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Articles 1 - 30 of 115
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Repositioning Propranolol To Block Mitogenic Signaling In Breast Cancer, Alexa Noel Montoya
Repositioning Propranolol To Block Mitogenic Signaling In Breast Cancer, Alexa Noel Montoya
Open Access Theses & Dissertations
Breast cancer is the second most diagnosed cancer among women and is about 30% of all new cases of female cancers each year. It is projected that 1 in 8 every U.S. woman (about 13%) develop invasive breast cancer over the course of her lifetime. While advances in cancer research have made it possible to elucidate several breast cancer genomic subtypes, and develop new novel therapies, many of these agents are associated with significant toxicity, as well as high costs. A retrospective cross-sectional study of 404 breast cancer patients was performed to determine the effect of β-blocker usage on tumor …
Interfacial Interactions Between Engineered Nanoplastics And Biological Systems: Towards An Atomic And Molecular Understanding Of Plastics- Driven Cellular Dyshomeostasis, Afroz Karim
Open Access Theses & Dissertations
The persistent presence of micro (nano) plastics in our environment has raised concerns regarding potential health risks associated with human exposure. With the extensive use of plastic materials and the widespread consumption of plastic-contaminated food items, two types of microplastics, polystyrene (PS) and polymethylmethacrylate (PMMA), have attracted increased attention. While the adverse effects of microplastics on animals and marine life have been extensively studied, their potential impact on human health remains largely unexplored. Specifically, the interaction between microplastics and biomolecules within the human body and their effect on human health have yet to be comprehensively investigated. This dissertation study focuses …
Functional Characterization Of The Human And Murine Schlafen Family Group Iii, Carlos A. Valenzuela
Functional Characterization Of The Human And Murine Schlafen Family Group Iii, Carlos A. Valenzuela
Open Access Theses & Dissertations
The Schlafen (SLFN) family of proteins are known for being encoded by interferon stimulated genes. The family is divided into three groups (I, II, III), for which the largest in size belong to the subgroup III. In humans, group III has the most members (SLFN5, SLFN11, SLFN13 and SLFN14); there is no member of group I and only one member of group II (SLFN12). All human SLFNs belonging to group III have been reported to impair viral protein expression or infection across a variety of viruses. The antiviral function is mediated in SLFN11 and SLFN13 by their tRNase activity, and …
X-Ray Crystal Structure Of E399q,E708q Ecm16 Double Mutant, Gileydis Guillama
X-Ray Crystal Structure Of E399q,E708q Ecm16 Double Mutant, Gileydis Guillama
Open Access Theses & Dissertations
The use of antibiotics has undoubtedly been a boon for humanity in combating infections and microbial threats. However, their widespread utilization has contributed to the emergence and spread of antibiotic resistance, which now poses a significant public health challenge. Streptomyces bacterium, produce diverse secondary metabolites with antibacterial, antifungal, antiviral, antitumoral, and immunosuppressant activities. Among these compounds is echinomycin, a nonribosomal peptide antibiotic synthesized by Streptomyces lasalocidi, which inhibits DNA replication and transcription by intercalating the DNA duplex at CpG steps. A gene called ecm16 was identified in the echinomycin biosynthetic gene cluster, which provides echinomycin self-resistance. Ecm16 recognizes DNA duplexes …
Structural Study Of Lsd13 And Lsd14 Type I Modular Polyketide Synthases From The Lasalocid A Biosynthesis Pathway, Dayan Viera
Structural Study Of Lsd13 And Lsd14 Type I Modular Polyketide Synthases From The Lasalocid A Biosynthesis Pathway, Dayan Viera
Open Access Theses & Dissertations
Bioactive natural products often possess a complex structure and have a large size which make their chemical synthesis highly challenging. To overcome this challenge, we are developing a biosynthetic method for production of natural products and their analogs. This technology is expected to decrease the synthesis time from years to weeks and reduce the cost of drug production by multiple orders of magnitude. We are investigating the biosynthesis pathway of lasalocid A, an anticancer antibiotic, to develop this technology. Specifically, we aim to characterize the enzymes structurally and biochemically in this pathway, thus paving the way for their rational engineering. …
