Готові списки джерел за темами / Protein vibration

Добірка наукової літератури з теми "Protein vibration"

Автор: Grafiati
Опубліковано: 14 березня 2023

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Статті в журналах з теми "Protein vibration"

1

Lu, Qin-Qin, Da-Chuan Yin, Yong-Ming Liu, Xi-Kai Wang, Peng-Fei Yang, Zheng-Tang Liu, and Peng Shang. "Effect of mechanical vibration on protein crystallization." Journal of Applied Crystallography 43, no. 3 (April 15, 2010): 473–82. http://dx.doi.org/10.1107/s0021889810009313.

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Анотація:
Mechanical vibration often occurs during protein crystallization; however, it is seldom considered as one of the factors influencing the crystallization process. This paper reports an investigation of the crystallization of five proteins using various crystallization conditions in a temperature-controlled chamber on the table of a mechanical vibrator. The results show that mechanical vibration can reduce the number of crystals and improve their optical perfection. During screening of the crystallization conditions it was found that mechanical vibration could help to obtain crystals in a highly supersaturated solution in which amorphous precipitates often normally appear. It is concluded that mechanical vibration can serve as a tool for growing optically perfect crystals or for obtaining more crystallization conditions during crystallization screening.
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2

Fournier, Frédéric, Elizabeth M. Gardner, Darek A. Kedra, Paul M. Donaldson, Rui Guo, Sarah A. Butcher, Ian R. Gould, Keith R. Willison, and David R. Klug. "Protein identification and quantification by two-dimensional infrared spectroscopy: Implications for an all-optical proteomic platform." Proceedings of the National Academy of Sciences 105, no. 40 (October 1, 2008): 15352–57. http://dx.doi.org/10.1073/pnas.0805127105.

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Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Two-dimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to <1 min per protein by using the same technology. Finally, we show that absolute quantification of protein levels is relatively straightforward to achieve and discuss the potential of an all-optical high-throughput proteomic platform based on two-dimensional infrared spectroscopic measurements.
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3

Nakai, Kumiko, Hideki Tanaka, Kyoko Fukuzawa, Jyunya Nakajima, Manami Ozaki, Nobue Kato, and Takayuki Kawato. "Effects of Electric-Toothbrush Vibrations on the Expression of Collagen and Non-Collagen Proteins through the Focal Adhesion Kinase Signaling Pathway in Gingival Fibroblasts." Biomolecules 12, no. 6 (June 1, 2022): 771. http://dx.doi.org/10.3390/biom12060771.

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Анотація:
Electric-toothbrush vibrations, which remove plaque, are transmitted to the gingival connective tissue via epithelial cells. Physical energy affects cell function; however, the effects of electric-toothbrush vibrations on gingival extracellular matrix (ECM) protein expression remain unknown. We aimed to examine the effects of these vibrations on the expression of ECM proteins—type I collagen (col I), type III collagen (col III), elastin, and fibronectin (FN)—using human gingival fibroblasts (HGnFs). HGnFs were seeded for 5 days in a six-well plate with a hydrophilic surface, exposed to electric-toothbrush vibrations, and cultured for 7 days. Subsequently, the mRNA and protein levels of col I, col III, elastin, and FN were examined. To investigate the role of focal adhesion kinase (FAK) signaling on ECM protein expression in vibration-stimulated cells, the cells were treated with siRNA against protein tyrosine kinase (PTK). Electric-toothbrush vibrations increased col I, col III, elastin, and FN expression; promoted collagen and non-collagen protein production; and enhanced FAK phosphorylation in HGnFs. Moreover, PTK2 siRNA completely blocked the effects of these vibrations on the expression of col I, col III and elastin mRNA. The results suggest that electric-toothbrush vibrations increase collagen, elastin, and FN production through the FAK-signaling pathway in fibroblasts.
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4

Hassanpour, Halimeh, Vahid Niknam, and Sadaf Salami. "Acceleration Breaks the Cells Defense Mechanisms against Vibration in Anthemis gilanica Calli." International Journal of Agronomy 2021 (March 20, 2021): 1–12. http://dx.doi.org/10.1155/2021/8862860.

