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Special Issue "Enzyme Chemistry"

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A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (20 September 2013)

Special Issue Editor

Guest Editor
Dr. Harvey F. Fisher

The Department of Biochemistry, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
Website | E-Mail
Interests: the determination of the chemical mechanism of the glutamate dehydrogenase reaction the energetics of this reaction; the energetics of this reaction; the relationship of the observed energetics to the resolved mechanistic features

Special Issue Information

Dear Colleagues,

Frank Westheimer once proclaimed that it is as if “mother nature has provided us with enzymes as a tool to teach physical-organic chemistry to scientists”. Thus far we have mastered only a minute part of her course. Our purpose in this special issue is to mark our current state in this endeavor. While our focus will be centered on the chemistry of the phenomenon, we will interpret that viewpoint quite broadly. A second objective of this issue is to take advantage ocf the ease of access to a broad audience provided by this journal’s policy and thus provide our colleagues a in related fields with a view of the various experimental and theoretical approaches available to today’s enzyme chemists.

Dr. Harvey F. Fisher
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 monthly 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 1800 CHF (Swiss Francs).

Keywords

  • intermediate complexes
  • structure-function relationships
  • energetics
  • steady and transient state kinetics
  • kinetic isotope effects
  • chemical bond formation
  • allosteric effects
  • single molecule reactions
  • quantum tunneling

Published Papers (4 papers)

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Research

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Open AccessArticle Unfolding Studies of the Cysteine Protease Baupain, a Papain-Like Enzyme from Leaves of Bauhinia forficata: Effect of pH, Guanidine Hydrochloride and Temperature
Molecules 2014, 19(1), 233-246; doi:10.3390/molecules19010233
Received: 8 October 2013 / Revised: 12 December 2013 / Accepted: 13 December 2013 / Published: 24 December 2013
Cited by 3 | PDF Full-text (731 KB) | HTML Full-text | XML Full-text
Abstract
Baupain belongs to the α+β class of proteins with a secondary structure-content of 44% α-helix, 16% β-sheet and 12% β-turn. The structural transition induced by pH was found to be noncooperative, with no important differences observed in the pH range from 3.0 to
[...] Read more.
Baupain belongs to the α+β class of proteins with a secondary structure-content of 44% α-helix, 16% β-sheet and 12% β-turn. The structural transition induced by pH was found to be noncooperative, with no important differences observed in the pH range from 3.0 to 10.5. At pH 2.0 the protein presented substantial non-native structure with strong ANS binding. Guanidine hydrochloride (GdnHCl)-induced unfolding did not change the protein structure significantly until 4.0 M, indicating the high rigidity of the molecule. The unfolding was cooperative, as seen by the sigmoidal transition curves with midpoints at 4.7 ± 0.2 M and 5.0 ± 0.2 M GdnHCl, as measured by CD and fluorescence spectroscopy. A red shift of 7 nm in intrinsic fluorescence was observed with 6.0 M GdnHCl. Temperature-induced unfolding of baupain was incomplete, and at least 35% of the native structure of the protein was retained, even at high temperature (90 °C). Baupain showed characteristics of a molten globule state, due to preferential ANS binding at pH 2.0 in comparison to the native form (pH 7.0) and completely unfolded (6.0 M GdnHCl) state. Combined with information about N-terminal sequence similarity, these results allow us to include baupain in the papain superfamily. Full article
(This article belongs to the Special Issue Enzyme Chemistry)
Open AccessArticle Modulation of the Microenvironment Surrounding the Active Site of Penicillin G Acylase Immobilized on Acrylic Carriers Improves the Enzymatic Synthesis of Cephalosporins
Molecules 2013, 18(11), 14349-14365; doi:10.3390/molecules181114349
Received: 9 September 2013 / Revised: 20 October 2013 / Accepted: 28 October 2013 / Published: 20 November 2013
Cited by 9 | PDF Full-text (648 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The catalytic properties of penicillin G acylase (PGA) from Escherichia coli in kinetically controlled synthesis of β-lactam antibiotics are negatively affected upon immobilization on hydrophobic acrylic carriers. Two strategies have been here pursued to improve the synthetic performance of PGA immobilized on epoxy-activated
[...] Read more.
The catalytic properties of penicillin G acylase (PGA) from Escherichia coli in kinetically controlled synthesis of β-lactam antibiotics are negatively affected upon immobilization on hydrophobic acrylic carriers. Two strategies have been here pursued to improve the synthetic performance of PGA immobilized on epoxy-activated acrylic carriers. First, an aldehyde-based spacer was inserted on the carrier surface by glutaraldehyde activation (immobilization yield = 50%). The resulting 3-fold higher synthesis/hydrolysis ratio (vs/vh1 = 9.7 ± 0.7 and 10.9 ± 0.7 for Eupergit® C and Sepabeads® EC-EP, respectively) with respect to the unmodified support (vs/vh1 = 3.3 ± 0.4) was ascribed to a facilitated diffusion of substrates and products as a result of the increased distance between the enzyme and the carrier surface. A second series of catalysts was prepared by direct immobilization of PGA on epoxy-activated acrylic carriers (Eupergit® C), followed by quenching of oxiranes not involved in the binding with the protein with different nucleophiles (amino acids, amines, amino alcohols, thiols and amino thiols). In most cases, this derivatization increased the synthesis/hydrolysis ratio with respect to the non derivatized carrier. Particularly, post-immobilization treatment with cysteine resulted in about 2.5-fold higher vs/vh1 compared to the untreated biocatalyst, although the immobilization yield decreased from 70% (untreated Eupergit® C) to 20%. Glutaraldehyde- and cysteine-treated Eupergit® C catalyzed the synthesis of cefazolin in 88% (±0.9) and 87% (±1.6) conversion, respectively, whereas untreated Eupergit® C afforded this antibiotic in 79% (±1.2) conversion. Full article
(This article belongs to the Special Issue Enzyme Chemistry)

