Дисертації: "Protein vibration"

1

SCARAMOZZINO, DOMENICO. "Elastic Lattice Models: From Proteins to Diagrid Tall Buildings." Doctoral thesis, Politecnico di Torino, 2021. http://hdl.handle.net/11583/2872326.

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2

Karjalainen, Eeva-Liisa. "The choreography of protein vibrations : Improved methods of observing and simulating the infrared absorption of proteins." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-60415.

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The work presented in this thesis has striven toward improving the capability to study proteins using infrared (IR) spectroscopy. This includes development of new and improved experimental and theoretical methods to selectively observe and simulate protein vibrations. A new experimental method of utilising adenylate kinase and apyrase as helper enzymes to alter the nucleotide composition and to perform isotope exchange in IR samples was developed. This method enhances the capability of IR spectroscopy by enabling increased duration of measurement time, making experiments more repeatable and allowing investigation of partial reactions and selected frequencies otherwise difficult to observe. The helper enzyme mediated isotope exchange allowed selective observation of the vibrations of the catalytically important phosphate group in a nucleotide dependent protein such as the sarcoplasmic reticulum Ca2+-ATPase. This important and representative member of P-type ATPases was further investigated in a different study, where a pathway for the protons countertransported in the Ca2+-ATPase reaction cycle was proposed based on theoretical considerations. The transport mechanism was suggested to involve separate pathways for the ions and the protons. Simulation of the IR amide I band of proteins enables and supports structure-spectra correlations. The characteristic stacking of beta-sheets observed in amyloid structures was shown to induce a band shift in IR spectra based on simulations of the amide I band. The challenge of simulating protein spectra in aqueous medium was also addressed in a novel approach where optimisation of simulated spectra of a large set of protein structures to their corresponding experimental spectra was performed. Thereby, parameters describing the most important effects on the amide I band for proteins could be determined. The protein spectra predicted using the optimised parameters were found to be well in agreement with experiment.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.

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3

Vural, Derya. "The vibrational amplitude of atoms in proteins." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 86 p, 2009. http://proquest.umi.com/pqdweb?did=1885607701&sid=3&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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4

Sowley, Hugh Richard. "Electron-vibration-vibration two-dimensional infrared spectroscopy as a structural probe of interactions in proteins and DNA." Thesis, Imperial College London, 2017. http://hdl.handle.net/10044/1/57959.

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Modern structural biology has a number of powerful tools but despite this there are a number of problems in structural biology that these methods are unable to address. Some of these pertain to the need for large number for precise comparative structures for the drug discovery process. EVV 2DIR has the potential to fill some of these gaps, having the potential to determine molecular binding geometry. This thesis presents the first steps in exploring the potential of EVV 2DIR to be applied to the analysis of the structure of inhibitor- protein binding and presents the first EVV spectra of an inhibitor-protein complex. For the inhibitor-protein complex studied, six vibrational couplings between seven vibrational modes were identified exclusively upon complex formation due to interactions between the two molecules. Experimental spectra were compared with ab initio calculations to assign these vibrations to specific motions on both the inhibitor and protein molecules. EVV 2DIR cross peaks can be sensitive to the geometry of the interacting groups which produce them. By measuring the spectra of the inhibitor-protein complex using two different polarisation schemes, quantitative comparison between calculated and experimental spectra was made possible. This allowed for the prospect of using calculation aided EVV 2DIR to determine the structure of protein-ligand complexes to be explored. This thesis also presents the first EVV spectra of DNA. EVV 2DIR spectra were measured of duplex and G-quadruplex structures and compared with those of unstructured controls. In the absence of calculated spectra, assignments were made to some of the spectral features observed. EVV 2DIR was shown to be sensitive to the structural form of the DNA samples, containing cross peaks indicative of WatsonCrick base pairing, G-quadruplex formation and glycosidic bond conformation. The DNA spectra contained many unassigned peaks leaving open the possibility to assign many more structural indicators.

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5

BASSANI, ANDREA. "Terahertz vibrations in proteins: experimental and numerical investigation." Doctoral thesis, Politecnico di Torino, 2017. http://hdl.handle.net/11583/2673736.

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The principal goal of this Doctorate thesis is to study high frequency vibrations (in the range between Gigahertz and Terahertz) in nanoscopic biological structures such as proteins. In particular, the idea of this thesis is to found, by means of experimental sessions and numerical simulations, natural frequencies of entire proteins or of large portions of that. The mechanical behaviour of proteins is receiving an increasing attention from the scientific community. Recently it has been suggested that mechanical vibrations play a crucial role in controlling structural configuration changes (folding) which govern proteins biological function. The mechanism behind protein folding is still not completely understood, and many efforts are being made to investigate this phenomenon. Complex Molecular Dynamics simulations and sophisticated experimental measurements are conducted to investigate protein dynamics and to perform protein structure predictions; however, these are two related, although quite distinct, approaches. Here we investigate the linearly free dynamics (frequencies and modes) of proteins by Modal Analysis. The input mechanical parameters are taken from the literature. We first give an estimate of the order of magnitude of the natural frequencies of protein crystals by considering both classical wave mechanics and structural dynamics formulas. Afterwards, we perform modal analyses of some relevant chemical groups and of the full lysozyme and Na-K ATPase proteins. The numerical results are compared to experimental data, obtained from both in-house and literature Raman measurements. Our present investigations are devoted to understand if stimulating protein samples with a laser that excites resonant mechanical vibrations (say, in the THz range) may induce variations in the vibrational spectra due to possible conformational changes of protein structure.

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6

Simpson, Niall. "Accessing ultrafast protein dynamics through 2DIR spectroscopy of intrinsic ligand vibrations." Thesis, University of Strathclyde, 2015. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=26003.

