The Biofilms Structural Database

Check our recent publication about “The Biofilms Structural Database”, a database devoted to the proteins involved in the biofilms’ formation.

Abstract

The Biofilms Structural Database (BSD) is a collection of structural, mutagenesis, kinetics, and inhibition data to understand the processes involved in biofilm formation. Presently, it includes curated information on 425 structures of proteins and enzymes involved in biofilm formation and development for 42 different bacteria. It is available at www.biofilms.biosim.pt.

Authors: Magalhães RP, Vieira TF, Fernandes HS, Melo A, Simões M, and Sousa SF

VMD Store – a VMD Plugin to Browse, Discover, and Install VMD Extensions

Henrique Silva Fernandes, Sérgio F. Sousa, and Nuno M.F.S.A. Cerqueira

Published on 21st October 2019
Journal: Journal of Chemical Information and Modeling

https://doi.org/10.1021/acs.jcim.9b00739 | Download citation

Abstract

Herein we present the VMD Store, an open-source VMD plugin that simplifies the way how users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism to install and configure VMD extensions. This plugin arises in an attempt to aggregate all VMD extensions in a single platform. The VMD Store is available, free of charge, for Windows, macOS, and Linux at https://biosim.pt/software/, and requires VMD 1.9.3 (or later).

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

Henrique S. Fernandes, Sérgio F. Sousa, and Nuno M.F.S.A. Cerqueira

Journal: Molecules

https://doi.org/10.3390/molecules24132462

Abstract

Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.

Amino Acid Deprivation Using Enzymes as a Targeted Therapy for Cancer and Viral Infections

Pages 283-297 | Received 29 Jul 2016, Accepted 25 Oct 2016, Accepted author version posted online: 04 Nov 2016, Published online: 15 Nov 2016

Introduction: Amino acid depletion in the blood serum is currently being exploited and explored for therapies in tumors or viral infections that are auxotrophic for a certain amino acid or have a metabolic defect and cannot produce it. The success of these treatments is because normal cells remain unaltered since they are less demanding and/or can synthesize these compounds in sufficient amounts for their needs by other mechanisms.

Areas covered: This review is focused on amino acid depriving enzymes and their formulations that have been successfully used in the treatment of several types of cancer and viral infections. Particular attention will be given to the enzymes L-asparaginase, L-arginase, L-arginine deiminase, and L-methionine-γ-lyase.

Expert opinion: The immunogenicity and other toxic effects are perhaps the major limitations of these therapies, but they have been successfully decreased either through the expression of these enzymes from other organisms, recombination processes, pegylation of the selected enzymes or by specific mutations in the proteins. In 2006, FDA has already approved the use of L-asparaginase in the treatment of acute lymphoblastic leukemia. Other enzymes and in particular L-arginase, L-arginine deiminase, and L-methioninase have been showing promising results in vitro and in vivo studies.