Functional Analysis Of The Gamma-Aminobutyric Acid Type A Receptor Subunit Alpha-1 (Gabra1) Gene During Zebrafish Development., Nayeli Gabriela Reyes-Nava
Functional Analysis Of The Gamma-Aminobutyric Acid Type A Receptor Subunit Alpha-1 (Gabra1) Gene During Zebrafish Development., Nayeli Gabriela Reyes-Nava
Open Access Theses & Dissertations
The GABRA1 gene encodes for the alpha-1 (α1) subunit of the Gamma-Aminobutyric acid type A receptor (GABAAR), which are the primary modulators of synaptic inhibition in the central nervous system (CNS). Alpha-1 subunits are essential for maintaining the normal function of native receptors and contribute to over 60% of all GABAARs in the CNS. Remarkably, a broad spectrum of neurodevelopmental and epilepsy-associated disorders have been linked with mutations in the GABRA1 gene. However, the developmental, behavioral, and molecular mechanisms underlying GABRA1-associated epileptic disorders remain to be fully understood. Hence, the overarching goal of this dissertation is to investigate the behavioral …
Analysis Of The Electrostatic Characteristics Of The Zika Virus Capsid Using Computational Methods, Cassandra Guadalupe Del Rio De Avila
Analysis Of The Electrostatic Characteristics Of The Zika Virus Capsid Using Computational Methods, Cassandra Guadalupe Del Rio De Avila
Open Access Theses & Dissertations
Zika virus (ZIKV) is a flavivirus that is usually transmitted through the bite of infected mosquitoes. This virus can cause a variety of neurological disorders, the most common being Guillain-Barré syndrome in adults. Moreover, it is of great concern in pregnant women, since can cause deformities in the brain and other organs of newborns.Studying the structural characteristics of the virus during its mature and infectious phase can provide crucial information on the mechanisms by which it enters and replicates within host cells, as well as its evolution, transmission, and interaction with other living organisms. The symmetric pattern present in the …
Microscopic And Spectroscopic Analysis Of Nordihydroguaiaretic Acid Effect On Astrocytes, Lizbeth Vanessa Martinez Lopez
Microscopic And Spectroscopic Analysis Of Nordihydroguaiaretic Acid Effect On Astrocytes, Lizbeth Vanessa Martinez Lopez
Open Access Theses & Dissertations
Astrocytes, one of the most abundant cell components in the central nervous system (CNS), have been a research target in the last few years. Several studies have found that astrocytes are not only mere supporters of neurons but also of essential processes developed in the CNS. Their malfunction could induce neurodegenerative diseases and brain tumors. Thus, further understanding of astrocytes and their role is of high interest to develop possible new treatments and methods of disease diagnosis, especially in brain cancer. The plant Larrea tridentata (La Gobernadora in Mexico or Creosote bush in the United States) is known to have …
Developing And Applying Computational Methods On Biomolecules, Shengjie Sun
Developing And Applying Computational Methods On Biomolecules, Shengjie Sun
Open Access Theses & Dissertations
Computational biophysics is an interdisciplinary subject that uses numerical algorithms to study the physical principles underlying biological phenomena and processes. Electrostatic interactions play an important role in computational molecular biophysics and their potential impact on disease mechanisms. At distances larger than several Angstroms, electrostatic interactions dominate all other forces, while the alteration of short-range electrostatic pairwise interactions can also have significant effects. The dual nature of electrostatic interactions, being dominant at long-range and specific at short-range, underscores their profound implications for wild-type structure and function. Any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could …
Exploring The Anticancer Mechanism Of Thienopyrazole Derivative Tpz-1 In Acute Myeloid Leukemia, Jessica Dyanne Hess
Exploring The Anticancer Mechanism Of Thienopyrazole Derivative Tpz-1 In Acute Myeloid Leukemia, Jessica Dyanne Hess
Open Access Theses & Dissertations
Anticancer drug discovery is a time and resource-consuming process for which exceedingly reliable and efficient modern approaches are needed. Phenotypic drug screenings can generate highly potent and innovative drug candidates; however, deconvolution of the drugâ??s target often presents significant barriers to drug development. To overcome this hurdle, we have originally combined in vitro and in silico analyses to uncover the molecular mechanism(s) driving the anticancer activity of the uniquely structured small molecule drug candidate, Tpz-1. Our study revealed that Tpz-1 is a multitargeted agent which induces the programmed death of HL-60 acute myeloid leukemia cells primarily through disruption of microtubule …