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Proteins are complex molecular machines that facilitate the chemical reactions fundamental to life. Their functions are encoded in a linear sequence of amino acids, of which only 20 species are found in nature. Yet the functional and structural diversity accessible through these building blocks is vast. Molecular and atomic-level protein studies have been crucial to our understanding of health and treatment of disease, with increasingly sophisticated experimental and computational methods continuing to provide new information with which to advance medicine. However, the requirement for more detailed understanding of proteins has risen through the emergence of multi-antibiotic-resistant bacteria and also through the potential to design synthetic proteins of novel function. Paradigms of protein function have evolved significantly since early studies, though few all-encompassing descriptions have been proposed, owing to the complex, dynamic structures of these large biomolecules. Presently, the relationship between protein structural motions at different timescales appears to hold vital significance to the elusive aspects of biological mechanisms. No single measurement technique is capable of accessing the multitude of timescales over which protein motions occur, and thus concerted investigation is necessary. Observation of dynamics at the femtosecond-picosecond timescale has only recently become possible through the development of new experimental techniques, allowing a new class of protein motions to be investigated. In this thesis, the advanced technique of two-dimensional infrared spectroscopy (2DIR) is employed to study three biomolecular systems with implications to ubiquitous protein interactions. The aims of these investigations are, firstly, to demonstrate the suitability of 2DIR spectroscopy in gathering novel dynamic information from biological systems that is not accessible via other methods, and secondly, to derive the potential physical significance of these dynamics as they relate to biological function. A description of the underlying theory of 2DIR is presented in this Chapter, along with the considerations that must be made in the application of such a technique to complex biological case-studies. In Chapter (2), descriptions are given for the experimental setups used to acquire infrared spectra, specifically, Fourier transform infrared (FTIR), pump-probe and 2DIR spectroscopies. In Chapter (3) the catalytic-site dynamics of two closely-related haem proteins are each studied by monitoring the vibrational evolution of a nitric oxide (NO) probe molecule bound to the haem centre. A comparison of the active site dynamics is performed in order to correlate the observed differences with discrepancies between the protein reaction mechanisms. Chapter (4) explores the potential of a coenzyme with high protein-binding promiscuity to serve as an intrinsic reporter of the dynamics that occur at substrate binding sites. Infrared analysis and categorisation of the free coenzyme molecule is performed in order to establish its effectiveness as a probe. In Chapter (5), method-development strategies are proposed for the extraction of 2DIR data from large, complex protein-protein systems, with the objective of expanding the range of interactions on which 2DIR can effectively report. Both well-established and novel strategies are employed, and the potential and limitations of the technique are discussed in the context of these demanding case-studies. Chapter (6) draws together conclusions and an overview of progress made and discusses future directions.

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7

Giraud, Gerard. "Ultrafast vibrational dynamics in liquids and proteins." Thesis, University of Strathclyde, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275153.

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8

Brewster, Victoria Louise. "Investigating protein modifications using vibrational spectroscopy and fluorescence spectroscopy." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/investigating-protein-modifications-using-vibrational-spectroscopy-and-fluorescence-spectroscopy(32ff24c8-326a-41cf-a076-11e067376525).html.

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Protein based biopharmaceuticals are becoming increasingly popular therapeutic agents. Recent changes to the legislation governing stem cell technologies will allow many further developments in this field. Characterisation of these therapeutic proteins poses numerous analytical challenges. In this work we address several of the key characterisation problems; detecting glycosylation, monitoring conformational changes, and identifying contamination, using vibrational spectroscopy. Raman and infrared spectroscopies are ideal techniques for the in situ monitoring of bioprocesses as they are non-destructive, inexpensive, rapid and quantitative. We unequivocally demonstrate that Raman spectroscopy is capable of detecting glycosylation in three independent systems; ribonuclease (a model system), transferrin (a recombinant biopharmaceutical product), and GFP (a synthetically glycosylated system). Raman data, coupled with multivariate analysis, have allowed the discrimination of a glycoprotein and the equivalent protein, deglycosylated forms of the glycoprotein, and also different glycoforms of a glycoprotein. Further to this, through the use of PLSR, we have achieved quantification of glycosylation in a mixture of protein and glycoprotein. We have shown that the vibrational modes which are discriminatory in the monitoring of glycosylation are relatively consistent over the three systems investigated and that these bands always include vibrations assigned to structural changes in the protein, and sugar vibrations that are arising from the glycan component. The sensitivity of Raman bands arising from vibrations of the protein backbone to changes in conformation is evident throughout the work presented in this thesis. We used these vibrations, specifically in the amide I region, to monitor chemically induced protein unfolding. By comparing these results to fluorescence spectroscopy and other regions of the Raman spectrum we have shown that this new method provides improved sensitivity to small structural changes. Finally, FT-IR spectroscopy, in tandem with supervised machine learning methods, has been applied to the detection of protein based contaminants in biopharmaceutical products. We present a high throughput vibrational spectroscopic method which, when combined with appropriate chemometric modelling, is able to reliably classify pure proteins and proteins ‘spiked’ with a protein contaminant, in some cases at contaminant concentrations as low as 0.25%.

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9

Ｊoutsuka, Tatsuya. "Proton/Electron Transfer and Vibrational Relaxation in Solution and Protein." 京都大学 (Kyoto University), 2012. http://hdl.handle.net/2433/157807.

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10

Wilson, Gary. "Vibrational Raman optical activity of peptides and proteins." Thesis, University of Glasgow, 1996. http://theses.gla.ac.uk/6144/.

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Vibrational Raman optical activity (ROA) which is the difference in the Raman scattering of left and right circularly polarised incident light, has recently emerged as a new and incisive probe of biomolecular structure. This thesis is based on new applications of ROA to some current biochemical problems. The first chapter is a brief explanation of the origin of chirality and the development of vibrational optical activity with special emphasis on ROA. Chapter 2 is a theoretical analysis of ROA and provides a fundamental explanation of the phenomenon. This involves a description as to how the ROA effect is generated using molecular property tensors. The third chapter concentrates on the instrumentation required to measure ROA and the importance of CCD detectors and holographic notch filters in establishing the technique with respect to biopolymers. Chapter 4 is a brief introduction to protein structure and includes an analysis of the strengths and weaknesses of current biophysical techniques used for structure determination. Chapters 5 and 6 describe detailed applications of ROA to polypeptides and native proteins. The polypeptides are a suitable starting point since from other spectroscopic techniques they are known to adopt certain conformations, such as -helix, -sheet and random coil. Native proteins are examined in Chapter 6 and the ability of ROA to detect not only secondary but also tertiary structure is highlighted. Chapter 7 is concerned with the important topics of the structure and dynamics of unfolded proteins, molten globules and ligand bound proteins. Finally, in the appendix there is a summary of the assignments made to secondary structure and to loops and turns.

