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Molecules
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Computational Spectroscopy of Protein Chromophores and Active Sites
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Computational Spectroscopy of Protein Chromophores and Active Sites

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (1 June 2021) | Viewed by 7263

Special Issue Editor

Prof. Dr. José A. Gascón

E-Mail Website
Guest Editor
Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA
Interests: molecular modeling of structure-function relationships in protein reaction centers, chromophores, and gold nanoclusters

Special Issue Information

Dear Colleagues,

One of the most powerful and functional aspects of Quantum Chemistry is that it can provide spectral properties. While the list is vast, the most widely computed properties include optical, rotational, and vibrational spectra; chemical shifts; magnetic couplings; and circular dichroism, among others. Electronic structure methods, such Density Functional Theory (DFT), are now an essential tool to help discern structure–spectrum relationships in proteins. Computational spectroscopy has found applications in many research fields that deal with protein complexes where spectral assignment to structural fingerprints is complicated by the heterogenous protein environment. The incorporation of these effects also presents a challenge from a computational point of view. The most natural computational approach to deal with these type of questions is Quantum Mechanics/Molecular Mechanics (QM/MM).  

This Special Issue of Molecules, “Computational Spectroscopy of Protein Chromophores and Active Sites”, presents recent developments and applications of electronic structure methods specifically designed to help interpret all sorts of spectroscopy experiments in the context of proteins and enzymes. QM/MM approaches are anticipated to play a central role in all these studies.

Prof. Dr. José A. Gascón
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Enzyme catalysis
  • Molecular mechanics
  • Multiscale modeling
  • Photochemistry
  • IR spectroscopy
  • Polarization
  • Quantum mechanics
  • DFT
  • TDDFT
  • QM/MM

Published Papers (3 papers)

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Research

19 pages, 4458 KiB  
Article
Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method
by Chenfei Shen, Xinsheng Jin, William J. Glover and Xiao He
Molecules 2021, 26(15), 4486; https://doi.org/10.3390/molecules26154486 - 25 Jul 2021
Cited by 8 | Viewed by 2235
Abstract
Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) [...] Read more.
Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules. Full article
(This article belongs to the Special Issue Computational Spectroscopy of Protein Chromophores and Active Sites)
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10 pages, 1815 KiB  
Article
Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach
by Kevin Clark, Natalia B. Pigni, Kithmini Wijesiri and José A. Gascón
Molecules 2021, 26(9), 2441; https://doi.org/10.3390/molecules26092441 - 22 Apr 2021
Cited by 2 | Viewed by 1812
Abstract
The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some [...] Read more.
The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid–protein interactions. Full article
(This article belongs to the Special Issue Computational Spectroscopy of Protein Chromophores and Active Sites)
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13 pages, 1928 KiB  
Article
Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides
by Francesco Segatta, David M. Rogers, Naomi T. Dyer, Ellen E. Guest, Zhuo Li, Hainam Do, Artur Nenov, Marco Garavelli and Jonathan D. Hirst
Molecules 2021, 26(2), 396; https://doi.org/10.3390/molecules26020396 - 13 Jan 2021
Cited by 2 | Viewed by 2487
Abstract
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been [...] Read more.
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. Full article
(This article belongs to the Special Issue Computational Spectroscopy of Protein Chromophores and Active Sites)
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