Development Of A Ph-Triggered Cargo Delivery System With Esxa Mutants, Shuchen Chen
Development Of A Ph-Triggered Cargo Delivery System With Esxa Mutants, Shuchen Chen
Open Access Theses & Dissertations
Tuberculosis (TB) is a communicable disease caused by Mycobacterium tuberculosis (Mtb). It was the leading cause of human death generated by a single infectious agent before the Coronavirus (COVID-19) pandemic. Mtb has a special mechanism to evade the hostâ??s immune system and utilize macrophages as reservoirs. Latent TB infections have been a threat to public health. Liposome has been widely used for drug delivery. Immunoliposomes are special liposome carriers coated with ligands, such as antigens, targeting certain cells or organs to regulate the uptake of liposome. By constructing the liposome components, or surface modification, cargo release of liposome can be …
Eluication Of Lipid Metabolic Pathways In Differentiating Giardia Lamblia Using High Resolution Mass Spectrometry, Cameron Ellis
Eluication Of Lipid Metabolic Pathways In Differentiating Giardia Lamblia Using High Resolution Mass Spectrometry, Cameron Ellis
Open Access Theses & Dissertations
Giardia lamblia is an intestinal protozoan found worldwide, including the U.S. This parasite exists in two morphologic stages - a replicative trophozoite and a relatively dormant yet viable cyst. While exposures of cysts to gastric acid during passage through the human stomach induces excystation, factors in the small intestine, where trophozoites colonize trigger encystation or cyst formation. Transformation into cyst stage is essential for Giardia to survive in the environment for months before infecting new hosts. Because of its small genome size (11.7 Mb), metabolic pathways in Giardia are highly reduced. As far as lipid metabolism is concerned, only limited …
Characterization Of Esxa/Esxb Heterodimer Membrane Interaction With A Novel Popc/Popg Liposome Model, Salvador Vazquez Vazquez Reyes
Characterization Of Esxa/Esxb Heterodimer Membrane Interaction With A Novel Popc/Popg Liposome Model, Salvador Vazquez Vazquez Reyes
Open Access Theses & Dissertations
EsxA and EsxB are co-secreted as a heterodimer and have been shown to play critical roles in phagosome rupture and translocation of Mycobacterium tuberculosis into the cytosol. Current in vitro studies support a model in which the EsxA:EsxB heterodimer is dissociated upon acidification, which might allow EsxA insertion into liposome membranes. While the membrane permeabilizing activity (MPA) of EsxA has been well characterized in liposomes composed of di-oleoyl-phosphatidylcholine (DOPC), the MPA of EsxA:EsxB heterodimer has not been detected with the DOPC liposome. In this study, we established a new in vitro membrane assay to test the MPA of EsxA and …
Utilizing Computational Methods To Study The Biomolecules, Wenhan Guo
Utilizing Computational Methods To Study The Biomolecules, Wenhan Guo
Open Access Theses & Dissertations
COVID-19 is increasingly affecting human health and global economy. Understanding the fundamental mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is highly demanded to develop treatments for COVID-19. SARS-CoV and SARS-CoV-2 share 92.06% identity in their N protein RBDs' sequences, which results in very similar structures. However, the SARS-CoV-2 is more easily to spread. Utilizing multi-scale computational approaches, this work studied the fundamental mechanisms of the nucleocapsid (N) proteins of SARS-CoV and SARS-CoV-2, including their stabilities and binding strengths with RNAs at different pH values. Electrostatic potential on the surfaces of N proteins show that both the N proteins …
Regulation Of C-C Chemokine Receptor 7 (Ccr7) Ligand-Mediated Internalization And Chemotaxis By G Protein-Coupled Receptor Kinase Family 4 (Grk-4, 5, 6) In Human Pediatric T-Cell Acute Lymphoblastic Leukemia (T-All), Eduardo Elias Chaib
Open Access Theses & Dissertations
Background and Significance: The Hispanic population is disproportionally affected by T-ALL (T-cell acute lymphoblastic leukemia) when compared to other races in the US. C-C Chemokine Receptor 7 (CCR7) in T-ALL is used during disease progression, and may lead to migration of cancerous cells into the Central Nervous System (CNS) of patients. Goals and Objectives: This project aims to find relevant rates and risk factors for T-ALL for the Hispanic population in the US/Mexico border region. The other aim is to assess the effect of the G protein-coupled Receptor Kinase 4 (GRK-4) family proteins on migration and receptor internalization through CCR7 …
Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda
Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda
Open Access Theses & Dissertations
Giardia lamblia, a protozoan parasite, is a major cause of waterborne infection, worldwide. While the trophozoite form of this parasite induces pathological symptoms in the gut, the cyst forms transmit the infection via contaminated water. Since Giardia is a non-invasive parasite, the actual mechanism by which it causes infection remains elusive. We have previously reported that Giardia assembles cholesterol and GM1 glycolipid-enriched lipid rafts (LRs) that participate in encystation and cyst production. To further delineate the role of LRs in pathogenesis, we isolated LRs from Giardia and subjected them to proteomic analysis. Various cellular proteins including the virulent proteinsâe.g., giardins, …
Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie
Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie
Open Access Theses & Dissertations
Computational biology is an interdisciplinary area that applies computational approaches in biological big data, including protein amino acid sequences, genetic sequences, etc., which is widely used to analyze protein-protein interactions, make predictions in drug discovery, develop vaccines, etc. Popular methods include mathematical modeling, molecular dynamics simulations, data science mythology, etc. With the help of computational algorithms and applications, drug development is much faster than traditional processes, as it reduces risks early on in a drug discovery process and helps researchers select target candidates that have the highest potential for success. In my doctoral research, I applied multi-scale computational approaches to …
Nanotechnology-Based Approaches To Mitigate Environmental Pollutants -- Induced Neurological Disorders, Jyoti Ahlawat
Nanotechnology-Based Approaches To Mitigate Environmental Pollutants -- Induced Neurological Disorders, Jyoti Ahlawat
Open Access Theses & Dissertations
Neurodegenerative diseases such as Parkinson's disease (PD), Alzheimerâ??s Disease (AD) and Huntingtonâ??s Disease (HD) have no cure despite intensive research efforts geared towards therapeutics development. In the USA, patients with PD and AD alone cost the nation ~ $200 billion annually in patient care and lost productivity. Therefore, there remains an urgent and unmet need to develop novel drugs and drug carriers with the potential to slow down, halt and ideally reverse the course of neurodegenerative disorders. The dissertation focuses on developing approaches towards targeting PD using multifactorial mechanisms including the targeting of protein aggregation and oxidative stress. This is …
Small Heat Shock Protein 27 And Its Role In Human Disease, Bianka Andrea Holguin
Small Heat Shock Protein 27 And Its Role In Human Disease, Bianka Andrea Holguin
Open Access Theses & Dissertations
Small heat shock protein 27 (Hsp27) is a ubiquitously expressed molecular chaperone with roles in many physiological processes. As an ATP-independent molecular chaperone, Hsp27 protects substrates from irreversible aggregation and holds them in a folding competent state for later recycling into the proteome. Hsp27 proteins form dimers that are assembled into large oligomeric complexes. Phosphorylation of Hsp27 dissembles the oligomers into chaperone active dimers. Several missense mutations of Hsp27 are causative for the neurodegenerative disorders Charcot-Marie-Tooth disease 2F and distal Hereditary Motor Neuropathy IIB. Here I show that the oligomerization and chaperoning ability of Hsp27 are altered by the Hsp27 …
The Electrostatic Features Of Dengue Virus Capsid Assembly, Alan Eduardo Lopez Hernandez
The Electrostatic Features Of Dengue Virus Capsid Assembly, Alan Eduardo Lopez Hernandez
Open Access Theses & Dissertations
Dengue virus causes serious diseases and considerable deaths each year all around the globe. Dengue virus undergoes assembly in a capsid, matures and becomes viral. Revealing mechanisms of the viral capsid protein may lead to the discovery of novel drugs that prevent this assembly to happen and stop the virus from spreading. Here I present a computational work which is focused on the stability and assembly of the dengue viral capsid. The E and M proteins conform a heterotetramer, which consists of two copies of E and M proteins. The heterotetramers form a highly ordered capsid. In the electrostatic analysis …