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11

Wong, Hing-wan. "Study of chemically modified food proteins by vibrational spectroscopy." View the Table of Contents & Abstract, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36995939.

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12

Horness, Rachel E. "Application and Development of Site?specific Vibrational Probes of Proteins." Thesis, Indiana University, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10977701.

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Conformational heterogeneity and protein dynamics play important roles in molecular recognition, but are experimentally difficult to characterize with sufficient temporal and spatial resolution. Infrared (IR) spectroscopy can probe protein dynamics on sub-ps timescales; and further, the small size of vibrational chromophores combined with site-selective incorporation of spectrally isolated IR probes provides high spatial resolution. Herein, we site-specifically introduce nitrile and carbon-deuterium bonds at distinct sites in the Src-homology 3 (SH3) domain from yeast protein Sho1 and its proline-rich peptide binding partner from Pbs2 to examine the underlying mechanisms of molecular recognition via IR spectroscopy. Further, we present efforts at developing instrumentation aimed at improving characterization of weakly absorbing vibrational probes in strongly absorbing solvent.

Nitrile probes were introduced at six distinct sites in the SH3 domain via amber codon suppression. Variation between the observed absorbance bands indicates site specific differences in conformational heterogeneity imposed by protein domain. Residue-specific changes upon peptide binding are observed at incorporated nitrile moieties, but are more dramatically observed for deuterated vibrational probes incorporated within the peptide binding partner. Deuterated amino acids were incorporated at highly conserved proline residues within the peptide ligand. Upon binding, absorbance bands are observed which indicate population of multiple conformational states in the bound complex. Only single resonances were observed by characterization of the same labeled bonds by NMR, suggesting rapid interconversion on the NMR timescale. Results suggest that the SH3 domain recognizes its peptide binding partner with at least elements of an induced-fit mechanism.

Characterization of the vibrational probes used above can be challenging due to the path length limitation imposed by the presence of strongly absorbing solvent water. This places an upper bound on the achievable signal strength which can obscure small (µOD) absorbance bands. To confront this limitation we have constructed an absorbance spectrometer with a quantum cascade laser (QCL) source. The instrument allows characterization of samples of increased path length with similar signal-to-noise ratios as in FT IR measurements. Achievable signal-to-noise ratios are limited by QCL source noise; we present several approaches, one electronic and one interferometric, aimed at limiting the deleterious effect of QCL fluctuations.

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13

Hertel, Sebastian. "Pulmonary delivery of pharmaceutical proteins by means of vibrating mesh nebulization." Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-172792.

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14

Raj, Sharad K. "Chemical Information Based Elastic Network Model: A Novel Way To Identification Of Vibration Frequencies In Proteins." Amherst, Mass. : University of Massachusetts Amherst, 2009. http://scholarworks.umass.edu/theses/261/.

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15

Schmüser-Steger, Lars [Verfasser]. "Vibrational sum frequency generation pectroscopy of proteins at interfaces / Lars Schmüser-Steger." Mainz : Universitätsbibliothek Mainz, 2018. http://d-nb.info/1166350223/34.

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16

Yegres, Michelle. "Probing the effect of conformational changes in protein complexes by vibrational spectroscopy : bioenergetics and allostery." Phd thesis, Université de Strasbourg, 2014. http://tel.archives-ouvertes.fr/tel-01048738.

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The mechanism of enzyme regulation through conformational changes is a key pattern in governing cell behavior. In this thesis the focus is on three protein complexes that reflect how protein activity can be regulated by different effectors. Different spectroscopic techniques, like IR and Raman spectroscopy, were used is order to follow the secondary and tertiary conformational changes in protein structure to identify their roles. The first protein of interest was PDZ1 from MAGI-1, involved in cellular signaling. This scaffold domain is known to interact with the E6 protein from HPV16. It was demonstrated that the different conformational states and their affinities to the C-terminus of the viral protein is regulated by the dynamics of the hydrogen bonding network formed by the connection of specific amino acids in three regions of the protein. Study of mutations around the C-terminal area of the protein and the βC strand were performed; demonstrating that both regions are crucial for assembly of the hydrogen bonding network to stabilize the substrate binding. These results leads to conclude that the pathogenicity and prevalence of a particular virus like HPV16 is in its ability to build a stronger hydrogen bonding network in comparison to the natural binder. The allosteric model and the "shift population" model agree that, upon binding, conformational changes distant from a carboxylate binding group might be the key to understanding the binding dynamics between the PDZ domains and the viral proteins.The second protein of interest was a model that constitutes a small scale prototype of the conformational changes observed in more complex proteins; it is a short Copper-binding peptide, the amyloid-beta peptide, known to beinvolved in Alzheimer's disease. The objective with this model was to describe the effect of histidine ligands in the metal centers upon Copper (Cu) reduction, a key electrochemical reaction in the development of Alzheimer's. FTIR difference spectroscopy showed two different spheres of coordination for Cu(II) and Cu(I). The major changes in the structure are dominated by the contribution of the imidazole ring of His residues (His6, His13 and His14), in addition to Asp1 and Tyr10 residues. Changes in the coordination geometry could be key to the pH-dependency of the aggregation observed in the presence of Cu(I). Accordingly, it can be suggested that the formation of the fibrils observed in Alzheimer's patients is not only triggered by the presence of Cu but it is strongly affected by its redox state. The last system of interest was a metalloprotein, the NADH:ubiquinone oxidoreductase (complex I), which plays a key role in the cellular bioenergetics. This protein bears several Fe-S clusters and one flavin and its activity is regulated by the energy produced by a bound substrate and the electron transfer of its cofactors. The metal ligand-vibrations of the cofactors are described in their oxidized and reduced states. Using electrochemistry coupled to FTIR, Resonance Raman and Fluorescence spectroscopies, the investigation of complex I led to the conclusion that the properties of the metal centers are dictated, to a large extent, by their surrounding environment. [...]

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17

Hertel, Sebastian [Verfasser], and Gerhard [Akademischer Betreuer] Winter. "Pulmonary delivery of pharmaceutical proteins by means of vibrating mesh nebulization / Sebastian Hertel. Betreuer: Gerhard Winter." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2014. http://d-nb.info/1063874890/34.

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18

Asses, Yasmine. "Conception par modélisation et criblage in silico d'inhibiteurs du récepteur c-Met." Phd thesis, Université Henri Poincaré - Nancy I, 2011. http://tel.archives-ouvertes.fr/tel-00653609.

