Article
Biotechnology & Applied Microbiology
Allison Z. Werner, Rita Clare, Thomas D. Mand, Isabel Pardo, Kelsey J. Ramirez, Stefan J. Haugen, Felicia Bratti, Gara N. Dexter, Joshua R. Elmore, Jay D. Huenemann, George L. Peabody, Christopher W. Johnson, Nicholas A. Rorrer, Davinia Salvachua, Adam M. Guss, Gregg T. Beckham
Summary: The study demonstrates the conversion of PET waste into beta-ketoadipic acid (beta KA) through a combination of catalytic deconstruction and biological conversion in Pseudomonas putida KT2440. The results showcase the potential of tandem catalytic approaches for upcycling waste PET into higher-value products.
METABOLIC ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Xuehui Guo, Yiming Jiang, Daiqian Xie, Yanzi Zhou
Summary: Poly(ethylene terephthalate) (PET) is widely used in daily life, but its non-degradability causes environmental and health problems. PETase from Ideonella sakaiensis has shown the highest PET degradation activity, but the crystal structure of the PET-PETase complex remains unknown. Molecular docking and dynamics simulations were used to study the binding and interactions between PET and PETase. The PET oligomers adopt stable conformations in a shallow cleft on PETase, with only four moieties fitting in the binding cleft. This study provides insights into PET binding and can aid the design of more efficient PETase variants for plastic degradation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Krit Charupanit, Varomyalin Tipmanee, Thana Sutthibutpong, Praopim Limsakul
Summary: This study utilized computational methods to construct the protein sequence space of PETase-PET binding energy and identified mutation sites and appropriate side-chain properties that could enhance PETase activity. Molecular dynamics simulations revealed that PETase variants with S238C or Q119F may improve PETase efficiency. The findings have important implications for protein engineering and PETase improvement.
Article
Biochemistry & Molecular Biology
Anil Ranu Mhashal, Neeraj T. Kumar, Nitheeshkumar Kumar, Anshul Singhal, Akash Ravandur, Pandian Sokkar, Naveen Kulkarni
Summary: This study investigated the reasons behind the improved catalytic activity of the engineered IsPETase enzyme through molecular dynamics simulations. The results showed that the mutations reshaped the active site structure, volume, and dynamics, crucial for substrate binding, and demonstrated that adding aromatic and hydrogen bond-forming residues near the catalytic site improves binding affinity. This work provides insights for the rational design of mutants with enhanced PET degrading activity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Dong Hyun Kim, Dong Oh Han, Kyu In Shim, Jae Kyun Kim, Jeffrey G. Pelton, Mi Hee Ryu, Jeong Chan Joo, Jeong Woo Han, Hee Taek Kim, Kyoung Heon Kim
Summary: PET, widely used in various industries, poses major environmental challenges due to its low degradability and recycling rate. An integrated process for depolymerizing PET and converting it to high-value products has been developed, showing great potential for upcycling waste PET.
Review
Biochemistry & Molecular Biology
Rita P. Magalhaes, Jorge M. Cunha, Sergio F. Sousa
Summary: Plastics are durable and widely used materials, but current methods for degradation and recycling are flawed. Biodegradation has emerged as a viable alternative, with enzymes capable of degrading PET being discovered and engineered. Despite progress, further efforts are needed to improve enzyme activity and thermal stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Physics, Applied
Connor J. Morris, Dennis Della Corte
Summary: Molecular docking and molecular dynamics are powerful tools for studying protein-ligand interactions, predicting binding poses, affinities, and stability. They are widely used in drug discovery and further research on combining common molecular docking and MD methods is recommended for enhanced results.
