The Journal of Physical Chemistry B (JPC B) will publish a Virtual Special Issue (VSI) on “Computational Advances in Protein Engineering and Enzyme Design.” The VSI will be led by Guest Editors Professor Lynn Kamerlin of Uppsala University and Professor Etienne Derat of Sorbonne University. Together they encourage researchers to submit their new and unpublished work by Sept 15, 2021.
Research areas of particular interest include:
- computational biochemistry
- in silico protein design
- protein engineering
In conceiving this Virtual Special Issue, the Guest Editors were inspired by some recent exciting innovations and discoveries, including:
Enzymes are among the most complicated molecular objects and it was long thought it would be impossible to conceive a functional enzyme starting from scratch. Using natural enzymes to perform interesting chemical transformations has been feasible for a long time, but was historically limited to a range of specific reactions like alcohol oxidation. Extending the scope of unnatural enzymatic reactions was therefore a primary goal. Here, several ideas have been developed over the recent years: either using existing enzymes and extending their capabilities by exploiting their promiscuity, or adapting/adjusting a known active site to perform a new reaction. But, a more exciting challenge would be to develop ex nihilo an enzyme to catalyze a specific and new reaction. Here, computation is playing an increasingly important role, whether through identifying ancestral scaffolds that can be used as starting points for new enzyme engineering efforts, exploiting conformational dynamics for enzyme engineering using computational tools, exploiting machine learning approaches in enzyme design, or an explosion of online tools and web servers that can simplify the engineering process. The field is expanding and maturing rapidly, and taking on many new and different directions. The goal of this special issue will be to highlight computational advances in protein engineering and enzyme design, focusing on both methodology development and applications, and we welcome research articles or reviews from all broadly defined areas of this discipline.
Some articles already published as part of the VSI include:
Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations
J. Phys. Chem. B 2021, 125, 18, 4701–4713
Introduction of a Glycine Linker Connecting the Heavy and Light Chains in Synthetic Cardosin B-Derived Rennet Changes the Specificity of Subpocket S3′
J. Phys. Chem. B 2021, 125, 17, 4368–4374
Combined MD and QM/MM Investigations of Hydride Reduction of 5α-Dihydrotestosterone Catalyzed by Human 3α-Hydroxysteroid Dehydrogenase Type 3: Importance of Noncovalent Interactions
J. Phys. Chem. B 2021, 125, 19, 4998–5008
The review process for all submissions for this VSI will be handled by JPC Senior Editor Benoit Roux.
To ensure an unbiased peer-review process, the journal asks that you do not indicate within your manuscript that the submission is intended for the VSI. If you do, your manuscript will be returned for correction. Instead, when you submit your manuscript, please indicate this on your cover letter and note what part and section you feel will be the best fit. You can find a complete list of sections and other important information for authors in the JPC Author Guidelines.
As with all submissions to JPC, your manuscript should represent a rigorous scientific report of original research, as it will be peer-reviewed as a regular article. Manuscripts are expected to provide new physical insight and/or present new theoretical or computational methods of broad interest.
If you are unsure if your research is within the VSI’s scope or have other questions about submitting a manuscript to this VSI, please email JPC B Deputy Editor Martin Zanni’s office at firstname.lastname@example.org.