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L'enjeu des travaux effectués au cours de cette thèse est l'extraction in silico de molécules potentiellement intéressantes dans le processus d'inhibition du récepteur tyrosine kinase c-Met. La faculté de cette protéine à interagir dans les phénomènes d'embryogenèse et de réparation tissulaires rendent son inhibition cruciale dans les traitements contre les développements tumoraux où c-Met se trouve impliquée. Dans ce but, la stratégie que nous avons employée implique l'utilisation de plusieurs méthodes in silico de conception rationnelle de médicaments. Nous avons utilisé comme support les multiples structures cristallographiques publiées sur la ProteinData Base (PDB). Un travail de modélisation par homologie fut tout d'abord nécessaire pour combler les lacunes des structures cristallographiques collectées. Afin d'échantillonner au mieux l'espace conformationnel du récepteur kinase c-Met et de caractériser sa flexibilité, une longue campagne de simulation de Dynamique Moléculaire (DM) fut menée concernant les formes apo et holo des structures cristallographiques disponibles. Pour compléter ces simulations, une partie du travail consista à utiliser également la méthode des modes normaux de vibration (NM). De ces 2 approches (DM et NM), nous avons extrait un ensemble de 10 conformères considérés comme les plus représentatifs de l'espace conformationnel simulé pour la kinase c-Met et avons proposé un mode de fonctionnement de ce récepteur. Utilisant les conformations extraites de l'échantillonnage conformationnel, nous avons ensuite mené une importante campagne de criblage virtuel sur plusieurs chimiothèques constituant au total environ 70.000 composés. L'analyse des résultats de l'arrimage moléculaire nous a conduits à la sélection de plusieurs molécules intéressantes possédant théoriquement une bonne affinité pour la kinase c-Met. Ces molécules ont été soumises aux tests expérimentaux effectués par l'équipe de biologistes associée à nos travaux.

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19

Wilcox, Kieaibi. "Using regression analyses for the determination of protein structure from FTIR spectra." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/using-regression-analyses-for-the-determination-of-protein-structure-from-ftir-spectra(1ad037eb-f237-4efe-867a-597239bd913e).html.

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One of the challenges in the structural biological community is processing the wealth of protein data being produced today; therefore, the use of computational tools has been incorporated to speed up and help understand the structures of proteins, hence the functions of proteins. In this thesis, protein structure investigations were made through the use of Multivariate Analysis (MVA), and Fourier Transformed Infrared (FTIR), a form of vibrational spectroscopy. FTIR has been shown to identify the chemical bonds in a protein in solution and it is rapid and easy to use; the spectra produced from FTIR are then analysed qualitatively and quantitatively by using MVA methods, and this produces non-redundant but important information from the FTIR spectra. High resolution techniques such as X-ray crystallography and NMR are not always applicable and Fourier Transform Infrared (FTIR) spectroscopy, a widely applicable analytical technique, has great potential to assist structure analysis for a wide range of proteins. FTIR spectral shape and band positions in the Amide I (which contains the most intense absorption region), Amide II, and Amide III regions, can be analysed computationally, using multivariate regression, to extract structural information. In this thesis Partial least squares (PLS), a form of MVA, was used to correlate a matrix of FTIR spectra and their known secondary structure motifs, in order to determine their structures (in terms of "helix", "sheet", “310-helix”, “turns” and "other" contents) for a selection of 84 non-redundant proteins. Analysis of the spectral wavelength range between 1480 and 1900 cm-1 (Amide I and Amide II regions) results in high accuracies of prediction, as high as R2 = 0.96 for α-helix, 0.95 for β-sheet, 0.92 for 310-helix, 0.94 for turns and 0.90 for other; their Root Mean Square Error for Calibration (RMSEC) values are between 0.01 to 0.05, and their Root Mean Square Error for Prediction (RMSEP) values are between 0.02 to 0.12. The Amide II region also gave results comparable to that of Amide I, especially for predictions of helix content. We also used Principal Component Analysis (PCA) to classify FTIR protein spectra into their natural groupings as proteins of mainly α-helical structure, or protein of mainly β-sheet structure or proteins of some mixed variations of α-helix and β-sheet. We have also been able to differentiate between parallel and anti-parallel β-sheet. The developed methods were applied to characterize the secondary structure conformational changes of an unfolding protein as a function of pH and also to determine the limit of Quantitation (LoQ).Our structural analyses compare highly favourably to those in the literature using machine learning techniques. Our work proves that FTIR spectra in combination with multivariate regression analysis like PCA and PLS, can accurately identify and quantify protein secondary structure. The developed models in this research are especially important in the pharmaceutical industry where the therapeutic effect of drugs strongly depends on the stability of the physical or chemical structure of their proteins targets; therefore, understanding the structure of proteins is very important in the biopharmaceutical world for drugs production and formulation. There is a new class of drugs that are proteins themselves used to treat infectious and autoimmune diseases. The use of spectroscopy and multivariate regression analysis in the medical industry to identify biomarkers in diseases has also brought new challenges to the bioinformatics field. These methods may be applicable in food science and academia in general, for the investigation and elucidation of protein structure.

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20

Schkolnik, Gal [Verfasser], and Peter [Akademischer Betreuer] Hildebrandt. "Vibrational Stark Spectroscopy as a Tool for Probing Electrostatics at Protein Surfaces and Self Assembled Monolayers / Gal Schkolnik. Betreuer: Peter Hildebrandt." Berlin : Universitätsbibliothek der Technischen Universität Berlin, 2012. http://d-nb.info/1028912951/34.

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21

Agathangelou, Damianos. "Anabaena Sensory Rhodopsin : effect of mutations on the ultrafast photo-isomerization dynamics." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAE001/document.