MODERN PHYSICS LETTERS B
(2021)
Article
Agriculture, Multidisciplinary
Lixia Shi, Haifeng Liu, Songfeng Gao, Yunxuan Weng, Leilei Zhu
Summary: In this study, the researchers successfully increased the secretion efficiency of PETase by using an engineered signal peptide, leading to more efficient enzymatic degradation of PET.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Environmental Sciences
Yidi Liu, Zhanzhi Liu, Zhiyong Guo, Tingting Yan, Changxu Jin, Jing Wu
Summary: In this study, a enzyme called DuraPETase-4M was designed through protein engineering to improve the efficiency of PET plastic biodegradation. The design included addition of disulfide bonds to enhance thermal stability, adjustment of key region flexibility to enhance degradation capacity, and optimization of protein surface electrostatic charge to improve binding ability with PET plastic.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biology
Mohd Afzal, Abdullah Alarifi, Naaser. A. Y. Abduh, Arusha Ayub, Mohd. Muddassir
Summary: Apoptosis is regulated by the BCL-2 family, and inhibition of the pro-apoptotic and anti-apoptotic protein-protein interactions has been studied for developing anticancer drugs. In this study, the hydrophobic nature of 74 organometallic compounds was analyzed, and their effectiveness against the BCL-2 protein was determined using molecular docking. The results identified several important compounds that could bind to the less solvent-accessible site of BCL-2.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Bethany Kolbaba-Kartchner, I. Can Kazan, Jeremy H. Mills, S. Banu Ozkan
Summary: The study explores the relationship between protein dynamics and enzymatic function in beta-lactamases, revealing that allosteric coupling of rigid residues to the active site has profound effects on enzyme function. By altering the dynamic profile of TEM-1 using computational protein design methods, it was found that changing residues surrounding highly coupled rigid residues significantly affected enzymatic activity and stability. This integration of computational protein design methods with analyses of protein dynamics represents a general approach to extend understanding of the relationship between dynamics and function in other enzyme classes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Applied
Fuqiang Liang, Yumeng Shi, Jiayi Shi, WeiWei Cao
Summary: This study investigated the interaction between apigenin and pumpkin seed protein (PSP) using multi-spectroscopic analysis and molecular simulation approaches. The results showed that apigenin interacted with PSP through hydrophobic interactions. Molecular docking and molecular dynamics simulations revealed that apigenin maintained binding stability in the hydrophobic pockets of the protein. The interaction induced changes in the protein's structure and conformation. This study provides theoretical evidence for the potential application of PSP and apigenin complex products in the food industry.
FOOD HYDROCOLLOIDS
(2023)
Review
Agriculture, Multidisciplinary
Abraham Vidal-Limon, Jose E. Aguilar-Toala, Andrea M. Liceaga
Summary: The use of in silico tools, such as molecular docking, to study biological activity of proteins and peptides can sometimes produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) offer a solution to overcome sampling limitations in docking analysis and provide valuable information in deciphering functional mechanisms of proteins and peptides. This review discusses the traditional use of in silico models, like molecular docking, and highlights the importance of MDS in predicting structural and functional dynamics of food proteins and bioactive peptides.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Mohd Sajid Ali, Mohd Waseem, Naidu Subbarao, Abdullah Nasser Alahamed, Hamad A. Al-Lohedan
Summary: The interaction between lysozyme and cefoperazone was studied using spectroscopic and computational approaches. The UV-visible spectrum showed a change in lysozyme in the presence of cefoperazone, indicating complex formation. Fluorescence spectroscopy suggested a fair interaction via dynamic quenching, with a binding ratio of approximately 1:1. In silico studies revealed that hydrophobic forces played a major role in the interaction, with some involvement of hydrogen bonding and electrostatic interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Lea R. Rapp, Sergio M. Marques, Bernd Nebel, Jiri Damborsky, Bernhard Hauer
Summary: The catalytic space of the P450 monooxygenase CYP153A(M.aq) was transformed from a fatty acid hydroxylase to a catalyst capable of omega-hydroxylation of dodecylamine. A rapid screening method called RAPP was established to measure saturation libraries directly from a 96-deepwell plate. Molecular modeling and dynamics simulations revealed significant effects of the mutations on the substrate tunnel architectures.
Article
Engineering, Civil
Clara Cordeiro, Ana Borges, M. Rosario Ramos
Summary: This study aims to address apparent water losses faced by water companies by proposing a strategy to detect decreasing water usage patterns. Statistical methods are used to analyze time series data of water consumption and identify potential issues.
