Enzymes Sliding on the New BiophysJ Cover

Alfonso De Simone, an author on the latest paper to be featured on the Biophysical Journal cover, describes the background of the image below. The paper, “Substrate Dynamics in Enzyme Action: Rotations of Monosaccharide Subunits in the Binding Groove are Essential for Pectin Methylesterase Processivity,” was co-authored by De Simone, Davide Mercadante (also the image artist), Laurence D. Melton, Geoffrey B. Jameson, and Martin A. K. Williams.

bpj_104_8_cover-1The cover image originated from an idea of Davide Mercadante and favored by discussions with the other authors. Davide generated the image by using a number of programs including Origin, Visual Molecular Dynamics and Adobe Photoshop. As happened with the research, to be featured in the Biophysical Journal, the cover art is the result of back and forth interactions between the UK and New Zeeland.

The image was created on the basis of our investigation and shows how the conformational transitions of the substrate facilitate processive action in pectin methylesterase enzymes. The sliding of the enzyme on the polysaccharide chain has been represented in the lower left corner of the figure while the conformational variations of the substrate are represented in the upper right corner. We have rendered the enzyme sliding along the polymer by blurring the image of the protein surface to suggest the enzyme motion. Symbolically, a hand-lens that magnifies the enzyme-substrate complex represents the ability of molecular dynamics to “magnify” insights into macromolecular interactions at an atomic level. In the upper right corner of the figure, the energetic variations coupled to the conformational transitions of the saccharide residues along the biopolymer, has been rendered with a yellow curve representing the energy profile of the conformational transitions. Scatter plots have also been added to the figure to create a direct link between the artistic representation and the research data. Optimizing the colors of the graphs, background and other images “did the trick.”

Cover art pages represent an important opportunity to enhance the visibility of research, as well as a unique mean to communicate complex models or scientific news and views. In our case, we tried to achieve this by exploiting the ability of the whole team to describe a complex biomolecular mechanism without words and, at the same time, trying to render an appealing cover by matching colors, lines and shapes. The availability of cutting edge programs for molecular visualization and rendering has impacted the way by which modern researchers are reported.

Using more effective and “artistic” images is a part of the natural evolution of the scientific reports, which currently includes also contemporary channels such as for instance blogs and social networks. As long as the quality of the science is solid, we see positively the employment of these modern tools for the scientific communication as well as the influence of art in the preparation of figures and cover images. Art is probably the finest expression of the human being and passion for art is very common among scientists.

It is a great honor to present our results on the front cover of an issue of the prestigious Biophysical Journal. This is highly rewarding, especially considering the intense research activity associated with this article. The Journal is a reference point for a highly interdisciplinary scientific community represented by the Biophysical Society. This is an extraordinary experience and in the future we will try to repeat it. In this respect, we are carrying out new studies giving us evidence that pectin methylesterase enzyme can be considered an electrostatic Brownian ratchet. This will seed new cover arts on the complex molecular behavior that belongs to this extremely interesting protein.

For more from the paper’s authors, visit their websites:
Dr. Davide Mercadante: http://www.h-its.org/english/research/mbm/people.php?we_objectID=947
Prof. Laurie Melton: http://web.chemistry.auckland.ac.nz/staffprofilejahia.aspx?staffid=18
Dr. Bill Williams: http://ifs.massey.ac.nz/people/staff.php?personID=66
Prof. Geoff Jameson: http://ifs.massey.ac.nz/people/staff.php?personID=22
Dr. Alfonso De Simone: http://www3.imperial.ac.uk/people/a.de-simon


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