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ASR, est une protéine photo réceptrice qui lie la base protonée de la rétine de Schiff dans deux conformations de l'état fondamental. La protéine particulière consiste en un système modèle dans lequel I'effet de l'environnement protéique sur la dynamique d'isomérisation des deux isomères peut être étudié. Dans cette thèse, une étude approfondie sur les protéines mutées ponctuellement est présentée, où la variable est l'environnement protéique. Les résultats montrent des différences significatives entre les durées de vie des états excités des deux isomères et les durées de vie plus courtes ou plus longues commentées en termes de mélange électronique Sl/S2. En complément, le développement expérimental d'un spectromètre à absorption transitoire (T.A) et d'un dispositif de spectroscopie électronique bidimensionnelle (2DES) fonctionnant respectivement dans les domaines spectral NIR et UV-Vis. Avec cette configuration, deux impulsions colinéaires à verrouillage de phase d'une durée inférieure à 10fs sont générées, où. la précision interférométrique sur le contrôle du retard entre les deux impulsions de pompe permet d'effectuer des mesures 2DES
ASR, is a photoreceptor protein that binds the protonated Schiff base of retinal in two ground state conformations. The particular protein consists a model system where the effect of the protein environment on the isomerization dynamics of the two isomers can be investigated. In this thesis an extended study on point mutated proteins is presented where the variable is the protein environment. The results show significant differences between the two isomers excited state lifetimes with the shorter or longer lifetimes commented in terms of Sl/S2 electronic mixing. Supplementary, the experimental development of a Transient absorption spectrometer (T.A) and a Two-dimensional electronic spectroscopy setup (2DES) operating in the NIR and UV-Vis spectral range respectively are described. The 2DES spectrometer is based on translating wedges made out of birefringent material producing two collinear phase-locked pulses with sub-I Ofs duration. The interferometric precision on controlling the delay between the two pump pulses allows to perform 2DES measurements on systems absorbing in the 360-430 nm range allowing to resolve the excitation process spectrally

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22

Maggi, Luca [Verfasser], Paolo [Akademischer Betreuer] Carloni, and Benjamin [Akademischer Betreuer] Stamm. "How vibrational energy exchange study in proteins can shed the light on important biological functions / Luca Maggi ; Paolo Carloni, Benjamin Stamm." Aachen : Universitätsbibliothek der RWTH Aachen, 2020. http://d-nb.info/1240689373/34.

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23

Forbrig, Enrico [Verfasser], Peter [Akademischer Betreuer] Hildebrandt, Peter [Gutachter] Hildebrandt, Thomas [Gutachter] Gutsmann, and Peter [Gutachter] Hegemann. "Investigation of membrane-active peptides and proteins by vibrational spectroscopy / Enrico Forbrig ; Gutachter: Peter Hildebrandt, Thomas Gutsmann, Peter Hegemann ; Betreuer: Peter Hildebrandt." Berlin : Technische Universität Berlin, 2018. http://d-nb.info/1165138891/34.

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24

Polander, Brandon C. "The hydrogen-bonded water network in the oxygen-evolving complex of photosystem II." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50222.

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Protein dynamics play a key role in enzyme-catalyzed reactions. Vibrational spectroscopy provides a method to follow these structural changes and thereby describe the reaction coordinate as a function of space and time. A vibrational spectroscopic technique, reaction-induced FTIR spectroscopy, has been applied to the study of the oxygen-evolving complex (OEC) of photosystem II (PSII). In plant photosynthesis, PSII evolves oxygen from the substrate, water, by the accumulation of photo-oxidizing equivalents at the OEC. Molecular oxygen and protons are the products of this reaction, which is responsible for the maintenance of an aerobic atmosphere on earth. The OEC is a Mn4CaO5 cluster with nearby bound chloride ions. Sequentially oxidized states of the OEC are termed the S states. The dark-stable state is S1, and oxygen is released on the transition from S3 to S0. Using short laser flashes, individual S states are generated, allowing vibrational spectroscopy to be used to study these different oxidation states of the OEC. In current X-ray crystal structures, hydrogen bonds to water molecules are predicted to form an extensive network around the Mn4CaO5 cluster. In the OEC, four peptide carbonyl groups are linked to the water network, which extends to two Mn-bound and two Ca-bound water molecules. This dissertation discusses a vibrational spectroscopic method that uses these peptide carbonyl frequencies as reporters of solvatochromic changes in the OEC. This technique provides a new, high-resolution method with which to study water and protein dynamics in PSII and other enzymes.

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25

Sintorn, Johan. "Enclosing and Mounting an Electronic Component on Articulated Haulers : A proposition on how to protect, and where to place, an intelligent node on the environmentally harsh exterior of construction equipment with respect to multiple parameters." Thesis, Linköpings universitet, Maskinkonstruktion, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-134053.

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As is the case with many other manufacturers of vehicles, Volvo Construction Equipment has a constantly increasing amount of electric and electronic equipment in their articulated haulers. These are of great use in modern machines, bringing functions, and safety that were not possible before, but they also bring more cables to handle. In the case of the articulated haulers a quite thick cable harness of about 15 meters in length reaches from the driver’s cabin in the front to the components in the far back end of the vehicle. This is not only a lot of long cables to handle both during assembly and service, but the nature of signals traveling in cables is that the voltage gets weaker with distance. This phenomenon has to be accounted for by measuring devices dependent on the voltage. It has been suggested that a device referred to as an intelligent node, or ICCS-module, which communicates digitally via CAN could be installed in the back of the articulated haulers. This module would be independent of the mentioned drop in voltage. The ICCS-module will be receiving a small bundle of cables being routed from the driver’s cabin. From it cables would go out to a majority of the components in its vicinity. The components connected to the node would not need to have any other cables. This thesis is focused on the mechanical aspects of installing this ICCS-module. Having electric and electronic equipment on construction vehicles is a challenge when it comes to protecting the device from the harsh environment that is the hauler’s exterior. It will have to withstand being immersed in water for long periods of time, greatly varying temperatures, vibrations and shocks as well as being hit by projectiles. The placement as well as the design of the enclosure should be chosen with respect to both the devices length of life and how well it fulfils its intended role and achieves the expected results. To produce an enclosure and find a placement aiming to satisfy these conditions, a traditional product development process were executed. The articulated haulers as well as relevant literature were researched. Concepts were generated and evaluated by both the author and by employees at Volvo Construction Equipment until a final concept for the enclosure and placement were found. The enclosure were then designed in detail specifying the material, manufacturing techniques, controlled for thermodynamic circumstances, modelled in Catia V5 and controlled for vibrations. It was concluded that the enclosure should be able protect the ICCS-module after some more development and that the placement and cable routing results in a much shorter total cable length.

