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Articles 1 - 30 of 72

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese May 2019

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese

MSU Graduate Theses

Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered ...


Automatic 13C Chemical Shift Reference Correction Of Protein Nmr Spectral Data Using Data Mining And Bayesian Statistical Modeling, Xi Chen Jan 2019

Automatic 13C Chemical Shift Reference Correction Of Protein Nmr Spectral Data Using Data Mining And Bayesian Statistical Modeling, Xi Chen

Theses and Dissertations--Molecular and Cellular Biochemistry

Nuclear magnetic resonance (NMR) is a highly versatile analytical technique for studying molecular configuration, conformation, and dynamics, especially of biomacromolecules such as proteins. However, due to the intrinsic properties of NMR experiments, results from the NMR instruments require a refencing step before the down-the-line analysis. Poor chemical shift referencing, especially for 13C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR. There is no available method that can rereference carbon chemical shifts from protein NMR without secondary experimental information such as structure or resonance assignment.

To solve this problem, we ...


The Molecular Basis Of Rna Recognition And Transcriptional Regulation By Fus And Prc2, Xueyin Wang Aug 2018

The Molecular Basis Of Rna Recognition And Transcriptional Regulation By Fus And Prc2, Xueyin Wang

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

RNA and protein interact with each other in the cell nucleus to form RNP (ribonucleoprotein) complexes. These RNPs play key roles in various steps of gene expression. This thesis focuses on two nuclear RNA-binding proteins: Fused in Sarcoma (FUS) and Polycomb Repressive Complex 2 (PRC2).

The normal functions of FUS are not fully understood, but RNA binding has been suggested to be crucial for FUS function and many RNA targets have been identified. Yet the features of RNAs necessary for FUS binding had not been systematically characterized. FUS bound all five published RNA motifs and other RNAs tightly, including fragments ...


The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn Aug 2018

The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn

Electronic Theses and Dissertations

Protein, DNA, and RNA methyltransferases have an ever-expanding list of novel substrates and catalytic activities. Even within families and between homologs, it is becoming clear the intricacies of methyltransferase specificity and regulation are far more diverse than originally thought. In addition to specific substrates and distinct methylation levels, methyltransferase activity can be altered through formation of complexes with close homologs. This work involves the N-terminal methyltransferase homologs NRMT1 and NRMT2. NRMT1 is a ubiquitously expressed distributive trimethylase. NRMT2 is a monomethylase expressed at low levels and in a tissue-specific manner. They are both nuclear methyltransferases with overlapping target consensus sequences ...


Detrital Protein Contributes To Oyster Nutrition And Growth In The Damariscotta Estuary, Maine, Usa, Cheyenne M. Adams May 2018

Detrital Protein Contributes To Oyster Nutrition And Growth In The Damariscotta Estuary, Maine, Usa, Cheyenne M. Adams

Electronic Theses and Dissertations

Oyster aquaculture is an expanding industry that relies on identifying and utilizing natural estuarine conditions for the economically viable production of a filter-feeding crop. The eastern oyster, Crassostrea virginica, is the principal species currently cultured in Maine. In addition to preferentially consumed phytoplankton, various detrital complexes (non-algal and/or non-living organic matter) may provide some nutrition to C. virginica between times of phytoplankton abundance. Here I investigated the importance of detrital proteins in supporting the growth of oysters cultured in the upper Damariscotta Estuary. Oyster aquaculture in this area is highly successful and previous reports indicate that labile detrital protein ...


Higher-Order Organization Principles Of Pre-Translational Mrnps, Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, Melissa J. Moore Mar 2018

Higher-Order Organization Principles Of Pre-Translational Mrnps, Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, Melissa J. Moore

University of Massachusetts Medical School Faculty Publications

Compared to noncoding RNAs (ncRNAs) such as rRNAs and ribozymes, for which high resolution structures abound, little is known about the tertiary structures of mRNAs. In eukaryotic cells, newly made mRNAs are packaged with proteins in highly compacted mRNPs, but the manner of this mRNA compaction is unknown. Here we developed and implemented RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem), a transcriptome-wide method for probing the 3D conformations of RNAs stably-associated with defined proteins, in this case exon junction complex (EJC) core factors. EJCs multimerize with other mRNP components to form megadalton sized complexes that protect large swaths of ...


Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman Jan 2018

Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman

Electronic Theses and Dissertations

Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using ...


An Investigation Of Atomic Structures Derived From X-Ray Crystallography And Cryo-Electron Microscopy Using Distal Blocks Of Side-Chains, Lin Chen, Jing He, Salim Sazzed, Rayshawn Walker Jan 2018

An Investigation Of Atomic Structures Derived From X-Ray Crystallography And Cryo-Electron Microscopy Using Distal Blocks Of Side-Chains, Lin Chen, Jing He, Salim Sazzed, Rayshawn Walker

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2-4 Å resolutions. The results show that the normalized probability density function of ...