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Анотація:
Vibration is a mechanical stress which happens in nature and affects many biological aspects of plants. In this research, the effect of acceleration and vibration was investigated on some physiological and biochemical responses of Anthemis gilanica in vitro. Calli were induced from leaf (LS) and root segments (RS) and were applied to different frequencies of vibrations (0, 50, and 100 Hz) and accelerations (1, 2, and 4 g) on the A. gilanica calli for 30 min. Results showed that vibration significantly increased relative water content (RWC), growth parameters, protein and proline contents, ascorbate peroxidase (APX), peroxidase (POX), and superoxide dismutase (SOD) activities and decreased total carbohydrate, malondialdehyde (MDA), H2O2 contents, and polyphenol oxidase (PPO) activity in both LS and RS calli. Inversely, increase of acceleration in vibrated calli decreased growth parameters, RWC, protein content, and POX activity and induced proline and carbohydrate accumulations, SOD, APX, and PPO activities as compared to vibration alone. Different responses of two callus types were observed, and the highest growth, protein content, and membrane stability were observed in LS calli as compared to RS calli. It found that high acceleration amplitude intensified the resonance effect of vibration by induction of lipid peroxidation and oxidative stress damage in A. gilanica.
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5

Gronenberg, Wulfila, Ajay Raikhelkar, Eric Abshire, Jennifer Stevens, Eric Epstein, Karin Loyola, Michael Rauscher, and Stephen Buchmann. "Honeybees ( Apis mellifera ) learn to discriminate the smell of organic compounds from their respective deuterated isotopomers." Proceedings of the Royal Society B: Biological Sciences 281, no. 1778 (March 7, 2014): 20133089. http://dx.doi.org/10.1098/rspb.2013.3089.

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Анотація:
The understanding of physiological and molecular processes underlying the sense of smell has made considerable progress during the past three decades, revealing the cascade of molecular steps that lead to the activation of olfactory receptor (OR) neurons. However, the mode of primary interaction of odorant molecules with the OR proteins within the sensory cells is still enigmatic. Two different concepts try to explain these interactions: the ‘odotope hypothesis’ suggests that OR proteins recognize structural aspects of the odorant molecule, whereas the ‘vibration hypothesis’ proposes that intra-molecular vibrations are the basis for the recognition of the odorant by the receptor protein. The vibration hypothesis predicts that OR proteins should be able to discriminate compounds containing deuterium from their common counterparts which contain hydrogen instead of deuterium. This study tests this prediction in honeybees ( Apis mellifera ) using the proboscis extension reflex learning in a differential conditioning paradigm. Rewarding one odour (e.g. a deuterated compound) with sucrose and not rewarding the respective analogue (e.g. hydrogen-based odorant) shows that honeybees readily learn to discriminate hydrogen-based odorants from their deuterated counterparts and supports the idea that intra-molecular vibrations may contribute to odour discrimination.
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6

Goldsmith, P. C., F. Abadia Molina, C. B. Bunker, G. Terenghi, T. A. Leslie, Clare J. Fowler, J. M. Polak, and Pauline M. Dowd. "Cutaneous Nerve Fibre Depletion in Vibration White Finger." Journal of the Royal Society of Medicine 87, no. 7 (July 1994): 377–81. http://dx.doi.org/10.1177/014107689408700703.

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Анотація:
Vibration white finger or hand-arm vibration syndrome is the episodic blanching of the fingers in response to cold occurring in those who work with hand held vibrating tools. Clinically the condition differs from primary Raynaud's phenomenon as persistent paraesthesiae and pain are common in the hands and arms and these occur independently from the ‘white attacks’. Symptoms can become severe enough to warrant a change of occupation. Industrial compensation may be awarded for vibration white finger but, at present, no simple or reliable objective diagnostic test is available. Calcitonin gene-related peptide (CGRP) is a neuropeptide with powerful vasodilator properties. A deficiency of immunoreactive CGRP nerve fibres has been previously demonstrated in the digital cutaneous microvasculature of patients with primary and secondary Raynaud's phenomenon with the distribution and quantity of other types of nerve fibres not being significantly altered. To determine if the innervation of the cutaneous microvasculature in vibration white finger was also abnormal skin biopsy samples from the fingers of 15 patients with vibration white finger, six healthy age matched controls who worked with vibrating machinery and 26 healthy age matched controls who were heavy manual workers without exposure to vibrating machinery were examined by immunohistochemistry. To try to correlate any histological abnormalities with clinical neurological deficit sensory nerve conduction studies have so far been performed in six patients with vibration white finger. There was a significant reduction in both the number of CGRP and protein gene product 9.5 (PGP) immunoreactive nerve fibres in the digital cutaneous biopsies from the patients with vibration white finger when compared to the biopsies from the heavy manual workers and the healthy workers exposed to vibration. The pattern of the loss of CGRP immunoreactive nerve fibres was similar to that described previously in Raynaud's phenomenon and may account for the episodic vasospasm seen in both conditions. PGP is a constitutive protein of all nerves therefore the reduced PGP immunostaining indicates generalized structural neuronal damage which could account for the persistent pain and paraesthesiae characteristic of vibration white finger. The nerve conduction studies revealed sensory nerve action potentials within the low range of normal in five patients with vibration white finger and mild median nerve compression in the remaining patient implying that the neuronal damage in the patients with vibration white finger is confined mainly to the small unmyelinated nerve fibres. The immunohistochemical findings may provide the basis for a diagnostic test for vibration white finger.
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7

