Day :
- Molecular Biology| Structural Biology| Gene regulation and Cell Signalling
Location: Webinar
Session Introduction
Ivan BarvÃk
Charles University, Czech Republic
Title: Computer modeling of TRPC channels gating
Biography:
Ivan Barvík is expert in computer modeling of biomolecules (molecular dynamics simulations, homology modeling, docking, quantum chemical calculations, and rational drug design), high performance computing, parallelization (Open MP, MPI, CUDA), numerical methods. He is author and co-author of 59 papers in impacted international journals (>757 citations, h-index 16). In many of these papers, the so-called TRP channels were studied: Sinica et al. Cells 9 (2020) 57; Zimova et al. Frontiers in Physiology 11 (2020) 189; Zimova et al. Science Signaling 11 (2018) 8621 etc. His research is supported by the Czech Science Foundation (22-13750S).
Abstract:
Statement of the problem: Transient Receptor Potential (TRP)-related channels are a large, diverse superfamily of proteins consisting of six families (TRPV, TRPC, TRPM, TRPA, TRPP, TRPML) and 30 subtypes [1-3]. TRP channels are activated by diverse cellular and environmental signals. Inhibition of TRP channels expressed on nociceptive neurons represents a viable therapeutic pain target. All TRP channels form functional tetramers, with each subunit consisting of six transmembrane segments (S1-S6) flanked by amino- and carboxyl-terminal cytosolic domains. The S1-S4 helices form isolated sensor domains arranged radially around the periphery of the central-ion conducting pore, which is lined with four S5-S6 domains. The central cavity involved in the ion permeation exhibits major constrictions at the selectivity filter, as well as at the lower gate. Unfortunately, not all TRP channels have their closed and open structure resolved.
Juha M. Linnanto
University of Tartu, Estonia
Title: Energy transfer in the photosynthetic unit of green sulphur bacterium
Biography:
Juha Matti Linnanto is from the Institute of Physics, University of Tartu, Estonia. He is computational/theoretical chemist. His research interest cover various aspects of theory and modeling of electronic, optical, structural and transport properties of photosynthetic pigments, pigment-protein complexes, self-aggregates, dendrimers and metal-organic compounds. His computation competence includes classical molecular mechanic methods; molecular dynamic methods; semi-empirical quantum chemical methods; density functional methods; ab-initio methods; configuration interaction methods; time-dependent Hartree-Fock/density functional methods; and molecular exciton theory. He has published >50 articles in international peer-review journals, has >1400, H index 24 (Web of Science). Currently he is an associate professor (Laboratory of Biophysics) at the Institute of Physics of Tartu University
Abstract:
Statement of the problem: Photosynthesis is the most important biological energy conservation pathway on the Earth, and oxygenic photosynthesis produces most of the oxygen we breathe. Photosynthetic organisms make use of solar energy to create free chemical energy that is used in their metabolic reactions. For light energy to be store by photosynthesis, it must first be absorbed by pigment molecules associated with the photosynthetic apparatus. The Light-Harvesting (LH) antenna systems collect sunlight and transfer excitation energy rapidly to the photosynthetic Reaction Centers (RCs), where the energy is trapped in an electron-transfer reaction. Photosynthetic Units (PSUs) of phototrophic organisms have such structural architecture that light energy absorbed by an LH antenna is transferred to a RC through efficient Energy Transfer (ET). To investigate these processes both experimental and theoretical methods are needed. There are available only a few experimentally solved atomic-resolution X-ray LH and RC structures. Thus, different computational methods together with experimental structural and spectroscopic information are needed to generate three-dimensional pigment-protein LH antenna model structures. The purpose of this study is to generate atomistic model for the PSU of Green Sulphur Bacteria (GSB) and to explain solar energy transfer processes in this system. Experimental X-ray, electron microscopy, and cryo-electron microscopy LH and RC structures of GSB are used as initial structure models in this study. The PSU of GSB is very interesting system because it contains both self-aggregated pigment oligomer LH complexes as also pigment-protein LH complexes. All of these complexes have their own specific absorption spectrum and energy levels. The PSU of the GSB allows some of GSB to live in extraordinarily low light conditions under which no other photosynthetic organisms can grow, such as in the bottom of stratified lakes, deep in the sea and near geothermal vents.
