrinsic FeC and CO bond strength in MbCO, as well as for CO⋯H bonding, based on the local vibrational mode analysis, originally developed by Konkoli and Cremer. We investigated a gas phase model, two models of the wild-type protein, and 17 protein mutations that change the distal polarity of the heme pocket, as well as two protein mutations of the heme porphyrin ring. Based on local mode force constants, we could quantify for the first time the suggested inverse relationship between the CO and FeC bond strength, the strength of CO⋯H bonding, and how it weakens the CO bond. Combined with the natural orbital analysis, we could also confirm the key role of π back donation between Fe and the CO moiety in determining the FeC bond strength. We further clarified that CO and FeC normal modes couple with other protein motions in the protein environment. Therefore, normal mode frequencies/force constants are not suited as bond strength descriptors and instead their local mode counterparts should be used. Our comprehensive results provide new guidelines for the fine-tuning of existing and the design of MbCO models with specific FeC, CO, and CO⋯H bond strengths.Graphical abstract.

Indexed as

Models, MolecularAlgorithmsCarbon MonoxideHydrogen BondingMolecular StructureMutationMyoglobinVibrationCarbon MonoxidecarboxymyoglobinMyoglobinDFTLocal mode force constantsLocal vibrational theoryMyoglobinQM/MMVibrational spectroscopy

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.