Analysis Of Rice Grain Protein Composition In The Context Of Rice Grain Quality, Jeanette D. Lescano-Balindong Jan 2018

Analysis Of Rice Grain Protein Composition In The Context Of Rice Grain Quality, Jeanette D. Lescano-Balindong

Theses

Protein (composed of prolamin, glutelin, globulin and albumin) is the second most abundant component in the milled rice grain. It has very diverse properties that may contribute to rice grain quality. Rice grain protein extraction and high-performance liquid chromatography methods were developed and applied into different sets of short, medium and long grain advanced breeding lines. Rice prolamin and albumin were extracted with 60% n-propanol, while the glutelin and globulin were extracted with 5M acetic acid. Analyses of protein extracts revealed differences in rice grain storage protein composition which were associated with rice grain texture and head rice yield.


Registration And Grouping Algorithms In Protein Nmr Derived Peak Lists And Their Application In Protein Nmr Reference Correction, Andrey Smelter, Xi Chen, Eric C. Rouchka, Hunter N. B. Moseley Oct 2017

Registration And Grouping Algorithms In Protein Nmr Derived Peak Lists And Their Application In Protein Nmr Reference Correction, Andrey Smelter, Xi Chen, Eric C. Rouchka, Hunter N. B. Moseley

Commonwealth Computational Summit

Nuclear magnetic resonance spectroscopy of proteins (protein NMR) is a powerful analytical technique for studying structure and dynamics of proteins. Almost all aspects of protein NMR have been accelerated by the development of software tools that enable the analysis of NMR spectral data and its utilization in studying protein structure and dynamics. This includes software for raw NMR processing, spectral visualization, protein resonance assignment, and structure determination. However, full automation of protein NMR data analysis is still a work in progress and data analysis still requires an expert NMR spectroscopist utilizing an array of software tools.

While manual resonance assignment ...


Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz Jul 2017

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz

CSE Journal Articles

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too. With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within ...


Caveolin Binding Motif Mutation Yields A Variance In Follicle Stimulating Hormone Receptor Signaling, Justin Fleischer Jun 2017

Caveolin Binding Motif Mutation Yields A Variance In Follicle Stimulating Hormone Receptor Signaling, Justin Fleischer

Honors Theses

The human follicle stimulating hormone receptor (hFSHR) is a glycoprotein hormone receptor belonging to the g protein-coupled receptor family. It is important in both male and female reproductive processes; defects in hFSHR can lead to infertility, delayed puberty, reduced muscle bulk, and osteoporosis. Work in other labs has shown that GPCRs can be localized to microdomains located within the cell membrane called lipid rafts. These regions are highly resistant to detergents because of the high concentration of sphingolipids and cholesterol. Also within these domains, an intracellular protein, caveolin, is present. Our lab has shown that hFSHR also localizes to lipid ...


Studies Into The Structure And Function Of Various Domains Of Obscurin And Titin, Rachel A. Policke May 2017

Studies Into The Structure And Function Of Various Domains Of Obscurin And Titin, Rachel A. Policke

Senior Honors Projects, 2010-current

Muscles give our bodies the ability to move by stretching and contracting. While contraction is accomplished by the well-known actin-myosin interaction, not much is known about stretch. Two integral muscle proteins involved in stretch are titin and obscurin; both are long rope-like protein molecules that seem to act as molecular springs. Mutations in these two proteins can lead to diseases such as hypertrophic cardiomyopathy and muscular dystrophy, as well as a variety of cancers. In an effort to understand muscle stretch and signaling on a more fundamental level, here we present the high resolution structure of obscurin Ig59, a domain ...


Protocols And Pitfalls In Obtaining Fatty Acid-Binding Proteins For Biophysical Studies Of Ligand-Protein And Protein-Protein Interactions, Qian Wang, Samar Rizk, Cédric Bernard, May Poh Lai, David Kam, Judith Storch, Ruth E. Stark May 2017

Protocols And Pitfalls In Obtaining Fatty Acid-Binding Proteins For Biophysical Studies Of Ligand-Protein And Protein-Protein Interactions, Qian Wang, Samar Rizk, Cédric Bernard, May Poh Lai, David Kam, Judith Storch, Ruth E. Stark

Publications and Research

Adipocyte fatty acid-binding protein (AFABP: FABP4) is a member of the intracellular lipid-binding protein family that is thought to target long-chain fatty acids to nuclear receptors such as peroxisome proliferatoractivated receptor gamma (PPARγ), which in turn plays roles in insulin resistance and obesity. A molecular understanding of AFABP function requires robust isolation of the protein in liganded and free forms as well as characterization of its oligomerization state(s) under physiological conditions. We report development of a protocol to optimize the production of members of this protein family in pure form, including removal of their bound lipids by mixing with ...