JOURNAL OF WATER RESOURCES PLANNING AND MANAGEMENT
(2022)
Article
Green & Sustainable Science & Technology
A. Pacheco, J. Monteiro, J. Santos, C. Sequeira, J. Nunes
Summary: This paper contributes to the understanding of the importance of community engagement in energy transition processes. It presents a case study of a small island in Portugal, showing how the community is successfully leading the green transition and achieving socio-economic benefits by tailoring technological solutions to the specific needs of the island.
Article
Social Sciences, Interdisciplinary
Silvia Monteiro Fonseca, Sara Faria, Sonia Cunha, Marcio Silva, M. Joaquina Ramos, Guilherme Azevedo, Rui Campos, Antonio Ruao Barbosa, Cristina Queiros
Summary: The study found that EMS personnel showed adequate psychological adjustment during COVID-19, with age, COVID-19 fear, and workplace security measures' adequacy contributing to whether they belonged to the well-adjusted or poorly-adjusted pattern. It underscores the need to further explore other COVID-19 fears, perceptions of workplace security measures, COVID-19 valid instruments, pre-COVID-19 data, and mental health patterns among different rescuers.
INTERNATIONAL JOURNAL OF EMERGENCY SERVICES
(2022)
Article
Biochemistry & Molecular Biology
Carla F. Sousa, Joao T. S. Coimbra, Robert Richter, Joao H. Morais-Cabral, Maria J. Ramos, Claus-Michael Lehr, Pedro A. Fernandes, Paula Gameiro
Summary: The misuse and overuse of fluoroquinolones in recent years have led to alarming levels of antibiotic resistance. The development of ternary copper complexes with fluoroquinolones is a potential strategy to overcome resistant bacteria. However, the permeation of metalloantibiotics through OmpF, a common porin in Gram-negative bacteria, is less favorable than free fluoroquinolones. Permeability studies confirmed the lower rate of permeation for metalloantibiotics compared to free antibiotics, suggesting a porin-independent mechanism for their influx into bacterial cells.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Chemistry, Physical
Rui P. P. Neves, Ana Cunha, Pedro A. Fernandes, Maria J. Ramos
Summary: In this study, QM/MM molecular dynamics simulations were used to investigate the rate-limiting step of the glycosylation reaction of pancreatic alpha-amylase. By carefully selecting different starting conformations and performing umbrella sampling simulations, Gibbs energy profiles were calculated. The results showed that the starting conformation has a significant impact on the reaction energy and activation energy.
Article
Chemistry, Multidisciplinary
Pedro A. Fernandes, Oscar Passos, Maria J. Ramos
Summary: The COVID-19 pandemic has posed challenges to teaching, and this article proposes the use of modern technology to create a virtual classroom for hands-on molecular bioinformatics courses, allowing students to learn effectively despite the lockdowns. The outcomes of this virtual classroom are comparable to the traditional teaching method.
JOURNAL OF CHEMICAL EDUCATION
(2022)
Article
Chemistry, Medicinal
Luis M. C. Teixeira, Joao T. S. Coimbra, Maria Joao Ramos, Pedro Alexandrino Fernandes
Summary: Efficient drugs are urgently needed to treat patients infected with SARS-CoV-2, despite the availability of vaccines. Human transmembrane protease serine 2 (TMPRSS2) is a promising target for drug development due to its vital role in the infection mechanism of the virus. Using quantum mechanics/molecular mechanics (QM/MM) calculations, the mechanism of the acylation step in the cleavage of the virus spike protein (S protein) was determined, providing valuable insights for the design of transition-state analogue inhibitors with higher affinity. These findings are important for the development of more effective drugs against SARS-CoV-2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Luisa M. P. F. Amaral, Tania Moniz, Andreia Leite, Ana Oliveira, Pedro Fernandes, Maria Joao Ramos, Alberto N. Araujo, Marisa Freitas, Eduarda Fernandes, Maria Rangel
Summary: This study evaluated the inhibitory effect of twelve 3-hydroxy-4-pyridinones (3,4-HPO) on tyrosinase and investigated their binding modes with human and mushroom enzymes using molecular docking. Ligands I6 and I11 showed the highest inhibitory activity in both reaction steps. The research clarified the inhibition type of kojic acid and highlighted the differences in potential tyrosinase inhibitors among the studied set of 3,4-HPO chelators.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Joao T. S. Coimbra, Rui P. P. Neves, Ana Cunha, Maria J. Ramos, Pedro A. Fernandes
Summary: This study investigates the influence of enzyme's dynamical flexibility on reaction mechanisms, using the first step of HIV-1 protease catalyzed reaction as a case study. The results reveal a mechanistic divergence in the enzyme, with two different reaction pathways exhibiting equivalent barriers. An active-site water molecule is suggested to play a role in influencing the mechanistic pathway.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Matilde F. Viegas, Rui P. P. Neves, Maria J. Ramos, Pedro A. Fernandes
Summary: This study describes the catalytic mechanism of the fungal Thermothelomyces thermophila glucuronoyl esterase (TtGE) using QM/MM methods. Two nearly-degenerate rate-determining transition states were found, and a mutation was proposed to enhance the catalytic rate of TtGE.
