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

Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan May 2019

Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan

Quest

Independent Research Paper

Research in progress for PHYS 2426: University Physics II

Faculty Mentor: Raji Kannampuzha, Ph.D.

The following paper represents research work done by students in a University Physics 2426 class, the second half of a two-semester introductory course in physics. It is a calculus-based physics course, intended primarily for physics, chemistry, math, and engineering majors. Students are introduced to the concept of academic research by learning to ask research-focused questions and then use the library resources to pursue outside research to find answers. For this assignment, students are asked to investigate a physical science, biological science, or ...


Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner Jul 2018

Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner

Department of Physics Papers

We give detailed recipes for a number of classroom demonstrations relevant to biological physics instruction. We developed them mainly for use in 2nd-3rd year undergraduate Physics courses. But you can (and we do) use them for primary school, through high school, up to PhD candidates. You adapt the words for each audience, but a phenomenon is a phenomenon.

We also outline a 1-hour introduction to Python for undergraduate scientific computing.

Finally we document some outcomes from courses taught at U Pennsylvania using these resources and others cited here. This material was presented at a workshop at the AAPT meeting in ...


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 ...


Improving The Usage Of Unnatural Amino Acids In Proteins: Thioamides And Other Biophysical Probes, Christopher Russell Walters Jan 2017

Improving The Usage Of Unnatural Amino Acids In Proteins: Thioamides And Other Biophysical Probes, Christopher Russell Walters

Publicly Accessible Penn Dissertations

Methods for genetically and synthetically manipulating protein composition enable a greater flexibility in the study of protein dynamics and function. However, current techniques for incorporating biophysical probes in the form of unnatural amino acids (Uaas) can suffer from poor yield, limited selectivity for the desired probe, and an insufficient understanding of the impact that the probe has on protein structure and function. Each of the studies discussed herein addresses one or more of these shortcomings in an effort to improve the usage of Uaas in biochemistry. We have shown that using inteins as traceless, cleavable purification tags enables the separation ...


Symmetry And Reconstruction Of Particle Structure From Random Angle Diffraction Patterns, Sandi Wibowo Dec 2016

Symmetry And Reconstruction Of Particle Structure From Random Angle Diffraction Patterns, Sandi Wibowo

Theses and Dissertations

The problem of determining the structure of a biomolecule, when all the evidence from experiment consists of individual diffraction patterns from random particle orientations, is the central theoretical problem with an XFEL. One of the methods proposed is a calculation over all measured diffraction patterns of the average angular correlations between pairs of points on the diffraction patterns. It is possible to construct from these a matrix B characterized by angular momentum quantum number l, and whose elements are characterized by radii q and q’ of the resolution shells. If matrix B is considered as dot product of vectors, which ...


X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar Jan 2016

X-Ray Characterization Of Mesophases And Phase Transitions Of Dna Analogues In Solutions, Mustafa Selcuk Yasar

Doctoral Dissertations

We think of DNA as double-stranded helices (duplex), but the polymer exists in many conformations. Several triplex and quadruplex DNA structures can be formed in laboratory settings and exist in nature. This thesis first provides a brief description of the nature of the order in arrays of duplex DNA under biologically relevant molecular crowding conditions. Then we compare the duplex DNA mesophases with the corresponding liquid crystalline phase behavior of the triplex and quadruplex DNA analogues. In particular, we focus on G-quadruplexes.

Observed in the folds of guanine-rich oligonucleotides, G-quadruplex structures are based on G-quartets formed by hydrogen bonding and ...


Statistical Biophysics Blog: A Hello: The Point Of This Blog, Daniel M. Zuckerman Apr 2015

Statistical Biophysics Blog: A Hello: The Point Of This Blog, Daniel M. Zuckerman

Scholar Archive

No abstract provided.


Sucralose Destabilization Of Protein Structure, Lee Chen, Nimesh Shukla, Inha Cho, Erin F. Cohn, Erika A. Taylor, Christina M. Othon Mar 2015

Sucralose Destabilization Of Protein Structure, Lee Chen, Nimesh Shukla, Inha Cho, Erin F. Cohn, Erika A. Taylor, Christina M. Othon

Erika A. Taylor, Ph.D.

Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence ...


De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains, Bernard Howard Everson Feb 2015

De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains, Bernard Howard Everson

All Dissertations, Theses, and Capstone Projects

In this work, I describe an approach to the rational, iterative design and characterization of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by generating libraries of sequences, which were then expressed and evaluated for function. One successful sequence is shown to bind a variety of porphyrin-like cofactors, and exhibits light- activated electron transfer in mixed hemin:chlorin e6 and hemin:Zn(II)-protoporphyrin IX complexes. These results imply that many sophisticated functions such ...