Thylakoid Protein Targeting/Insertion By A Signal Recognition Particle In Chloroplasts, Priyanka Sharma May 2017

Thylakoid Protein Targeting/Insertion By A Signal Recognition Particle In Chloroplasts, Priyanka Sharma

Theses and Dissertations

Protein targeting is a fundamental cellular process that directs proteins from their site of synthesis to the site where they function. The signal recognition particle (SRP) dependent targeting pathway is conserved in both eukaryotes and prokaryotes where it co-translationally targets polypeptide chains emerging from ribosomes to the endoplasmic reticulum (eukaryotes) or cytoplasmic membrane (prokaryotes). A structurally unique form of SRP is found in chloroplasts where it functions to post-translationally bind and target a subset of integral thylakoid membrane proteins, the light harvesting chlorophyll binding proteins (LHCPs). Mature LHCPs bind chlorophyll a/b and function in photosynthetic light capture. Like many ...


Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver Apr 2017

Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver

Chemistry Honors Papers

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination ...


Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta Mar 2017

Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ticks secrete several anti-hemostatic factors in their saliva to suppress the host innate and acquired immune defenses against infestations. Using Ixodes scapularis ticks and age-matched mice purchased from two independent commercial vendors with two different immune backgrounds as a model, we show that ticks fed on immunodeficient animals demonstrate decreased fibrinogenolytic activity in comparison to ticks fed on immunocompetent animals. Reduced levels of D-dimer (fibrin degradation product) were evident in ticks fed on immunodeficient animals in comparison to ticks fed on immunocompetent animals. Increased engorgement weights were noted for ticks fed on immunodeficient animals in comparison to ticks fed on ...


Neuronal Gq Structures In Neurodegeneration, Damian S. Mcaninch Jan 2017

Neuronal Gq Structures In Neurodegeneration, Damian S. Mcaninch

Electronic Theses and Dissertations

This study investigates protein nucleic acid interactions between various proteins and G quadruplex (GQ) forming messenger RNAs (mRNAs) in human neurological disorders. GQ structures are formed in DNA/RNA, when four guanine residues form planar tetrads stabilized by Hoogsteen base pairing, that stack forming a GQ structure stabilized by potassium ions. These GQ structures are targeted by the arginine-glycine-glycine (RGG) repeat domain containing RNA-binding domain.

Three RGG domain containing RNA-binding proteins, all of which have been implicated in neurological disorders, and their interactions with GQ forming mRNAs, were investigated in this study: fused in sarcoma (FUS), fragile X mental retardation ...


Elucidating Structure, Function, And Small Molecular Interactions Of Human Immunodeficiency Virus And Chikungunya Virus, Kristin Nicole Slater Jan 2017

Elucidating Structure, Function, And Small Molecular Interactions Of Human Immunodeficiency Virus And Chikungunya Virus, Kristin Nicole Slater

Wayne State University Theses

Abstract HIV-1:

Human immunodeficiency virus-1 (HIV-1) is a widespread, incurable retrovirus known to cause

immunodeficiency and a shortened life span. Despite successful treatment methods, HIV-1

frequently mutates, resulting in antiviral resistance. Many therapies target the HIV-1 protease

(PR), which is responsible for cleaving the viral polyprotein essential for its life cycle. HIV-1 PR

often evades treatment by way of mutations and less commonly through residue insertions. We

have identified a clinical isolate with a five residue insertion between residues 28 and 29.

Through molecular dynamics simulations we analyzed the protease protein structure and

determined that the residue insertion created a ...


An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He Jan 2017

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He

Computer Science Faculty Publications

A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from alpha-proteins and ...


Toward A Mechanistic Understanding Of Outer Membrane Protein Biogenesis, Alex Hunt Hopkins Jan 2017

Toward A Mechanistic Understanding Of Outer Membrane Protein Biogenesis, Alex Hunt Hopkins

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The outer membranes of Gram-negative bacteria are essential to their survival and have a unique asymmetric structure that features an outer leaflet of lipopolysaccharide. Bacterial outer membranes are populated by integral membrane proteins with amphipathic transmembrane β-barrel domains called outer membrane proteins (OMPs). OMPs are translated in the cytoplasm and translocated across the inner membrane and periplasm before being inserted into the outer membrane. The β-barrel Assembly Machine (BAM), a hetero-pentameric protein complex at the outer membrane, recognizes, folds, and releases OMPs into the membrane. However, the functional contributions of individual BAM subunits, the architecture of the BAM, and the ...


