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).

The 19th YSF and 44th FEBS conferences

I was at the 19th YSF and 44th FEBS conferences, in Krakow – Poland, during the last week (July 3rd to 11th) presenting my work about “Enhancing the catalytic power of Serine Hydroxymethyltransferase to produce commercially valuable compounds”. It was an excellent congress where I got some new ideas for the future. Thank you

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.

Desenvolvimento de Software com Aplicação no Ensino Em Química e Biologia – VII Encontro da Divisão de Ensino e Divulgação da Química

Last Saturday (November 17th), I was presenting some of the software that we have developed at BioSIM research group to improve the way some chemical concepts are taught to our students.

VMD extensions, such as VMD Magazine, ToolBar, Protein Wars, and VMD Store were presented during the “VII Encontro da Divisão de Ensino e Divulgação da Química” conference. During the presentation, the software features were presented and were showed how these extensions can be used to engage young students to learn chemistry in a more pleasant and clear manner.

Moreover, the BioSIM Augmented Reality technology was presented for the first time, and it allows an easy and costless way to see molecules using augmented reality. See the video below:

Poster at UCIBIO Annual Meeting 2018 – Lisbon

On September 28-29, I was presenting my recently published work at the UCIBIO Annual Meeting in Lisbon (FCT-NOVA).

The catalytic mechanism of Serine Hydroxymethyltransferase: a drug target against Malaria

Henrique S. Fernandes, M. J. Ramos, Sérgio F. Sousa, and N. M. F. S. A. Cerqueira

The catalytic mechanism of the Serine Hydroxymethyltransferase – a computational ONIOM QM/MM study

Henrique Silva Fernandes, Maria João Ramos, and Nuno M.F.S.A. Cerqueira

Published on 18th September 2018
Journal: ACS Catalysis

http://dx.doi.org/10.1021/acscatal.8b02321 | Download citation

Abstract

Serine Hydroxymethyltransferase (SHMT) is an important drug target to fight malaria – one of the most devastating infectious diseases that accounted in 2016 with 216 million new cases and almost 450 thousand deaths. In this paper, computational studies were carried out to unveil the catalytic mechanism of SHMT using QM/MM methodologies. This enzyme is responsible for the extraordinary cyclisation of a tetrahydrofolate (THF) into 5,10-methylene-THF. This process is catalyzed by a pyridoxal-5’-phosphate (PLP) cofactor that binds L-serine and from which one molecule of L-glycine is produced. The results show that the catalytic process takes place in eight sequential steps that involve an α-elimination, the cyclization of the 5-hydroxymethyl-THF intermediate into 5,10-methylene-THF and the protonation of the quinonoid intermediate. According to the calculated energetic profile, the rate-limiting step of the full mechanism is the elimination of the hydroxymethyl group, from which results a formaldehyde intermediate that then becomes covalently bonded to the THF cofactor. The calculated barrier (DLPNO-CCSD(T)/CBS:ff99SB) for the rate-limiting step (18.0 kcal/mol) agrees very well with the experimental kinetic results (15.7-16.2 kcal/mol). The results also highlight the key role played by Glu57 during the full catalytic process and particularly in the first step of the mechanism that requires an anionic Glu57, contrasting with some proposals available in the literature for this step. It was also concluded that the cyclisation of THF must take place in the enzyme, rather than in solution as it has been proposed also in the past. All of these results together provide new knowledge and insight on the catalytic mechanism of SHMT that now can be used to develop new inhibitors targeting SHMT and therefore new anti-malaria drugs.

Workshop “Utilização de software na simulação molecular” – V Encontro Internacional da Casa das Ciências

Utilização de software na simulação molecular

Inf F0-I1

Nuno Cerqueira, Sérgio Sousa, Henrique Fernandes e Carla Teixeira- Investigadores do DQB-FCUP

As tecnologias de informação e comunicação são nos dias de hoje uma ferramenta apelativa para o ensino da química. Neste contexto, salientam-se os programas de computador utilizados em modelação molecular que permitem visualizar e interpretar vários fenómenos químicos e que são normalmente difíceis de lecionar ou entendidos pelos alunos. Este workshop tem por objetivo a apresentação de vários programas de modelação molecular (como por exemplo Avogadro ou VMD) que permitem a visualização e edição de estruturas moleculares, bem como o cálculo de propriedades químicas de algumas moléculas. Todas as ferramentas apresentadas serão de acesso livre e por isso poderão ser instaladas e usadas pelos professores e alunos sem qualquer custo. Os exemplos abordados poderão ser mais tarde utilizados na sala de aula e permitir a construção de um ambiente de aprendizagem mais dinâmico e interativo, tornando o conteúdo lecionado mais estimulante e elucidativo para os alunos.
Informação aos formandos: os participantes deverão fazer-se acompanhar dos seus portáteis.

Moléculas Magníficas – V Encontro Internacional da Casa das Ciências 2018

Conferência de especialidade

Dia 9 de Julho de 2018, 14h30

Auditório Grande do Centro Cultural Vila Flor

Moléculas Magníficas

Maria João Ramos, Pedro Alexandrino Fernandes e Henrique Fernandes – Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto

Todas as moléculas são magníficas, mas algumas são mais magníficas que outras. Nesta conferência vamos apresentar algumas das moléculas incrivelmente complexas que comandam a nossa biologia, falando do seu papel, da sua função e do que é que as faz tão magníficas e fascinantes. Vamos ainda mostrá-las de uma forma artística, recorrendo às mais modernas tecnologias gráficas, para criar obras de arte a partir da ciência e do conhecimento.
Esta conferência de especialidade será dividida em três partes. Numa primeira palestra, eu próprio apresentarei alguns dos recursos digitais que temos vindo a desenvolver para o ensino da química, que permitem levar as Moléculas Magníficas para a sala de aula, no sentido de não só facilitar o processo de aprendizagem, mas também, e fundamentalmente, para despertar nos estudantes o fascínio pela química e pela ciência. Numa segunda palestra, o nosso convidado Henrique Fernandes (estudante de doutoramento na Univ. do Porto) fará uma apresentação sobre um conjunto de Moléculas Magníficas específicas, mostrando a sua explicando o seu papel na nossa vida. Por fim, numa terceira e última palestra, a Prof.a Maria João Ramos apresentará a história da iniciativa Moléculas Magníficas, o seu nascimento, as várias iniciativas de disseminação que têm vindo a ser feitas, as várias exposições, e os projetos futuros.
Entre as palestras terão lugar momentos de debate com a assembleia de participantes.

Uma tarde FQ! #5ei_cdc

Uma publicação partilhada por fisicaequimica.com (@trap_photon) a

Photos