Hiv-1 Rna Dimerization At Single Molecule Level, Hansini R. Mundigala Jan 2014

Hiv-1 Rna Dimerization At Single Molecule Level, Hansini R. Mundigala

Wayne State University Dissertations

The Dimerization Initiation Sequence (DIS) is a conserved hairpin-loop motif on the 5' UTR of the HIV-1 genome. It plays an important role in genome dimerization through formation of a "kissing complex" intermediate between two homologous DIS sequences. This bimolecular kissing complex ultimately leads to the formation of an extended RNA duplex. Understanding the kinetics of this interaction is key to exploiting DIS as a possible drug target against HIV. We wish to report a novel study that makes an important contribution to understanding the dimerization mechanism of HIV-1 RNA in vitro. Our work has employed single-molecule fluorescence resonance energy ...


Escherichia Coli Heptosyltransferase I: Investigation Of Protein Dynamics Of A Gt-B Structural Enzyme, Erika A. Taylor, Daniel J. Czyzyk, Shreya S. Sawant, Carlos A. Ramirez-Mondragon Aug 2013

Escherichia Coli Heptosyltransferase I: Investigation Of Protein Dynamics Of A Gt-B Structural Enzyme, Erika A. Taylor, Daniel J. Czyzyk, Shreya S. Sawant, Carlos A. Ramirez-Mondragon

Erika A. Taylor, Ph.D.

Heptosyltransferase I (HepI), the enzyme responsible for the transfer of l-glycero-d-manno-heptose to a 3-deoxy-α-d-manno-oct-2-ulopyranosonic acid (Kdo) of the growing core region of lipopolysaccharide, is a member of the GT-B structural class of enzymes. Crystal structures have revealed open and closed conformations of apo and ligand-bound GT-B enzymes, implying that large-scale protein conformational dynamics play a role in their reaction mechanism. Here we report transient kinetic analysis of conformational changes in HepI reported by intrinsic tryptophan fluorescence and present the first real-time evidence of a GT-B enzyme undergoing a substrate binding-induced transition from an open to closed state prior to catalysis.


36 Degrees Step Size Of Proton-Driven C-Ring Rotation In Fof1-Atp Synthase, Monika Düser, Nawid Zarrabi, Daniel Cipriano, Stefan Ernst, Gary Glick, Stanley Dunn, Michael Börsch Oct 2012

36 Degrees Step Size Of Proton-Driven C-Ring Rotation In Fof1-Atp Synthase, Monika Düser, Nawid Zarrabi, Daniel Cipriano, Stefan Ernst, Gary Glick, Stanley Dunn, Michael Börsch

Stanley D Dunn

Synthesis of adenosine triphosphate ATP, the 'biological energy currency', is accomplished by F(o)F(1)-ATP synthase. In the plasma membrane of Escherichia coli, proton-driven rotation of a ring of 10 c subunits in the F(o) motor powers catalysis in the F(1) motor. Although F(1) uses 120 degrees stepping during ATP synthesis, models of F(o) predict either an incremental rotation of c subunits in 36 degrees steps or larger step sizes comprising several fast substeps. Using single-molecule fluorescence resonance energy transfer, we provide the first experimental determination of a 36 degrees sequential stepping mode of ...


Is The Curvature Of The Flagellum Involved In The Apparent Cooperativity Of The Dynein Arms Along The "9+2" Axoneme?, Christian Cibert, Andrei Ludu Jun 2010

Is The Curvature Of The Flagellum Involved In The Apparent Cooperativity Of The Dynein Arms Along The "9+2" Axoneme?, Christian Cibert, Andrei Ludu

Andrei Ludu

In a recent study [Cibert, 2008. Journal of Theoretical Biology, 253, 74-89], by assuming that the walls of microtubules are involved in cyclic compression/dilation equilibriums as a consequence of their cyclic curvature of the axoneme, it was proposed that local adjustments of spatial frequencies of both dynein arms and beta-tubulin monomers facing series create propagation of joint probability waves of interaction (JPI) between these two necessary partners. Modeling the occurrence of these interactions along the entire length of an axoneme between each outer doublet pair (without programming any cooperative dialog between the molecular complexes) and the cyclic attachment of ...