Review

Jump to: Research

Open AccessReview Carnosinases, Their Substrates and Diseases
Molecules 2014, 19(2), 2299-2329; doi:10.3390/molecules19022299
Received: 25 October 2013 / Revised: 7 January 2014 / Accepted: 28 January 2014 / Published: 21 February 2014
Cited by 8 | PDF Full-text (1717 KB) | HTML Full-text | XML Full-text
Abstract
Carnosinases are Xaa-His dipeptidases that play diverse functions throughout all kingdoms of life. Human isoforms of carnosinase (CN1 and CN2) under appropriate conditions catalyze the hydrolysis of the dipeptides carnosine (β-alanyl-L-histidine) and homocarnosine (γ-aminobutyryl-L-histidine). Alterations of serum carnosinase (CN1) activity has been associated
[...] Read more.
Carnosinases are Xaa-His dipeptidases that play diverse functions throughout all kingdoms of life. Human isoforms of carnosinase (CN1 and CN2) under appropriate conditions catalyze the hydrolysis of the dipeptides carnosine (β-alanyl-L-histidine) and homocarnosine (γ-aminobutyryl-L-histidine). Alterations of serum carnosinase (CN1) activity has been associated with several pathological conditions, such as neurological disorders, chronic diseases and cancer. For this reason the use of carnosinase levels as a biomarker in cerebrospinal fluid (CSF) has been questioned. The hydrolysis of imidazole-related dipeptides in prokaryotes and eukaryotes is also catalyzed by aminoacyl-histidine dipeptidases like PepD (EC 3.4.13.3), PepV (EC 3.4.13.19) and anserinase (EC 3.4.13.5). The review deals with the structure and function of this class of enzymes in physiological and pathological conditions. The main substrates of these enzymes, i.e., carnosine, homocarnosine and anserine (β-alanyl-3-methyl-L-histidine) will also be described. Full article
(This article belongs to the Special Issue Enzyme Chemistry)
Figures

Open AccessReview Cytochrome P450 Family 1 Inhibitors and Structure-Activity Relationships
Molecules 2013, 18(12), 14470-14495; doi:10.3390/molecules181214470
Received: 22 September 2013 / Revised: 15 November 2013 / Accepted: 19 November 2013 / Published: 25 November 2013
Cited by 14 | PDF Full-text (983 KB) | HTML Full-text | XML Full-text
Abstract
With the widespread use of O-alkoxyresorufin dealkylation assays since the 1990s, thousands of inhibitors of cytochrome P450 family 1 enzymes (P450s 1A1, 1A2, and 1B1) have been identified and studied. Generally, planar polycyclic molecules such as polycyclic aromatic hydrocarbons, stilbenoids, and flavonoids
[...] Read more.
With the widespread use of O-alkoxyresorufin dealkylation assays since the 1990s, thousands of inhibitors of cytochrome P450 family 1 enzymes (P450s 1A1, 1A2, and 1B1) have been identified and studied. Generally, planar polycyclic molecules such as polycyclic aromatic hydrocarbons, stilbenoids, and flavonoids are considered to potentially be effective inhibitors of these enzymes, however, the details of the structure-activity relationships and selectivity of these inhibitors are still ambiguous. In this review, we thoroughly discuss the selectivity of many representative P450 family 1 inhibitors reported in the past 20 years through a meta-analysis. Full article
(This article belongs to the Special Issue Enzyme Chemistry)

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