Biological physics is the branch of science that applies the principles of physics, chemistry, and mathematics to the biological system to understand the fundamental biological processes such as how biomolecules, cells, tissues, and organs perform vital life functions. Scientists from diverse backgrounds use an experimental, computational, and theoretical approach to explore the mysteries of life. Medical physics applies knowledge of physics in medicine to diagnose and treat human disease using methods like magnetic resonance imaging and radiation treatments. Soft matter physics is an interdisciplinary field where scientists from different areas of science come together to understand the behavior and properties of soft materials like liquid crystals, colloids, polymers, gels, membranes, and cytoskeletons. The Biological/Medical/Soft matter physics session of the ANPA conference taking place on July 15-17, 2022, aims to bring the scientist together to present their findings, discuss their research and foster new collaborations. We invite you and your colleagues to submit abstracts for presentations and look forward to seeing you at the conference.
In silico approach to tackling viral and bacterial diseases
Physics-based molecular modeling and simulations have recently led to numerous applications, including
the design of new drugs and enzymes. The emergence of the COVID-19 pandemic has brought interdisciplinary
biomedical researchers together at an unprecedented level, and computational techniques have
played a crucial role in understanding and tackling the disease. These include structure determination and
exploring molecular mechanisms as well as identifying therapeutic and vaccine candidates. In this talk,
I will discuss a few projects in my lab focusing on viral and bacterial diseases, including computational
investigations of cell attachment and immune evasion by SARS-CoV-2 variants, matrix protein-plasma
membrane interactions in viral assembly and budding of filoviruses and paramyxoviruses, and designing
novel antimicrobial compounds to confront the threat of antimicrobial resistance.
Current Development in Structural Biology Techniques for Studying Membrane Proteins
Biological systems perform critical functions in specific situations. Hence it is very important to
understand structural and dynamic properties of components of the systems in a suitable environment
to understand their proper function. Membrane proteins are involved in several biological process that
are required for the survival of living organisms: e. g., cellular transport, signaling, recognition and
catalysis. These proteins are targets of more than 50 % of all modern drugs. Mutations or misfolding
of membrane proteins are linked to several human dysfunctions, disorders and diseases such as Long QT
Syndrome, Alzheimer, etc. Despite the abundance and clear importance of membrane-associated molecules,
very little information about these systems exists. X-ray crystallography and Nuclear magnetic resonance
(NMR) spectroscopy are the most widely used biophysical techniques for obtaining detailed structural
information on biological systems. Challenges in studying membrane proteins arise due to the hydrophobic
nature of membrane proteins making overexpression, purification, and crystallization more difficult, and
lacking of suitable solubilizing membrane mimetic. Electron paramagnetic resonance spectroscopy (EPR)
is a very powerful and rapidly growing technique that can resolve the limitations associated with these
techniques and provide prominent solutions to obtain structural and dynamic information on peptides,
proteins, macromolecules, and nucleic acids. Recent developments in improving structural biology techniques
using some of the examples of biological problems associated with membrane proteins (potassium channel
proteins) will be presented. We are developing several advanced approaches of EPR spectroscopy .to study
membrane proteins.
Session Schedule
Please look below for detailed schedule.
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Abstract Number: ANPA2022_0157 Presenting Author: Indra D. Sahu (Invited) Presenter's Affiliation: Campbellsville University Title: Current Development in Structural Biology Techniques for Studying Membrane Proteins Show/Hide Abstract Biological systems perform critical functions in specific situations. Hence it is very important to understand structural and dynamic properties of components of the systems in a suitable environment to understand their proper function. Membrane proteins are involved in several biological process that are required for the survival of living organisms: e. g., cellular transport, signaling, recognition and catalysis. These proteins are targets of more than 50% of all modern drugs. Mutations or misfolding of membrane proteins are linked to several human dysfunctions, disorders and diseases such as Long QT Syndrome, Alzheimer, etc. Despite the abundance and clear importance of membrane-associated molecules, very little information about these systems exists. X-ray crystallography and Nuclear magnetic resonance (NMR) spectroscopy are the most widely used biophysical techniques for obtaining detailed structural information on biological systems. Challenges in studying membrane proteins arise due to the hydrophobic nature of membrane proteins making overexpression, purification, and crystallization more difficult, and lacking of suitable solubilizing membrane mimetic. Electron paramagnetic resonance spectroscopy (EPR) is a very powerful and rapidly growing technique that can resolve the limitations associated with these techniques and provide prominent solutions to obtain structural and dynamic information on peptides, proteins, macromolecules, and nucleic acids. Recent developments in improving structural biology techniques using some of the examples of biological problems associated with membrane proteins (potassium channel proteins) will be presented. We are developing several advanced approaches of EPR spectroscopy .to study membrane proteins.