A New Approach To Understanding Biological Control Of Quinone Electrochemistry, Bruce R. Lichtenstein May 2010

A New Approach To Understanding Biological Control Of Quinone Electrochemistry, Bruce R. Lichtenstein

Publicly Accessible Penn Dissertations

Oxidoreductases play pivotal roles in energy capturing and converting processes of life. During these processes, quinones shuttle protons and reducing equivalents between membrane-bound oxidoreductases that generate the proton motive force during oxidative phosphorylation and photophosphorylation. A key mechanistic feature of these oxidoreductases is their ability to tune the reduction potentials of the hydroquinone, semiquinone and oxidized states of their substrate quinones. This level of control allows for maximization of conversion efficiency between the energy of the quinone reducing equivalents and the proton motive force, and prevents side reactions that may be fatal to cells. A half-century of experimental study and ...


Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang Jan 2008

Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang

Retrospective Theses and Dissertations

Because of its appealing simplicity, the elastic network model (ENM) has been widely accepted and applied to study many molecular motion problems, such as the molecular mechanisms of chaperonin GroEL-GroES function, allosteric changes in hemoglobin, ribosome motions, motor-protein motions, and conformational changes in general. In this dissertation, the ENM is employed to study various protein dynamics problems, and its validity is also examined by comparing with experimental data. First, we apply principal component analysis (PCA) to identify the essential protein motions from multiple structures (X-ray, NMR and MD) of the HIV-1 protease. We find significant similarities between the first few ...


Molecular And Chemical Characterization Of Genes Involved In Maize Cuticular Wax Biosynthesis , M. Ann D. N. Perera Jan 2005

Molecular And Chemical Characterization Of Genes Involved In Maize Cuticular Wax Biosynthesis , M. Ann D. N. Perera

Retrospective Theses and Dissertations

The primary surfaces of the arial parts of plants, and the surfaces of reproductive organs are covered by an extra cellular layer called the cuticle. The cuticle provides the foremost protection to the plant in order to adapt to the terrestrial environment. The cuticle composed of a biopolymer (cutin), which is embedded in a coating of cuticular waxes. Understanding the biochemical, genetic and physiological mechanisms for the biosynthesis of these cuticular waxes is relatively poor. This body of work has established methods for the chemical analysis of the cuticular waxes of maize plants. I have used these methods to chemically ...


A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu Jul 2004

A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu

Doctoral Dissertations

Investigations on instantaneous skin burns are useful for an accurate assessment of burn-evaluation and for establishing thermal protections for various purposes. Meanwhile, hyperthermia with radiation is important in the treatment of cancer, and it is essential for developers and users of hyperthermia systems to predict, and interpret correctly the biomass thermal and vascular response to heating. In this dissertation, we employ the well-known Pennes' bioheat transfer equation to predict the degree of skin burn and the temperature distribution in hyperthermia cancer treatment.

A fourth-order compact finite difference scheme is developed to solve Pennes' bioheat transfer equation in a three-dimensional single ...


X-Ray Crystallographic Studies On Adenylosuccinate Synthetase From Escherichia Coli , Zhenglin Hou Jan 1998

X-Ray Crystallographic Studies On Adenylosuccinate Synthetase From Escherichia Coli , Zhenglin Hou

Retrospective Theses and Dissertations

Adenylosuccinate synthetase catalyzes the first committed step in de novo biosyntheses of AMP from IMP and aspartate, using GTP as the energy source. Metal cations, ligand-induced conformational transitions and metabolic effectors significantly influence the catalytic potential of the synthetase. The Mg2+, Mn2+, or Ca 2+ bind to the same site, coordinating alpha-, beta-, and gamma-phosphoryl groups of GTP. The level of catalysis supported by each cation is linked to its influence on the basicity of Asp13, a residue which abstracts the proton from N1 of IMP. Zn2+, a potent inhibitor of the synthetase, coordinates the beta- and gamma-phosphoryl groups of ...


Characterization Of Biomacromolecules By Nuclear Magnetic Resonance Spectroscopy , Wayne Robert Baker Jan 1996

Characterization Of Biomacromolecules By Nuclear Magnetic Resonance Spectroscopy , Wayne Robert Baker

Retrospective Theses and Dissertations

Two proteins were examined by Nuclear Magnetic Resonance (NMR) spectroscopy. The Emb-1 protein of Daucus carota was found to have few spectral characteristics indicative of a stable tertiary structure. In particular, line-widths were narrow, chemical shift dispersion was poor and nuclear Overhauser effect spectra were sparse. The NMR spectra of Ribonuclease A was examined at a range of pH values and the chemical shifts of a selected number of resonances was plotted as a function of the pH. From these titrations curves pKa values were determined and assigned to specific ionizing groups within the protein based, in part, on physical ...