The Functions Of The Cid And Lrg Operons In S. Aureus Programmed Cell Death, Xinyan Zhang Dec 2016

The Functions Of The Cid And Lrg Operons In S. Aureus Programmed Cell Death, Xinyan Zhang

Theses & Dissertations

Staphylococcus aureus cid/lrg operons regulate the formation of S.aureus biofilm formation and programmed cell death based on previous in vivo work done in Dr. Bayles's lab. cid operon, which encodes CidA/CidB/CidC proteins, has been shown to be an effector in leading to the lysis and death of the S.aureus; While lrg operon, encoding LrgA and LrgB proteins, is an inhibitor of the lysis and death. Recent studies suggest that CidA behaves like holin proteins from bacterial phage, by increasing the murein hydrolysis activity under aerobic culturing conditions. LrgA, together with LrgB, appears ...


Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas Jun 2016

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

All Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is ...


Protein Adsorption Using A Lattice Toy Model, Ari J. Weiland May 2016

Protein Adsorption Using A Lattice Toy Model, Ari J. Weiland

Macalester Journal of Physics and Astronomy

Protein adsorption is an important subfield of Biophysics particularly relevant in medical science. Using a computational simulation with a basic but configurable two-dimensional square lattice model of approximate amino acid interactions, I investigated the entropic effects of protein adsorption on a weakly attractive surface. These simulations allow for a precise calculation of the partition functions of these complex systems, from which I can then analyze other thermodynamic properties.


Mutant Study Of Sinorhizobium Meliloti Proline Utilization A (Puta), Jacob E. Wilkinson, John J. Tanner, Donald F. Becker Apr 2016

Mutant Study Of Sinorhizobium Meliloti Proline Utilization A (Puta), Jacob E. Wilkinson, John J. Tanner, Donald F. Becker

UCARE Research Products

The purpose of this project is to purify and characterize the reaction kinetics of mutant versions the enzyme Proline Utilization A (PutA) in Sinorhizobium meliloti. The enzyme catalyzes the first step in proline metabolism. It has two active sites. The first is proline dehydrogenase (PRODH) which converts proline to pyrroline-5-carboxylate (P5C). The second is P5C dehydrogenase (P5CDH) which converts P5C to glutamate. Although many bacterial organisms have PutA, there are still significant interspecies variations, resulting in an entire family of PutA enzymes. The main difference is the length of the amino acid sequence. This affects the protein’s structure or ...


Knowledge-Based Approaches For Understanding Structure-Dynamics-Function Relationship In Proteins, Kannan Sankar Jan 2016

Knowledge-Based Approaches For Understanding Structure-Dynamics-Function Relationship In Proteins, Kannan Sankar

Graduate Theses and Dissertations

Proteins accomplish their functions through conformational changes, often brought about by changes in environmental conditions or ligand binding. Predicting the functional mechanisms of proteins is impossible without a deeper understanding of conformational transitions. Dynamics is the key link between the structure and function of proteins. The protein data bank (PDB) contains multiple structures of the same protein, which have been solved under different conditions, using different experimental methods or in complexes with different ligands. These alternate conformations of the same protein (or similar proteins) can provide important information about what conformational changes take place and how they are brought about ...


A Computationally Designed Protein-Ligand Interaction Is Mechanically Robust, William John Van Patten Jan 2016

A Computationally Designed Protein-Ligand Interaction Is Mechanically Robust, William John Van Patten

Undergraduate Honors Theses

Protein-ligand interactions govern essential and ubiquitous biological processes such as immune response and gene regulation. Recently, the first computationally designed ligand-binding protein named DIG10.3 was developed by the Baker lab at the University of Washington. This artificially designed (rather than naturally evolved) ligand binding protein exhibited high affinity and selectivity to its target ligand, Digoxigenin (Dig). Such computationally designed ligand-binders offer promising capabilities in diagnostics and therapeutics for a wide range of diseases. By applying a mechanical force to a single DIG10.3::Digoxigenin interaction through atomic force microscope (AFM)-based single-molecule force spectroscopy (SMFS) we can extract unique ...


Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz Oct 2015

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

CSE Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.


An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien Aug 2015

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There ...


Conformational Dynamics Of Cytochrome P450cam Upon Ligand Binding, Ana Virginia Bernal Gomez Aug 2015

Conformational Dynamics Of Cytochrome P450cam Upon Ligand Binding, Ana Virginia Bernal Gomez

Masters Theses

Cytochrome P450s are a superfamily of metalloenzymes that are responsible for the monooxygenation of their hydrophobic substrates. P450’s retain the same general structural scaffold, however are able to bind promiscuously to substrates with distinct physico-chemical properties. It is believed that they possess considerable flexibility in the substrate binding regions as well as their active site to accomplish the diverse binding and catalytic chemistry with high regio- and stereo-specificity. In order to investigate the conformational dynamics inherent in these enzymes, especially in context of binding different ligands, we carried out amide proton exchange studies via NMR spectroscopy on a model ...