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Abstract Number: ANPA2022_0158 Presenting Author: Nawal Kishore Khadka Presenter's Affiliation: Boise State University Title: An AFM Approach in ?-Crystallin Membrane Association Studies Show/Hide Abstract The lens of the eye loses elasticity with age, while ?-crystallin association with the lens membrane increases with age. It is unclear whether there is any correlation between ?-crystallin association with the lens membrane and loss in lens elasticity. This research investigated ?-crystallin mem-brane association using atomic force microscopy (AFM) for the first time to study topographical images and mechanical properties (breakthrough force and membrane area compressibility modulus (KA), as measures of elasticity) of the membrane. ?-Crystallin extracted from the bovine lens cortex was incubated with a supported lipid membrane (SLM) prepared on a flat mica surface. The AFM images showed the time-dependent interaction of ?-crystallin with the SLM. Force spectroscopy revealed the presence of breakthrough events in the force curves obtained in the membrane regions where no ?-crystallin was associated, which suggests that the membrane�s elasticity was maintained. The force curves in the ?-crystallin submerged region and the close vicinity of the ?-crystallin associated region in the membrane showed no breakthrough event within the defined peak force threshold, indicating loss of membrane elasticity. Our results showed that the association of ?-crystallin with the membrane deteriorates membrane elasticity, providing new insights into understanding the molecular basis of lens hardening and presbyopia.
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Abstract Number: ANPA2022_0159 Presenting Author: Raju Timsina Presenter's Affiliation: Boise State University Title: Binding of Alpha-Crystallin with Lens Lipid Membranes Derived from a Single Lens Show/Hide Abstract This research investigates the binding of ?-crystallin with membranes prepared from total lipids isolated from a single bovine eye lens, measures the physical properties of membranes, and illustrates the feasibility that such experiments can be conducted for membranes prepared from total lipids isolated from a single human eye lens. Small unilamellar vesicles were prepared with and without decreasing the cholesterol (Chol) content from total lipids isolated from a single lens cortex of a two-year-old bovine using the rapid solvent exchange method and probe-tip sonication. Chol content in the cortical membranes was decreased by adding lipid (phospholipids and sphingolipid) mixtures resembling bovine lens lipid composition. The electron paramagnetic resonance spin-labeling method was used to measure the percentage of membrane surface occupied (MSO) by ?-crystallin, the binding affinity (Ka), and the physical properties (hydrophobicity, mobility parameter, and maximum splitting) of membranes. No significant binding of ?-crystallin with bovine lens lipid membranes derived from the single-lens cortex was observed. However, ?-crystallin binding with cortical membranes with reduced Chol content was observed. The smaller the Chol content in cortical membranes, the larger the MSO and Ka, and vice-versa. These results imply that the membrane Chol is a key component in preventing ?-crystallin binding with the bovine lens lipid membrane. Hydrophobicity near the surface of cortical membranes increased with the increased ?-crystallin binding, supporting the hypothesis that ?-crystallin binding with lens membranes forms a barrier to polar molecules. The profiles of mobility parameters decreased and maximum splitting showed no significant change with the increased ?-crystallin concentration, indicating that cortical membranes became less mobile with no significant change in order near the surface with the ?-crystallin binding. Our results show that the membrane Chol plays a crucial role in inhibiting ?-crystallin binding with the bovine lens lipid membrane, and such binding alters the physical properties of membranes playing a vital role in modulating the integrity of membranes. Moreover, this study demonstrates that it is feasible to investigate the binding of ?-crystallin with membranes derived from a single human lens.
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Abstract Number: ANPA2022_0160 Presenting Author: Leona Choi Presenter's Affiliation: California State Polytechnic University, Pomona Title: Investigation of Structure and Dynamics of the SecA Protein in Native Conditions via Atomic Force Microscopy Show/Hide Abstract Membrane proteins are responsible for various important cellular processes such as: protein export, signal transduction, enzymatic activities, and cell-to-cell communication. Membrane proteins also constitute more than half of all current drug targets. SecA is a member of the secretory system with the primary function of taking part in transporting nascent proteins through the inner membrane and into the periplasmic region of E. coli. Studies suggest dynamic interactions between the SecA protein and the lipid bilayer during this translocation process. Since structural details and conformational dynamics are tied to functions, we performed high-resolution imaging of SecA interacting with a lipid bilayer in physiological buffer conditions via atomic force microscopy (AFM).
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Abstract Number: ANPA2022_0161 Presenting Author: Prem Chapagain (Invited) Presenter's Affiliation: Florida International University, Miami, FL 33199 Title: In silico approach to tackling viral and bacterial diseases Show/Hide Abstract Physics-based molecular modeling and simulations have recently led to numerous applications, including the design of new drugs and enzymes. The emergence of the COVID-19 pandemic has brought interdisciplinary biomedical researchers together at an unprecedented level, and computational techniques have played a crucial role in understanding and tackling the disease. These include structure determination and exploring molecular mechanisms as well as identifying therapeutic and vaccine candidates. In this talk, I will discuss a few projects in my lab focusing on viral and bacterial diseases, including computational investigations of cell attachment and immune evasion by SARS-CoV-2 variants, matrix protein-plasma membrane interactions in viral assembly and budding of filoviruses and paramyxoviruses, and designing novel antimicrobial compounds to confront the threat of antimicrobial resistance.