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26

Kielb, Patrycja [Verfasser], Inez M. [Akademischer Betreuer] Weidinger, Peter [Akademischer Betreuer] Hildebrandt, Peter [Gutachter] Hildebrandt, Inez M. [Gutachter] Weidinger, and Arne [Gutachter] Thomas. "Redox processes of heme proteins and metalloporphyrins studied by vibrational spectroelectrochemistry / Patrycja Kielb ; Gutachter: Peter Hildebrandt, Inez M. Weidinger, Arne Thomas ; Inez M. Weidinger, Peter Hildebrandt." Berlin : Technische Universität Berlin, 2017. http://d-nb.info/1156014883/34.

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Eberl, Katharina Barbara [Verfasser], Jens [Akademischer Betreuer] Bredenbeck, Jens [Gutachter] Bredenbeck, and Josef [Gutachter] Wachtveitl. "Applying non-canonical amino acids for investigation of vibrational energy transfer and dynamic allostery in a synaptic protein domain / Katharina Barbara Eberl ; Gutachter: Jens Bredenbeck, Josef Wachtveitl ; Betreuer: Jens Bredenbeck." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2020. http://d-nb.info/1222102676/34.

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Müller-Werkmeister, Henrike [Verfasser], Jens [Gutachter] Bredenbeck, and Harald [Gutachter] Schwalbe. "Unnatural amino acids as novel probes for ultrafast 2D-IR spectroscopy of proteins : towards real-time investigation of biomolecular dynamics and vibrational energy flow / Henrike Müller-Werkmeister ; Gutachter: Jens Bredenbeck, Harald Schwalbe." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2017. http://d-nb.info/1139048546/34.

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29

Harb, Zeinab. "Détermination théorique des paramètres RMN de métabolites et protéines." Phd thesis, Université Claude Bernard - Lyon I, 2011. http://tel.archives-ouvertes.fr/tel-00740957.

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Ce travail présente une étude théorique des spectres RMN de molécules biologiques. Dans la première partie, les calculs DFT des paramètres RMN (déplacements chimiques et constantes de couplage spin-spin) pour les protons liés à des atomes de carbone ont été réalisés pour quatre métabolites de la prostate: la putrescine, la spermidine, la spermine, et la sarcosine, et trois métabolites du cerveau: l'acétate, l'alanine et la sérine. Une étude théorique systématique, dans l'approche DFT, des paramètres de RMN des métabolites a montré que la méthode B3LYP/6-311++G** est un bon compromis entre la précision et les coûts. Les contributions du solvant ont été évaluées en utilisant le modèle PCM, les effets des isomères, pondérés dans l'approximation de Boltzmann, ont été pris en compte, et les corrections de vibration de point zéro ont été estimées en utilisant une approche perturbative au second ordre. La comparaison avec l'expérience a démontré que tous ces effets sont nécessaires pour améliorer l'accord entre les données calculées et expérimentales, aboutissant à des résultats de grande précision. Dans la deuxième partie, nous avons développé un nouveau modèle, BioShift, qui permet la prédiction des déplacements chimiques des différents noyaux (H, N, C ...) pour des molécules biologiques (protéines, ADN, ARN, polyamine ...). Il est simple, rapide, et comporte un nombre limité de paramètres. La comparaison avec des modèles sophistiqués conçus spécialement pour la prédiction des déplacements chimiques des protéines a montré que Bioshift est concurrentiel avec de tels modèles.

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30

Ragain, Christina Marie. "Role of local electrostatic fields in protein-protein and protein-solvent interactions determined by vibrational Stark effect spectroscopy." Thesis, 2014. http://hdl.handle.net/2152/24949.

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This examines the interplay of structure and local electrostatic fields in protein-protein and protein-solvent interactions. The partial charges of the protein amino acids and the polarization of the surrounding solvent create a complex system of electrostatic fields at protein-protein and protein-solvent interfaces. An approach incorporating vibrational Stark effect (VSE) spectroscopy, dissociation constant measurements, and molecular dynamics (MD) simulations was used to investigate the electrostatic interactions in these interfaces. Proteins p21Ras (Ras) and Rap1A (Rap) have nearly identical amino acid sequences and structures along the effector-binding region but bind with different affinities to Ral guanine nucleotide dissociation stimulator (RalGDS). A charge reversion mutation at position 31 alters the binding affinity of Ras and Rap with RalGDS from 0.1 [mu]M and 1 [mu]M, to 1 [mu]M and 0.5 [mu]M, respectively. A spectral probe was placed at various locations along the binding interface on the surface of RalGDS as it was docked with Ras and Rap single (position 30 or 31) and double mutants (both positions). By comparing the probes' absorption energies with the respective wild-type (WT) analogs, VSE spectroscopy was able to measure molecular-level electrostatic events across the protein-protein interface. MD simulations provided a basis for deconvoluting the structural and electrostatic changes observed by the probes. The mutation at position 31 was found to be responsible for both structural and electrostatic changes compared to the WT analogs. Furthermore, previous identification of positions N27 and N29 on RalGDS as "hot spots" that help discriminate between structurally similar GTPases was supported. The RalGDS probe-containing variants and three model compounds were placed in aqueous solvents with varying dielectric constants to measure changes in absorption energy. We investigated the ability of the Onsager solvent model to describe the solvent induced changes in absorption energy, while MD simulations were employed to determine the location and solvation of the probes at the protein-solvent interface. The solvent accessible-surface area, a measure of hydration, was determined to correlate well with the change in magnitude of the probe's absorption energy and the displaced solvent by the probe.
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31

Fafarman, Aaron Thomas Boxer Steven G. Chidsey Christopher E. D. Pecora Robert. "Quantitative measurement of electrostatic fields in proteins using vibrational probes." 2010. http://purl.stanford.edu/mb274tk4375.

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32

Ritchie, Andrew William. "Quantifying electrostatic fields at protein interfaces using classical electrostatics calculations." Thesis, 2015. http://hdl.handle.net/2152/31346.

