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New Molecular Research and Perspective: Enzyme and Its Catalysis
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New Molecular Research and Perspective: Enzyme and Its Catalysis

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 6613

Special Issue Editor

Dr. Samuel De Visser

E-Mail Website
Guest Editor
Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
Interests: computational chemistry; density functional theory; QM/MM; reaction mechanisms; biomimetic models; enzyme catalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes are efficient molecular catalysts in nature that work under ambient pressures and temperatures and catalyse a large variety of chemical reactions by using environmentally benign systems. There is much to learn from nature on how to convert chemicals into useful products. In particular, enzymes react very fast and often, these fleeting intermediates are difficult to trap and characterize. Over the past few years, major breakthroughs in understanding enzymatic catalysis have been obtained and highlights of novel research problems and solutions are the topic of this Special Issue. This Special Issue will welcome review, opinion, and research articles that focus on, but are not limited to, the above topics.

Prof. Dr. Samuel De Visser
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • catalysts
  • enzyme reaction

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Published Papers (2 papers)

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Research

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19 pages, 5118 KiB  
Article
Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1?
by Thirakorn Mokkawes and Sam P. de Visser
Int. J. Mol. Sci. 2023, 24(4), 3651; https://doi.org/10.3390/ijms24043651 - 11 Feb 2023
Cited by 11 | Viewed by 3824
Abstract
Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. [...] Read more.
Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin. Full article
(This article belongs to the Special Issue New Molecular Research and Perspective: Enzyme and Its Catalysis)
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Review

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23 pages, 1207 KiB  
Review
Conditional Split Inteins: Adaptable Tools for Programming Protein Functions
by Callum Shepherd, Makeba Lawson-Williams, Alexandria Holland, Adebayo J. Bello, Darren W. Sexton and Femi J. Olorunniji
Int. J. Mol. Sci. 2025, 26(2), 586; https://doi.org/10.3390/ijms26020586 - 11 Jan 2025
Viewed by 2017
Abstract
Split inteins are biological mechanisms for the operation of the spatiotemporal control of protein activities. They function through protein trans-splicing, in which their N- and C-terminal fragments are expressed contiguously with two protein halves. The subsequent self-excision upon recognition of the complimentary [...] Read more.
Split inteins are biological mechanisms for the operation of the spatiotemporal control of protein activities. They function through protein trans-splicing, in which their N- and C-terminal fragments are expressed contiguously with two protein halves. The subsequent self-excision upon recognition of the complimentary fragment yields a mature, complete, and functional protein. The conditional regulation of protein splicing through environmental factors or the attachment of regulatory modules can be used to determine when and where a protein will operate, providing potential novel approaches for engineering biology applications. This review will discuss current split intein applications and the mechanistic basis for novel species classification. These considerations can provide guidance in intein and extein engineering through activation strategies, in the design of spatial arrangements, and in taking advantage of unique reaction environments. This can pave the way for the future implementation of novel split intein discoveries and the selection of appropriate intein species and aid in designing novel protein engineering strategies. Full article
(This article belongs to the Special Issue New Molecular Research and Perspective: Enzyme and Its Catalysis)
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