The journal for physical chemistry B (JPC B) will publish a Virtual Special Issue (VSI) on “Computational Advances in Protein Engineering and Enzyme Design”. The VSI is headed by guest editors Professor Lynne Kamerlin from Uppsala University and Professor Etienne Derat from Sorbonne University. Together they encourage researchers to submit their new and unpublished work 15.09.2021.
The main research areas of particular interest are:
- computational biochemistry
- in silico protein design
- Protein engineering
In creating this virtual special edition, the guest editors took inspiration from some of the latest exciting innovations and discoveries, including:
Enzymes are among the most complex of molecular objects, and it has long been thought impossible to create a working enzyme from scratch. The use of natural enzymes to perform interesting chemical transformations has long been possible, but has historically been limited to a number of specific reactions such as alcohol oxidation. Expanding the scope of unnatural enzymatic reactions has therefore been a primary goal. Several ideas have been developed here in recent years: either using existing enzymes and expanding their capabilities by taking advantage of their promiscuity, or adapting / adapting a known active center to perform a new reaction. A more exciting challenge, however, would be developing an ex nihilo enzyme to catalyze a specific and novel reaction. Computation is playing an increasingly important role here, be it through the identification of ancestral scaffolds that can be used as starting points for new enzyme engineering efforts, the use of conformational dynamics for enzyme engineering with computer tools, the use of machine learning approaches in enzyme design or an explosion of online tools and web servers that can simplify the engineering process. The field is rapidly expanding and maturing, taking many new and different directions. The aim of this special edition will be to highlight computational advances in protein engineering and enzyme design, with an emphasis on both method development and application. We welcome research articles or review articles from all broadly defined areas of this discipline.
Some articles already published under the VSI include:
Investigation of the minimum energy paths and free energy profiles of enzymatic reactions with QM / MM calculations
J.Phys. Chem. No. B. 2021, 125, 18, 4701-4713
DOI: 10.1021 / acs.jpcb.1c01862
Introduction of a glycine linker connecting the heavy and light chains in synthetic rennet derived from Cardosin B changes the specificity of Subpocket S3 ′
J.Phys. Chem. No. B. 2021, 125, 17, 4368-4374
DOI: 10.1021 / acs.jpcb.1c01826
Combined MD and QM / MM studies on the hydride reduction of 5α-dihydrotestosterone, catalyzed by human 3α-hydroxysteroid dehydrogenase type 3: Significance of non-covalent interactions
J.Phys. Chem. No. B. 2021, 125, 19, 4998-5008
DOI: 10.1021 / acs.jpcb.1c01751
The review process for all submissions for this VSI is handled by JPC Editor-in-chief Benoit Roux.
To ensure an impartial peer review process, the journal asks that you do not state in your manuscript that the submission is intended for the VSI. In this case your manuscript will be sent back for correction. Instead, indicate this in your cover letter when submitting your manuscript, making a note of which part and section you think fits best. A complete list of the categories and other important information for authors can be found in the JPC Guidelines for authors.
As with all submissions to JPC, your manuscript should be a rigorous scientific account of the original research as it will be peer-reviewed as a regular article. Manuscripts are expected to provide new physical knowledge and / or present new theoretical or computational methods of wide interest.
If you are unsure whether your research falls within the scope of the VSI or have any other questions about submitting a manuscript to this VSI, please send an email JPC B Assistant Editor Martin Zanni’s office at email@example.com.