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The functional aspects of proteins are largely dictated by highly selective protein- protein and protein-ligand interactions, even in situations of high structural homology, where electrostatic factors are the major contributors to selectivity. The vibrational Stark effect (VSE) allows us to measure electrostatic fields in complex environments, such as proteins, by the introduction of a vibrational chromophore whose vibrational absorption energy is linearly sensitive to changes in the local electrostatic field. The works presented here seek to computationally quantify electrostatic fields measured via VSE, with the eventual goal of being able to quantitatively predict electrostatic fields, and therefore Stark shifts, for any given protein-interaction. This is done using extensive molecular dynamics in the Amber03 and AMOEBA force fields to generate large ensembles the GTPase Rap1a docked to RalGDS and [superscript p]²¹Ras docked to RalGDS. We discuss how side chain orientations contribute to the differential binding of different mutations of Rap1a binding to RalGDS, where it was found that a hydrogen-bonding pocket is disrupted by the mutation of position 31 from lysine to glutamic acid. We then show that multi-dimensional umbrella sampling of the probe orientations yields a wider range of accessible structures, increasing the quality of the ensembles generated. A large variety of methods for calculating electrostatic fields are presented, with Poisson- Boltzmann electrostatics yielding the most consistent, reliable results. Finally, we explore using AMOEBA for both ensemble-generation as well as the electrostatic description of atoms for field calculations, where early results suggest that the electrostatic field due to the induce dipole moment of the probe is responsible for predicting qualitatively correct Stark shifts.

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Stafford, Amy Jo. "Electrostatic fields at the functional interface of the protein Ral guanine nucleotide dissociation stimulator determined by vibrational Stark effect spectroscopy." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-12-4685.

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Noncovalent factors, such as shape complementarity and electrostatic driving forces, almost exclusively cause the affinity and specificity for which two or more biological macromolecules organize into a functioning complex. The human oncoprotein p21Ras (Ras) and a structurally identical but functionally distant analog, Rap1A (Rap), exhibit high selectivity and specificity when binding to downstream effector proteins that cannot be explained through structural analysis alone. Both Ras and Rap bind to Ral guanine nucleotide dissociation stimulator (RalGDS) with affinities that differ tenfold instigating diverse cellular functions; it is hypothesized that this specificity of RalGDS to discriminate between GTPases is largely electrostatic in nature. To investigate this hypothesis, electrostatic fields at the binding interface between mutants of RalGDS bound to Rap or Ras are measured using vibrational Stark effect (VSE) spectroscopy, in which spectral shifts of a probe oscillator’s energy is related directly to that probe’s local electrostatic environment and measured by Fourier transform infrared spectroscopy (FTIR). After calibration, the probe is inserted into a known position in RalGDS where it becomes a highly local, sensitive, and directional reporter of fluctuations of the protein’s electrostatic field caused by structural or chemical perturbations of the protein. The thiocyanate (SCN) vibrational spectroscopic probe was systematically incorporated throughout the binding interface of RalGDS. Changes in the absorption energy of the thiocyanate probe upon binding were directly related to the change of the strength of the local electrostatic field in the immediate vicinity of the probe, thereby creating a comprehensive library of the binding interactions between Ras-RalGDS and Rap-RalGDS. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations with the results highlighting the complex structural and electrostatic nature of protein-water interface. Additional SASA studies of the nine RalGDS mutants that bind to Ras or Rap verified that experimentally measured thiocyanate absorption energies are negatively correlated with exposure to water at the protein-water interface. By changing the solvent composition, we confirmed that the cyanocysteine residues that are more exposed to solvent experienced a large difference in absorption energy. These studies reinforce the hypothesis that differences in the electrostatic environment at the binding interfaces of Ras and Rap are responsible for discriminating binding partners.
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34

Ogren, John Isaac. "Vibrational spectroscopy of an optogenetic rhodopsin: a biophysical study of molecular mechanisms." Thesis, 2015. https://hdl.handle.net/2144/16343.

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In this dissertation,the membrane protein channelrhodopsin-1 from the green flagellate algae Chlamydomonas agustae (CaChR1) is studied using a variety of spectroscopic techniques developed in the Rothschild Molecular Biophysics Laboratory at Boston University. Over the last decade, channelrhodopsins have proven to be effective optogenetic tools due to their ability to function as light-gated ion channels when expressed in neurons. This ability allows neuroscientists to optically activate an inward directed photocurrent which depolarizes the neuronal membranes and triggers an action potential. Although a variety of channelrhodopsins with different properties have been used, the underlying mechanisms of channelrhodopsin functionality is not yet fully understood. The protein studied here has several advantageous properties compared to the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii including a red shifted visible absorption and slower light inactivation despite having a lower channel current. Elucidating the internal molecular mechanisms underlying the function of CaChR1 provides critical insight into the large class of channelrhodopsin proteins leading toward improved bioengineering for specific optogenetic applications. Here near-IR pre-resonance Raman spectroscopy of CaChR1 provides information on the structure of the unphotolyzed (P0) retinal chromophore, the Schiff base protonation state, and presence of carboxylic acid residues interacting with the Schiff base. Low-temperature FTIR difference spectroscopy combined with site-directed mutagenesis and isotope labeling provide information on changes occurring in the retinal chromophore and protein during the primary phototransition (P0 to P1). This includes information about changes involving protonation state of binding-pocket residues, protein backbone structure, and internal water molecules. Further experiments combining low-temperature and time-resolved FTIR-difference spectroscopy reveal additional information about structural changes during the transition from the unphotolyzed state to the active (open channel) state of the protein (P0 to P2). This work has resulted in an initial model that describes key proton transfer events which occur between the Schiff base and carboxylic acid residues inside the active site of CaChR1. The model raises the possibility that ion channel gating and ion specificity is regulated by the protonation changes of two key residues (Glu 169 and Asp299) located near the Schiff base.

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35

"Calculating Infrared Spectra of Proteins and Other Organic Molecules Based on Normal Modes." Doctoral diss., 2012. http://hdl.handle.net/2286/R.I.15193.