Structural And Biochemical Studies On Disease Associated Proteins: Heat Shock Protein 60 And Hiv Capsid, Alejandro Rodriguez
Structural And Biochemical Studies On Disease Associated Proteins: Heat Shock Protein 60 And Hiv Capsid, Alejandro Rodriguez
Open Access Theses & Dissertations
Structural studies on proteins provide valuable knowledge, from information about their fundamental nature, to laying a foundation for rational drug design. Here, we study two proteins, a human mitochondrial chaperonin heat shock protein 60 (Hsp60) and the main structural HIV-1 protein capsid (CA). We focus on the structural nature of both proteins to try to understand their role in disease and elucidate the mechanism of potential drug treatments. Hsp60 is a chaperonin found in human mitochondria that is responsible for assisting client proteins reach their native, functional, state. The mechanism by which it catalyzes protein folding, however, has not been …
Utilizing Computational Approaches To Study Tubulin- Tubulin Electrostatic Interactions, Tolulope Ayodeji Ale
Utilizing Computational Approaches To Study Tubulin- Tubulin Electrostatic Interactions, Tolulope Ayodeji Ale
Open Access Theses & Dissertations
Microtubules play significant roles in transporting cargos within the cell, as well as the cell cycle. They are essentially the highway for the transportation of cell organelles. Understanding the interactions among microtubule components is crucial for the treatment of neurodegenerative diseases and cancer. In this study, we utilize a series of computational approaches to study the electrostatic interactions at the binding interfaces of interacting tubulin monomers. Our study revealed that the electrostatic attractive interactions in the αβ tubulin dimer is the strongest while the interaction between two αβ tubulin dimers in the longitude direction is the weakest. The result identified …
In Vitro Investigation Of Tumor Selective Piperidones As Therapeutic Agents Against Leukemia Cancer Cells, Lisett Contreras
In Vitro Investigation Of Tumor Selective Piperidones As Therapeutic Agents Against Leukemia Cancer Cells, Lisett Contreras
Open Access Theses & Dissertations
Cancer is a continuous global health issue. It is the second leading cause of death behind heart disease. Disparities across the emergence of cancer and resulting fatalities raise the importance of researching the disease. Treatments are available for certain types of cancers. However, these are typically accompanied by residual problems including side effects and the possibility for relapse. Some treatments attack all cells, leading to unwarranted side effects that make the possibility of living a comfortable life nearly impossible. Other treatments are specific to certain genetic alterations, making them only useful for a small percentage of patients. Not one treatment …
Molecular Mechanism Of Dna Bisintercalator Antibiotic Resistance, Priyanka Rajendra Gade
Molecular Mechanism Of Dna Bisintercalator Antibiotic Resistance, Priyanka Rajendra Gade
Open Access Theses & Dissertations
Class II UvrA is an ATP-binding cassette protein and a homolog of class I UvrA, the DNA lesion detection component of the universal prokaryotic nucleotide excision repair system. We show that Ecm16, a class II UvrA protein from Streptomyces lasalocidi, specifically recognizes DNA duplex that contains the DNA bisintercalator antibiotic echinomycin. Heterologous expression of Ecm16 in Escherichia coli renders host cells resistant to echinomycin. Interestingly, Ecm16’s antibiotic resistance activity does not require the DNA repair proteins UvrA/B/C/D, indicating that it operates independently of the cell’s nucleotide excision repair pathway. Unlike UvrA, Ecm16 uses the insertion domain to regulate its ATPase …
In The Search For Novel Treatments For Chagas' Disease Using Cutting-Edge Imaging Technology, Karsten Dieter Amezcua Winter
In The Search For Novel Treatments For Chagas' Disease Using Cutting-Edge Imaging Technology, Karsten Dieter Amezcua Winter
Open Access Theses & Dissertations
Chagas disease (ChD) is caused by Trypanosoma cruzi (T. cruzi), an intracellular protozoan parasite. ChD has a global mortality of 15,000 annual deaths, and approximately, 8-10 million people are infected. There is growing concern in the United States as autochthonous cases of ChD have been reported in the southern region. The two available treatments are only partially effective and highly toxic. N-aroyl derivatives and α, β-unsaturated ketones have been previously tested against Leishmania, a closely related parasite, demonstrating selective toxicity towards the microorganism. The objective of this study is to evaluate a drug library consisting of 21 α, β-unsaturated ketones …
