Crystallography of Enzymes (2nd Edition)

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Biomolecular Crystals".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 1398

Special Issue Editors

Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
Interests: biochemistry; structural biology; RNA biology; virology; neurobiology; cancer biology
Special Issues, Collections and Topics in MDPI journals
Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, USA
Interests: protein biochemistry; structural biology; collagen; post-translational modifications; cancer biology; matrix biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the success of the first Edition, we are pleased to announce the launch of the second Edition of the Special Issue of Crystals, entitled “Crystallography of Enzymes (2nd Edition).”

Enzymes—whether naturally evolved or human-designed—are remarkable biological catalysts that enable and regulate life’s chemical reactions. They accelerate diverse biochemical processes by lowering activation barriers, most of which exhibit extraordinary specificity, precision and efficiency. Despite decades of biochemical and structural investigation, our understanding of how enzymes achieve such remarkable selectivity and reactivity remains incomplete.

Crystallography remains a cornerstone for revealing the atomic details underlying enzyme catalysis, substrate recognition, conformational dynamics and inhibitor interactions. Advances in X-ray crystallography, serial femtosecond crystallography, cryo-electron microscopy and complementary computational approaches have opened unprecedented opportunities to visualize enzymes in action and to explore their mechanistic landscapes.

In this second Edition, we particularly encourage contributions that expand the frontier of enzyme discovery and design. This includes studies on:

  • Novel or uncharacterized natural enzymes, revealing new catalytic strategies;
  • De novo designed enzymes and artificial biocatalysts, showcasing how structural insights guide structural or AI-assisted design;
  • Ancestrally reconstructed enzymes, providing evolutionary perspectives on catalysis and stability;
  • Engineered enzymes with improved selectivity, altered substrate scope, or novel functionality;
  • Mechanistic and structural studies coupling crystallography with kinetics, spectroscopy or computation;
  • Crystallization innovations enabling previously intractable enzyme targets.

We welcome original research articles, reviews and perspectives from structural biologists, biochemists, enzymologists and computational modelers. Together, these contributions will deepen our understanding of how structure encodes catalytic power and continue Francis Crick’s timeless insight: “If you want to understand function, study structure.”

Dr. Bo Liang
Dr. Houfu Guo
Guest Editors

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 250 words) can be sent to the Editorial Office for assessment.

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. Crystals 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 2100 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 structure and function
  • X-ray and serial crystallography
  • de novo enzyme design
  • ancestral reconstruction
  • protein engineering
  • catalytic mechanism
  • structural dynamics
  • substrate and inhibitor interactions
  • computational modeling

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

10 pages, 2747 KB  
Article
Crystal Packing of Protomers Provides a Valuable Structural Insight into Protein Structure
by Dong-Hyun Lee, Ho-Phuong-Thuy Ngo, Thien-Hoang Ho, Jiwon Yun, Byung-Jin Lee, Yoon-Sik Park, Nam-Soo Jwa and Lin-Woo Kang
Crystals 2026, 16(4), 221; https://doi.org/10.3390/cryst16040221 - 26 Mar 2026
Viewed by 481
Abstract
The crystal structure of proteins is generally considered static due to the constraints imposed by crystal packing. We determined the crystal structure of rice NADP-malic enzyme 2 (OsNADP-ME2), an oxidative decarboxylase that converts malic acid to pyruvate and provides NADPH to generate reactive [...] Read more.
The crystal structure of proteins is generally considered static due to the constraints imposed by crystal packing. We determined the crystal structure of rice NADP-malic enzyme 2 (OsNADP-ME2), an oxidative decarboxylase that converts malic acid to pyruvate and provides NADPH to generate reactive oxygen species. The OsNADP-ME2 is crystallized as a tetramer in the space group of P21. In the crystal, all the crystal packing interactions are made through the NADP-binding domain of the enzyme. Interestingly, a protomer shows a conformational change, with a 7.4° tilt in the NADP-binding domain. Basically, the crystal packing consists of a horizontal arrangement of vertically parallel P21 screw axes. In the vertical direction, a protomer (Mol A) is tightly sandwiched by two protomers (Mol C) of nearby tetramers and vice versa. In the horizontal direction, two protomers (Mol B and D) of a tetramer are parallelly bound to nearby tetramers, of which one protomer (Mol B) has tighter interactions than the other protomer (Mol D). The protomer Mol D, with the least interaction surface in the crystal packing, adopts an open conformation of the NADP-binding domain, which may be the flexible part of the enzyme for NADP+ cofactor binding. Crystallization can provide valuable information for protein structure. Full article
(This article belongs to the Special Issue Crystallography of Enzymes (2nd Edition))
Show Figures

Figure 1

14 pages, 2339 KB  
Article
Crystal Structures of a Thermophilic Cutinase from Chaetomium thermophilum Reveal Conformational Dynamics of the Catalytic Lid Loop
by Ryohei Nojima, Lirong Chen, Minami Kurokawa, Sho Ito and Tatsuya Nishino
Crystals 2026, 16(4), 217; https://doi.org/10.3390/cryst16040217 - 24 Mar 2026
Viewed by 609
Abstract
Microbial cutinases are promising biocatalysts for polymer recycling. Here, we investigated the structural basis of catalytic activation in a thermophilic cutinase from Chaetomium thermophilum (CtCut). Differential scanning calorimetry revealed a three-state thermal unfolding pathway (Tm = 66.4 °C and 69.5 °C), [...] Read more.
Microbial cutinases are promising biocatalysts for polymer recycling. Here, we investigated the structural basis of catalytic activation in a thermophilic cutinase from Chaetomium thermophilum (CtCut). Differential scanning calorimetry revealed a three-state thermal unfolding pathway (Tm = 66.4 °C and 69.5 °C), indicating hierarchical stability. To capture distinct conformational states while avoiding affinity-tag artifacts, we employed both tag-free and tagged constructs. We determined apo-structures of wild-type and S136A mutant CtCut at 1.7 Å resolution and a complementary inhibitor complex at 2.65 Å. In the apo-state, a chloride ion coordinated the electrostatically pre-organized active site, while the catalytic H204 adopted a solvent-exposed, inactive loop conformation. In the inhibitor complex, p-nitrophenol displaced the chloride, establishing a characteristic oxyanion hole network. Concomitantly, the “lid” loop transitioned to an open state, with H204 exhibiting pronounced conformational heterogeneity across eight independent molecules. These complementary structures provide structural evidence for conformational dynamics of the catalytic lid loop, consistent with the conformational cycling model previously proposed for a mesophilic homolog. Full article
(This article belongs to the Special Issue Crystallography of Enzymes (2nd Edition))
Show Figures

Figure 1

Back to TopTop