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abstract: The goal of this theoretical study of infrared spectra was to ascertain to what degree molecules may be identified from their IR spectra and which spectral regions are best suited for this purpose. The frequencies considered range from the lowest frequency molecular vibrations in the far-IR, terahertz region (below ~3 THz or 100 cm-1) up to the highest frequency vibrations (~120 THz or 4000 cm-1). An emphasis was placed on the IR spectra of chemical and biological threat molecules in the interest of detection and prevention. To calculate IR spectra, the technique of normal mode analysis was applied to organic molecules ranging in size from 8 to 11,352 atoms. The IR intensities of the vibrational modes were calculated in terms of the derivative of the molecular dipole moment with respect to each normal coordinate. Three sets of molecules were studied: the organophosphorus G- and V-type nerve agents and chemically related simulants (15 molecules ranging in size from 11 to 40 atoms); 21 other small molecules ranging in size from 8 to 24 atoms; and 13 proteins ranging in size from 304 to 11,352 atoms. Spectra for the first two sets of molecules were calculated using quantum chemistry software, the last two sets using force fields. The "middle" set used both methods, allowing for comparison between them and with experimental spectra from the NIST/EPA Gas-Phase Infrared Library. The calculated spectra of proteins, for which only force field calculations are practical, reproduced the experimentally observed amide I and II bands, but they were shifted by approximately +40 cm-1 relative to experiment. Considering the entire spectrum of protein vibrations, the most promising frequency range for differentiating between proteins was approximately 600-1300 cm-1 where water has low absorption and the proteins show some differences.
Dissertation/Thesis
Ph.D. Physics 2012

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36

Pazderka, Tomáš. "Studium struktury a dynamiky proteinů pomocí optické spektroskopie." Doctoral thesis, 2018. http://www.nusl.cz/ntk/nusl-389831.

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Title: Study of protein structure and dynamics by means of optical spectroscopy Author: Tomáš Pazderka Institute: Institute of Physics of Charles University Supervisor: RNDr. Vladimír Kopecký, Ph.D., Institute of Physics of Charles University Abstract: The aim of this thesis is to improve understanding of protein structure and dynamics and extend experimental setup and data processing for such stud- ies. We focus on the extension of experimental feasability of vibrational optical activity (VOA). We have demonstrated a usability of intensity calibration in the field of Raman optical activity. Advantages for measurements on multiple instru- ments and/or using different configurations have been shown. A new instrumental setup has been developed for microsampling measurements of vibrational circular dichroism spectra with a spatial resolution of 1 mm. Using this technique, spatial inhomogeneities in a sample of protein fibrils have been observed. Model com- pounds for amide nonplanarity have been investigated utilizing several methods of optical spectroscopy and key spectral features for determination of amide non- planarity and the absolute configuration have been identified. A comprehensive set of Raman spectra of proteinogenic amino acids has been measured. Sample concentration dependencies and consequent...

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Víšová, Ivana. "Charakterizace proteinů dráhy 2'-5' oligoadenylátů pomocí vibrační spektroskopie." Master's thesis, 2015. http://www.nusl.cz/ntk/nusl-350883.

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The work concerns to structural characterization of two important proteins of 2'-5' oligoadenylate pathway participating in an immune response of organism to a viral infection. Studied proteins were ankyrin domain of mouse RNase L, the C-terminal part of human phosphodiesterase 12 and the complete human phosphodiesterase 12. The proteins were characterized by Raman spectroscopy, infrared spectroscopy, electronic circular dichroism, dynamic light scattering and in addition by two non-spectroscopic methods- differential calorimetry and electrophoresis. For each protein the secondary structures, thermal stability, weight of oligomers and generally a basic characterization by above mentioned methods were provided.

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Friedrich, Marcel Günther [Verfasser]. "Vibrational spectroscopic and electrochemical investigations of multi-centered heme proteins in biomimetic membrane architectures / vorgelegt von Marcel Günther Friedrich." 2009. http://d-nb.info/992048931/34.

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Krupová, Monika. "Teorie a aplikace optické aktivity biomolekul." Doctoral thesis, 2021. http://www.nusl.cz/ntk/nusl-447991.

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Title: Theory and Applications of Optical Activity of Biomolecules Author: Monika Krupová Supervisor: prof. RNDr. Petr Bouř, DSc. Institutions: Faculty of Mathematics and Physics, Charles University, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Abstract: This thesis describes how we used several chiroptical spectroscopic methods to study chiral molecules: vibrational circular dichroism (VCD), circularly polarized luminescence (CPL) and magnetic circular dichroism (MCD). VCD and induced lanthanide CPL were used to study the structure of amyloid protein fibrils. We found out that VCD is very sensitive to their structure and supramolecular chirality. It could be used to distinguish between various polymorphic fibrils. On the other hand, induced lanthanide CPL provided information on the local structure. VCD was also used to study the hydration polymorphism of nucleoside crystals. Due to the crystal packing, the VCD signal was strong and specific for different types of crystals. Finally, electronic structure of hydrated Ln3+ ions was studied by MCD. Molecular dynamics simulations together with crystal field theory (CFT) and multistate complete active space calculations with second order perturbation correction (MS-CASPT2) were used to interpret the spectra. CFT...

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40

Winkler, Kathrin. "Ultraschnelle, lichtinduzierte Primärprozesse im elektronisch angeregten Zustand des Grün Fluoreszierenden Proteins (GFP)." Doctoral thesis, 2003. http://hdl.handle.net/11858/00-1735-0000-0006-B0C1-3.

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Terrett, Richard Norman Leslie. "Computational Investigation of the Oxygen Evolving Complex of Photosystem II and Related Models via Density Functional Theory." Phd thesis, 2017. http://hdl.handle.net/1885/133592.

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The first step of photosynthetic metabolism effects the facile oxidation of water to dioxygen and hydrogen cations. This is achieved through an incompletely-understood process of light-driven four-electron oxidation at the Mn4CaO5 cofactor of the Oxygen Evolving Complex (OEC) of the Photosystem II (PSII) holoenzymatic complex in photosynthetic autotrophs. Biomimesis of this reaction—artificial photosynthesis—may offer energy-efficient routes to industrial hydrogen generation and value-added derivatives, with implications for solar energy fixation. This thesis consists of a compilation of four publications relating to Density Functional Theory (DFT) studies of structural and spectroscopic aspects of the OEC of PSII. These publications consist of research resolving the basis of structural anomalies in metal-substituted PSII, combinatoric simulation of difference spectra corresponding to proton-coupled oxido-reduction scenarios of PSII models, simulation of the hyperfine and superexchange magnetic interactions in PSII models, and the development of a methodology for obtaining vibrational intensities in the Mobiel Block Hessian (MBH) approximation, with applications to accelerated modeling of the vibrational structure of complex models of PSII, as well as other large molecules. These publications are presented alongside explanatory introductions and preceded by a general survey of the state of the art of photosynthesis research, context for the relevance of this research, and methodological discussion. Concluding remarks are also presented.

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