Bodienkova, G. M., and S. I. Kurchevenko. "EVALUATION OF CYTOKINES AND HEAT SHOCK PROTEIN IN VIBRATION DISEASE." Medical Immunology (Russia) 20, no. 6 (December 15, 2018): 895–98. http://dx.doi.org/10.15789/1563-0625-2018-6-895-898.

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Анотація:
The prolonged impact of industrial vibration on workers leads to the development of a vibrational disease (VB), which occupies a leading position in the structure of occupational pathology. VB from the impact of local vibration is a chronic occupational disease characterized by a predominant lesion of the nervous, vascular system and musculoskeletal system of the upper and lower extremities. One of the real ways to reduce the incidence is the early detection of the negative impact of vibration on the body of workers. In this regard, cytokines and heat shock proteins (HSP70) can be early and sensitive indicators that reflect the severity of health disorders from exposure to vibration. The aim of the study was to study changes in the content of pro- and antiinflammatory cytokines, extracellular HSP70 and their relationship in patients with VB. In the immunological study included 43 male patients with a diagnosis of VB. The criteria for inclusion in this group were: a verified diagnosis, written informed consent to participate in the study, the harmful effects of local vibration in the workplace. According to the data of hygienic control, the working conditions of workers in dangerous occupations by vibration belong to the 4 (dangerous) class due to intensive local vibration. The content of cytokines: IL-1β, IL-8, IL-10, TNFα and HSP70 in the serum of patients was determined by enzyme immunoassay. The blood sampling for the study was taken from patients only once on admission to the hospital before the treatment. Statistical processing of data was carried out with the help of packages of application programs Statistica for Windows 6.0 and Microsoft Excel. It was established that the development of VB disease is accompanied by imbalance of the cytokine profile, characterized by a decrease in the levels of IL-1β, IL-10 and an increase in IL-8. The inhibition of production of IL-1β and IL-10 is a consequence of the chronic process that has developed in the body of the patients examined. And the revealed decrease in extracellular concentration of HSP70 in comparison with practically healthy people can be caused by the accumulation of it inside the cell or on its surface. Correlation analysis revealed the relationship between a decrease in HSP70 and an increase in IL-1β, and a decrease in IL-10 levels. Synthesis of HSP is an intracellular defense mechanism that prevents cell damage by activating the synthesis and secretion of pro-inflammatory cytokines. The obtained relationships between cytokines and HSP70 testify to the involvement of HSP70 in immunoinflammatory processes in VB. The revealed changes contribute to the chronic inflammatory process and justify the progressive course of the VB.
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8

Niessen, Katherine A., Mengyang Xu, Yanting Deng, Edward H. Snell, and Andrea G. Markelz. "Importance of Protein Vibration Directionality on Function." Biophysical Journal 112, no. 3 (February 2017): 353a. http://dx.doi.org/10.1016/j.bpj.2016.11.1916.

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9

Lu, Qin-Qin, Bin Zhang, Liang Tao, Lu Xu, Da Chen, Jing Zhu, and Da-Chuan Yin. "Improving Protein Crystal Quality via Mechanical Vibration." Crystal Growth & Design 16, no. 9 (July 26, 2016): 4869–76. http://dx.doi.org/10.1021/acs.cgd.6b00227.

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10

Sun, Chao, Ruixia Zeng, Ge Cao, Zhibang Song, Yibo Zhang, and Chang Liu. "Vibration Training Triggers Brown Adipocyte Relative Protein Expression in Rat White Adipose Tissue." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/919401.