Pacific Black Duck Ecology And Habitat Assessment In Aunu'u, American Samoa, And Their Relationship To Other Mallard-Like Ducks Of Oceania, Greater Indonesia, And The Philippines, Marissa Kaminski
Open Access Theses & Dissertations
Determining a species’ ecological needs, assessing the quality of their habitat, and determining genetic differentiation and connectivity among populations is essential to their conservation. My dissertation focuses on obtaining such a holistic view for a population of Pacific Black Ducks recently established on the Island of Aunu’u, American Samoa. Specifically, I present the first evaluation of the ecology and habitat of a recently established population of Pacific Black Ducks on the Island of Aunu’u, American Samoa, in Chapter 1, while I assess the genetic connectivity and relationship of this population to other Mallard-like ducks found in Greater Indonesia, Oceania, and …
The Role Of Calcium Ions In Signaling And Regulation Of Efflux Pump Genes In Staphylococcus Aureus, Amy Rebecca Nava
The Role Of Calcium Ions In Signaling And Regulation Of Efflux Pump Genes In Staphylococcus Aureus, Amy Rebecca Nava
Open Access Theses & Dissertations
Calcium ions (Ca2+) play an important role in eukaryote cell signaling and regulation of physiological functions. Although evidence of a similar role for Ca2+ in prokaryotes has been difficult to demonstrate, there is mounting evidence that Ca2+ acts as a cell regulator in bacteria. The purpose of this study was to investigate Ca2+ signaling and the effect of Ca2+ on gene expression of various multidrug resistant (MDR) efflux pumps and their regulator MgrA in Staphylococcus aureus and clinically isolated MRSA. We hypothesized that the presence of Ca2+ increased gene expression of multidrug resistance pumps, LmrS, NorA, and the regulator, MgrA. …
Molecular And Cellular Characterizations Of Glucosylceramide Transferase (Synthase) In Giardia Lamblia, Vanessa Enriquez
Molecular And Cellular Characterizations Of Glucosylceramide Transferase (Synthase) In Giardia Lamblia, Vanessa Enriquez
Open Access Theses & Dissertations
Giardiasis, caused by an intestinal protozoan, Giardia lamblia, is a major public health problem worldwide. Giardia infection is spread through the fecal-oral route via contaminated water and food. It is estimated that over 280 million people are infected with Giardia across the globe. Giardia is a non-invasive parasite and consists of a two-stage life cycle: trophozoites and cysts. Ingested cysts undergo excystation in the proximal small intestine, releasing two trophozoites (excyzoites). Upon reaching the distal small intestine and colonizing there, trophozoites transform into cysts by encystation. It has been reported earlier that the process of encystation induced the synThesis of …
A Genomic Approach To Assessing The Fkbp52-Regulated Androgen Receptor Cistrome And Transcriptome, Nina Raquelle Ortiz
A Genomic Approach To Assessing The Fkbp52-Regulated Androgen Receptor Cistrome And Transcriptome, Nina Raquelle Ortiz
Open Access Theses & Dissertations
Androgen receptor (AR)-regulated genes contribute to the initiation and progression of prostate cancer. Receptor signaling persists and plays a pivotal role in late-stages of the disease, for which there is currently no treatment. Thus, there is a need to understand the mechanisms regulating AR function as a means to identify drug targets for potential therapeutics. The FKBP52 cochaperone has emerged in recent years as a regulator of AR activity that is functionally linked in the AR signaling pathway. FKBP52 is a known positive regulator of AR and believed to interact with AR at its binding function 3 surface (BF3), a …
The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun
The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun
Open Access Theses & Dissertations
Fast and accurate calculations of the electrostatic features for highly charged biomolecules such as DNA, RNA, highly charged proteins, are crucial but challenging tasks. Traditional implicit solvent methods calculate the electrostatic features fast, but they are not able to balance the high net charges in the biomolecules effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we developed a novel method, the Hybridizing Ions Treatment (HIT) method, which hybridizes the implicit solvent method with the explicit method to realistically calculate the electrostatic potential for highly …