Sarwan Dhir
Fort Valley State University, USA
Title: Establishment of plant regeneration and genetic transformation in hemp (Cannabis Sativa L.) using Agrobacterium-mediated
Biography:
Sarwan Dhir is a tenured Professor of Plant Biotechnology and Director of the Center for Biotechnology at Fort Valley State University, Fort Valley, GA. He received post-doctoral training at the University of Illinois at Urbana-Champaign and Monsanto Agricultural Company in St. Louis (Bayer) in the area of genetic engineering and plant biotechnology. Since 2001, as a faculty member, he played a leadership role in the establishment of the Center for Biotechnology (Supported by NSF since 2001), developed the Plant Science-Biotechnology major (by restricting and developing 6 new courses), and founding director for Undergraduate Research Program. Besides full-time teaching appointments, as the PI, we received more than 15 million dollars from various funding agencies such as NSF (from 2001 to 2025), NIFA, and DoE. He has successfully directed NSF-funded “National Role Model” programs such as REU-Site in Biotechnology, HBCU-UP, and S-STEM scholarship program since 2001. He has served as a faculty mentor to place more than 485 students in summer internship programs at major institutions, federal labs, and industries and mentored more than 625 undergraduates to prepare their abstracts and present their research at national and international scientific meetings, winning more than 105 awards. He has mentored, 212 Pre-bridge program students, and out of those, 198 enrolled at FVSU and 152 chose STEM majors. Every year, he provides financial support to students enrolled in the Plant Science-Biotech program to 35-40 students in scholarships amounting to $4,200 per academic year for 4-years. He has served as a research mentor for more than 55 middle and high school students and helped them to develop award-winning science fair presentations at national and international science fair competitions. He is a winner of the 2005 White House-Presidential Awards for Excellence in Science, Mathematics, and Engineering Mentoring (PAESMEM) from President George Bush in STEM, a two-time Outstanding Mentoring Excellence Award from NSF HBCU-UP program, and the John W. Davidson Award for Outstanding Teaching and Outstanding Million Dollar Grantsmanship Award given by the FVSU Foundation.
Abstract:
Hemp (Cannabis sativa L.) is an annual and typically dioecious crop and is cultivated in many parts of the world for its fiber, oil, seed and in the therapeutic potential for human diseases, phytocannabinoids as a medical therapy are getting more attention recently. The species is also widely utilized as a source of fiber (such as fabrics, ropes, and paper), food, oil, and medicines plus it has a reputation as being used in religious ceremonies and/or for recreational purposes [1]. The development of new hemp cultivars with improved traits such as resistance to biotic and abiotic stresses, better nutritional and processing qualities, and with increased yields among others [2,3]. However, before the implementation of this technique in C. sativa species, it is imperative to develop an efficient plant regeneration and transformation protocol that allows the regeneration of transgenic plants. Micro propagation can facilitate high throughput propagation in many species and forms the basis of disease-free plants for certified clean plant programs. Thus, developing an optimized in vitro method for propagating clean plants is a crucial strategy to produce large-scale genetically identical plants, retain genetic integrity and maintain the long-term sustainability of the economically valuable crop [4,5,6]. The purpose of this study was to establish a protocol for Agrobacterium-mediated transformation for foreign gene introduction in Hemp. Several factors influence transformation efficiency including the effect of explant type, age of leaf explants, the concentration of silver nitrate and or calcium chloride, bacteria concentration, infection time, acetosyringone concentration, wounding, and different co-culture periods of bacteria were evaluated to optimize the transformation efficiency for Hemp.