Article
Chemistry, Medicinal
Rui P. P. Neves, Pedro A. Fernandes, Maria J. Ramos
Summary: We studied the conformational dynamics and glycosylation step of a human pancreatic alpha-amylase:maltopentose complex. Molecular dynamics simulations showed that the distance between the nucleophile Asp197 and the buried glucoside is responsible for enzyme active site fluctuations. Quantum mechanics/molecular mechanics simulations indicated that the reaction occurs in an asynchronous concerted step involving an acid-base reaction with Glu233 followed by a nucleophilic substitution by the Asp197. Thermodynamic analysis revealed that a water molecule tightly bonded to the substrate's glycosidic oxygen formed a short hydrogen bond with Glu233 at the transition state, lowering the Gibbs barrier.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Review
Chemistry, Multidisciplinary
Ana L. Oliveira, Matilde F. Viegas, Saulo L. da Silva, Andreimar M. Soares, Maria J. Ramos, Pedro A. Fernandes
Summary: This review discusses the chemistry of snake venom and its potential for medicinal purposes. It focuses on the molecular structure, chemical reactivity, and target recognition of bioactive toxins found in snake venom, and how they can be developed into bioactive drugs. The design and working mechanisms of snake-venom-derived drugs are illustrated, along with the strategies for transforming toxins into therapeutics. The challenges in realizing the curative potential of snake venom are also discussed, and chemical strategies for deriving new drugs from snake venom are proposed.
NATURE REVIEWS CHEMISTRY
(2022)
Article
Chemistry, Physical
Alexandre V. Pinto, Pedro Ferreira, Pedro A. . Fernandes, Alexandre L. Magalhaes, Maria J. Ramos
Summary: In this paper, a new molecular dynamics (MD) model is proposed to accurately describe the structure of graphene oxide (GO) and its interaction with a solvent and other adsorbate molecules. The new force field parameters are derived through linear-scaling density functional theory calculations, which better reproduce the solvent structure observed in ab initio MD simulations. The effect of ionic strength and the carbon-to-oxygen ratio on the distribution of charges surrounding GO sheets is also analyzed, and the force field is validated by simulating the adsorption of natural amino acid molecules to GO sheets and estimating their free energy of binding.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Medicinal
Rui P. P. Neves, Maria J. Ramos, Pedro A. Fernandes
Summary: Here we present an approach to identify enzyme mutants with increased turnover by recalculating barriers and analyzing charge interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Review
Biochemistry & Molecular Biology
Jose R. Almeida, Bruno Mendes, Marcelo Lancellotti, Gilberto C. Franchi Jr, Oscar Passos, Maria J. Ramos, Pedro A. Fernandes, Claudia Alves, Nuno Vale, Paula Gomes, Saulo L. da Silva
Summary: This study found that peptides derived from snake venom have potential as antineoplastic and antibacterial therapies. Two short peptides were synthesized and evaluated for their bioactivity against bacteria and tumor cells. The peptides showed dual activity, with one peptide showing more significant activity. The study highlights the importance of studying biomembrane remodeling proteins and their potential use in developing therapeutic peptides.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