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Abstract Number: ANPA2022_0162 Presenting Author: Bhim M Adhikari Presenter's Affiliation: MPRC, University of Maryland School of Medicine, Baltimore, USA Title: Brief overview of neuroimaging methods in brain functions and dysfunctions Show/Hide Abstract The human brain, a complex dynamical system, consists of highly interconnected neurons, its behaviors relating to brain functions and dysfunctions can be described by the physics of network phenomena. Neuronal interactions and synchrony of neuronal oscillations are central to normal brain functions. Breakdowns in interaction patterns and modifications in synchronization behaviors are the hallmarks of brain dysfunctions. In this talk, the speaker plans to provide a brief overview of some of the neuroimaging techniques that are widely used for measuring brain activities during various tasks or at rest. In addition, a brief summary on Enhancing NeuroImaging Genetics through Meta-Analysis Consortium, studying the human brain in health and disease will be provided.
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Abstract Number: ANPA2022_0163 Presenting Author: BISHAL PANTHI Presenter's Affiliation: KATHMANDU MODEL COLLEGE Title: Using Nobel Metal Nanoparticles for S protein Modification in Coronavirus treatment: An approach from Quantum Mechanical Study Show/Hide Abstract In response to the recent outbreak of COVID-19, scientists have been devoted to find discover and efficient treatment to tackle the virus such as mRNA vaccines. Although contemporary methods of combating COVID-19 such as vaccinations and social distancing had been effective methods, the evolution of new variants had continuously posed threat to the world. To overcome and tackle those challenges, more in-depth understanding of the SARS-C0V-2 virus is highly needed.
METHOD:
By using the quantum mechanical method through the density functional theory (DFT), we are able to efficiently monitor the reactions between virus and the noble metal nanoparticles as the potential curing treatments for the COVID-19. Therefore, theoretical explorations in this field will be significant for supplying key information for future curing methods. In this project, I have carried out quantum mechanical based theoretical calculations to investigate the interactions between noble metal nanoparticles and the S proteins. In this project, I have carried out quantum mechanical based theoretical calculations to investigate the interactions between noble metal nanoparticles and the S proteins. During the project, I will try several different noble metals including Au, Ag, Cu, Pt, and Pd, etc to interact with the S protein. For the proteins with extremely complicated structures and functional groups, I will focus on several key fragments of S protein. This project will reveal the interactions between the S protein fragments and noble metal nanoparticles regarding the binding strength, electronic structures, and stability of the fragments, etc.
RESULT:
As the COVID-19 situation still developing in all countries, more efficient treatments should be developed alongside traditional vaccination developments. To disfunction the SARS-CoV-2 virus in the human body, we propose using the noble metal to disfunction the key S protein. In previous study on treatments for Alzheimer�s disease, metal NPs have been found to modify proteins and induce disfunction. Therefore, we also expect that such a strategy is also effective for the SARS-CoV-2 virus. However, owing to the high risks of the virus, the theoretical investigations are of great significance to perform preliminary studies of the potential interactions between Au and proteins. This strategy not only can lower the biomedical risks of COVID-19 but also save the large experiment time costs to find out the most possible candidates.
Keywords: COVID-19, S protein Modification, Noble Metal Nanoparticle, Quantum Mechanics, Density Functional Theory
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Abstract Number: ANPA2022_0164 Presenting Author: Bidhya Thapa Presenter's Affiliation: Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu, Nepal. Title: Investigating Kaiso-Nuclear Co-repressor (N-CoR) Protein-Protein Interactions Using Molecular Simulations Show/Hide Abstract Zinc finger (ZF) protein Kaiso mediates the transcription repression by recruiting the nuclear co-repressor (N-CoR) complex through its N-ternimal BTB/POZ domain. The investigation of molecular mechanism of Kaiso binding to N-CoR protein is helpful to understand the role of Kaiso in the transcription repression process. A detailed study on the molecular mechanism of the interaction of Kaiso with N-CoR complex is still lacking despite some prior studies on this system. In this work, we first modeled the Kaiso (BTB/POZ domain)-NCoR complex using molecular docking and then utilized molecular dynamics (MD) simulation to investigate the structural features of Kaiso-NCoR interactions. Our MD simulation results show the complex between Kaiso and N-CoR is stable for 600 ns of simulation time as revealed by RMSD measurements. In addition, we identified the major interacting residues responsible for binding of the two proteins. Since the POZ domain of Kaiso is highly hydrophobic, the hydrophobic interaction plays an important role in the binding of Kaiso with N-CoR. We explored binding interactions such as formation of salt bridges and hydrogen bonding that are responsible for the Kaiso-NCoR complex formation.
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