Safoura Ghalamkari
University of Debrecen, Hungary
Title: A novel carcinogenic PI3Kα mutation suggesting the role of helical domain in transmitting nSH2 regulatory signals to kinase domain
Biography:
I am Safoura Ghalamkari second-year PhD student from Department of laboratory of medicine, Medical School, University of Debrecen, Debrecen, Hungary. My research interests are functional and computational genetic study to figure out the effect of mutations on the protein structure and function. Now I am doing functional studies on rare genetic disorders under supervision of prof. Istvan Balogh, head of human genetics department. My previous research has been published in two international journals.
Abstract:
Mutations in PIK3CA, which encodes p110α subunit of PI3K class IA enzymes are highly frequent (~40%) in breast cancer. Most of the hotspot gain-of-function PIK3CA mutations are clustered in exon 9 and 20 of this gene. In this study, we aimed to probe mutations in exon 9 of PIK3CA and computationally simulate their function since MD simulation is a powerful tool for predicting conformational dynamics of mutant protein kinases. Firstly PCR/HRM and PCR/sequencing were used for mutation detection in 40 breast cancer specimens. The identified mutations were queried via in-silico algorithms to check the pathogenicity.
Biography:
Ezgi Sen is a Master Student in Biology Department at Georgia State University. Her interest is working with Dopamine pathways to investigate how dopamine levels can impact on monogamy in the Dr. Sylvester Lab. She has gained experiences, knowledge on developmental biology, evolutionary perspective of neural development and most importantly passion on doing research.
Abstract:
Monogamy has long been a subject of scientific interest for researchers. Visual observations have shown that Convict cichlid fish stay together after mating. Zebra fish (Danio rerio) were chosen as an alternative model for non-monogamous behavior. In this research study, dopamine receptors will be investigated because dopamine plays an important role in monogamous behavior. Dopamine is a modulatory neurotransmitter used in several ways, such as learning and memory, cognition, attention, reward pathways, and social behavior. For these reasons, I propose that the number of dopaminergic neurons in the midbrain of zebra fish will be fewer than in the membrane of Convict cichlid. This results in Convict cichlid monogamous behavior. The expression of dopaminergic neurons will be visualized by in-situ hybridization and with antibody immunohistochemistry. This research study will bring guidance to the future studies on monogamy.
Alejandro A Gutiérrez-Hernández
Autonomous University, Mexico
Title: In silico evaluation of SNPs at the interface of ACE2 forming the ligandreceptor complex with the Spike protein
Biography:
Alejandro A. Gutiérrez-Hernández is a student in Autonomous University of Zacatecas, Mexico. He is interested in working with Pathology and Molecular Diagnosis Laboratory, Academic Unit of Chemical Sciences.
Abstract:
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has recently emerged in China and caused the disease COVID-19, the virus spread rapidly around the world, causing a global outbreak. Protein-protein binding assays have confirmed that Angiotensin-Converting Enzyme 2 (ACE2) is the cellular receptor through which the virus invades the host cell. The severity of the symptoms and the rapid progression of the disease have led to in-depth investigation of this virus, suggesting a response by which some populations are more susceptible to the entry of the SARS-CoV-2 virus and this may be due to polymorphisms of a Single Nucleotide (SNP) present in various populations in this case in the ACE2 receptor. In this study, nsSNPs present in the ACE2 interface were selected, the amino acid changes corresponding to each nsSNP were made from the base model that form the ACE2-SARS- CoV-2 complex, the binding energy and the binding constant were calculated. protein-protein interaction dissociation. The results of the analysis indicate that the presence of the Asp355Asn and Ser19Pro variants in ACE2 decrease the binding affinity in the protein-protein complex, therefore, we suggest a lower susceptibility to COVID-19 disease. However, the Glu329Gly and Glu37Lys variants indicate an increase in binding affinity according to the physicochemical parameters evaluated, so their presence in ACE2 would possibly increase susceptibility to COVID-19 disease.