Modeling and simulations of single stranded rna viruses

The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA.PhDCommittee Chair: Stephen C. Harvey; Committee Member: Adegboyega Oyelere; Committee Member: Loren Williams; Committee Member: Rigoberto Hernandez; Committee Member: Roger Wartel

Structural and Electrostatic Characterization of Pariacoto Virus: Implications for Viral Asembly

This is the peer reviewed version of the following article:Devkota, B., Petrov, A., Lemieux, S., Boz, M. B., Tang, L., Schneemann, A., … Harvey, S. C. (2009). Structural and Electrostatic Characterization of Pariacoto Virus: Implications for Viral Asembly. Biopolymers, 91(7), 530–538. http://doi.org/10.1002/bip.21168, which has been published in final form at doi.org/10.1002/bip.21168. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-ArchivingWe present the first all-atom model for the structure of a T=3 virus, pariacoto virus (PaV), which is a non-enveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal structure, which reveals about 88% of the protein structure but only about 35% of the RNA structure. Evaluation of alternative models confirms our earlier observation that the polycationic protein tails must penetrate deeply into the core of the virus, where they stabilize the structure by neutralizing a substantial fraction of the RNA charge. This leads us to propose a model for the assembly of small icosahedral RNA viruses: nonspecific binding of the protein tails to the RNA leads to a collapse of the complex, in a fashion reminiscent of DNA condensation. The globular protein domains are excluded from the condensed phase but are tethered to it, so they accumulate in a shell around the condensed phase, where their concentration is high enough to trigger oligomerization and formation of the mature virus

GPS bozucular için bütünleşik l-bant güç yükselticisi

This paper includes the analysis, design and implementation of Power Amplifiers (PA) operating in the specified frequency ranges (L1, L2, L5) in the L Band. This PA provides 18 W output power with 58% efficiency. The PA consist three different amplifier stage. GaN-on-SiC transistor is used in PA. The focus of the realized structure is efficiency and linearity. These requirements have been achieved with the choice of transistor technology, impedance matching circuit design and bias point selection. With this design, a Power Amplifier that can be used in signal jammers or amplifier units operating in the L band range has been produced

Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association

<div><p>Substantial evidence in support of the formation of opioid receptor (OR) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions. In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations of different combinations of the three major OR subtypes, i.e., μ-OR, δ-OR, and κ-OR, in an explicit lipid bilayer. Specifically, we ran multiple, independent MD simulations of each homomeric μ-OR/μ-OR, δ-OR/δ-OR, and κ-OR/κ-OR complex, as well as two of the most studied heteromeric complexes, i.e., δ-OR/μ-OR and δ-OR/κ-OR, to derive the preferred supramolecular organization and dimer interfaces of ORs in a cell membrane model. These simulations yielded over 250 microseconds of accumulated data, which correspond to approximately 1 millisecond of effective simulated dynamics according to established scaling factors of the CG model we employed. Analysis of these data indicates similar preferred supramolecular organization and dimer interfaces of ORs across the different receptor subtypes, but also important differences in the kinetics of receptor association at specific dimer interfaces. We also investigated the kinetic properties of interfacial lipids, and explored their possible role in modulating the rate of receptor association and in promoting the formation of filiform aggregates, thus supporting a distinctive role of the membrane in OR oligomerization and, possibly, signaling.</p></div

Evaluation of Oral Glucose Tolerance Test in Hyperlipidemic Normoglycemic Patients

Background: Atherosclerotic coronary artery disease is an important health issue and a leading mortality reason in developed countries. In this study; we aimed to diagnose diabetes and other glucose disturbances early by evaluating the glycemic profi le in hyperlipidemic patients and to decrease the cardiovascular morbidity and mortality by an early intervention. Methods: 46 female and 19 male, totally 65 hyperlipidemic normoglycemic patients were included in the study. Patients had no history of diabetes and normal fasting blood glucose levels and were diagnosed with hyperlipidemia during routine blood tests. There were no limitations for age, gender or body mass index. Coronary heart disease risk factors were questioned and fi ndings were used to determine the pathological low density lipoprotein (LDL) levels. 2-hour oral glucose tolerance test (OGTT) was performed for all patients. Results were evaluated according to American Diabetes Association (ADA) 1997 criteria. Results: Mean total cholesterol level of patients was 236±41 mg/dl, mean trigliserid level was 223±141 mg/dl and mean LDL level was 153±38 mg/dl. According to OGTT results ; mean fasting blood glucose level was 95±13 mg/dl and mean 2nd hour glucose level was 128±34 mg/dl. According to ADA 97 criteria; OGTT of 33 (51%) patients were normal. 2 (3%) patients had impaired fasting glucose (IFG), 11 (17%) patients had impaired glucose tolerance (IGT) and 19 patients (29%) had diabetes. Conclusions: Hyperlipidemia and diabetes are important risk factors for cardiovascular disease and they usually coexist. Identifi cation and early intervention of these risk factors are prognostically important. Thus; patients who are diagnosed with hyperlipidemia should be screened for glucose disturbances as a secondary risk factor and by early intervention of both risk factors, cardiovascular morbidity and mortality should be decreased

Fraction of the observed hetero-dimeric interfaces during five independent MD simulations of the μ-OR/δ-OR and δ-OR/κ-OR systems.

<p>Best estimate of the fraction of each hetero-dimeric arrangement and its (2.5%,97.5%) confidence intervals (in parenthesis) are calculated as reported in the Methods section.</p><p>Fraction of the observed hetero-dimeric interfaces during five independent MD simulations of the μ-OR/δ-OR and δ-OR/κ-OR systems.</p

Superposition of the highly frequent homo-dimer configurations of δ-OR onto the closest available crystal structures of parallel receptors.

<p>Specifically, these are: TM1,2,H8/TM1,2,H8, TM1,2/TM5,6, and TM4,5/TM5,6, in panels A (RMSD of 3.57 Å from 4DJH), B (RMSD of 6.48 Å from 3OE8), and C (RMSD of 6.62 Å from 3OE8), respectively.</p

An example of OR setup at different simulation times.

<p>Location of the 16 simulated receptor molecules in one of the five runs executed for the κ-OR system (run #1), at different simulation times, (specifically: 0, 2, 6, and 10 μs)</p

Fraction of the observed homo-dimeric interfaces during five independent MD simulations of the μ-OR/μ-OR, δ-OR/δ-OR, and κ-OR/κ-OR systems.

<p>Best estimate of the fraction of each homo-dimeric arrangement and its (2.5%,97.5%) confidence intervals (in parenthesis) are calculated as reported in the Methods section.</p><p>Fraction of the observed homo-dimeric interfaces during five independent MD simulations of the μ-OR/μ-OR, δ-OR/δ-OR, and κ-OR/κ-OR systems.</p