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Анотація:
Recently, vibration training is considered as a novel strategy of weight loss; however, its mechanisms are still unclear. In this study, normal or high-fat diet-induced rats were trained by whole body vibration for 8 weeks. We observed that the body weight and fat metabolism index, blood glucose, triglyceride, cholesterol, and free fatty acid in obesity rats decreased significantly compared with nonvibration group(n=6). Although intrascapular BAT weight did not change significantly, vibration enhanced ATP reduction and increased protein level of the key molecule of brown adipose tissue (BAT), PGC-1α, and UCP1 in BAT. Interestingly, the adipocytes in retroperitoneal white adipose tissue (WAT) became smaller due to vibration exercise and had higher protein level of the key molecule of brown adipose tissue (BAT), PGC-1α, and UCP1 and inflammatory relative proteins, IL-6 and TNFα. Simultaneously, ATP content and PPARγprotein level in WAT became less in rats compared with nonvibration group. The results indicated that vibration training changed lipid metabolism in rats and promoted brown fat-like change in white adipose tissues through triggering BAT associated gene expression, inflammatory reflect, and reducing energy reserve.
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Дисертації з теми "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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Анотація:
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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Анотація:
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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Анотація:
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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Анотація:
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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Анотація:
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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Книги з теми "Protein vibration"

1

R, Baugher Charles, and United States. National Aeronautics and Space Administration., eds. G-jitter effects in protein crystal growth: A numerical study. [Washington, D.C: National Aeronautics and Space Administration, 1995.

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2

R, Baugher Charles, and United States. National Aeronautics and Space Administration., eds. G-jitter effects in protein crystal growth: A numerical study. [Washington, D.C: National Aeronautics and Space Administration, 1995.

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3

R, Baugher Charles, and United States. National Aeronautics and Space Administration., eds. G-jitter effects in protein crystal growth: A numerical study. [Washington, D.C: National Aeronautics and Space Administration, 1995.

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Protein, NATO Advanced Research Workshop on Self-Trapping of Vibrational Energy in. Davydov's soliton revisited: Self-trapping of vibrational energy in protein. New York: Plenum Press, 1990.

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5

N, Uversky Vladimir, and Permi͡akov E. A, eds. Methods in protein structure and stability analysis. New York: Nova Biomedical Books, 2007.

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6

G-jitter effects in protein crystal growth: A numerical study. [Washington, D.C: National Aeronautics and Space Administration, 1995.

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7

Vibrational Spectroscopy in Protein Research. Elsevier, 2020. http://dx.doi.org/10.1016/c2018-0-02644-4.

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8

Ozaki, Yukihiro, Malgorzata Baranska, Igor Lednev, and Bayden R. Wood. Vibrational Spectroscopy in Protein Research. Elsevier Science & Technology Books, 2020.

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9

Ozaki, Yukihiro, Malgorzata Baranska, Igor Lednev, and Bayden R. Wood. Vibrational Spectroscopy in Protein Research. Elsevier Science & Technology, 2020.

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(Editor), Vladimir N. Uversky, and Eugene A. Permyakov (Editor), eds. Methods in Protein Structure and Stability Analysis: Vibrational Spectroscopy (Molecular Anatomy and Physiology of Proteins). Nova Biomedical Books, 2007.

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Частини книг з теми "Protein vibration"

1

Singh, Pushpendra, Kanad Ray, D. Fujita, and Anirban Bandyopadhyay. "Complete Dielectric Resonator Model of Human Brain from MRI Data: A Journey from Connectome Neural Branching to Single Protein." In Engineering Vibration, Communication and Information Processing, 717–33. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-1642-5_63.

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2

Frauenfelder, Hans. "Vibrations." In The Physics of Proteins, 377–91. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-1044-8_27.

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Keiderling, Timothy A., Petr Pancoska, Sritana C. Yasui, Marie Urbanova, and Rina K. Dukor. "Conformational studies of proteins using vibrational circular dichroism." In Proteins, 165–70. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-010-9063-6_24.

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Scaramozzino, Domenico, Giuseppe Lacidogna, and Alberto Carpinteri. "Protein Vibrations and Elastic Network Models." In Waves in Biomechanics, 21–42. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-02614-0_3.

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Williams, Robert W. "Experimental Determination of Membrane Protein Secondary Structure Using Vibrational and CD Spectroscopies." In Membrane Protein Structure, 181–205. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4614-7515-6_8.

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Teixeira-Dias, J. J. C., E. M. V. Pires, P. J. A. Ribeiro-Claro, L. A. E. Batista de Carvalho, M. Aureliano, and Ana Margarida Amado. "A Vibrational Raman Spectroscopic Study of Myosin and Myosin - Vanadate Interactions." In Cellular Regulation by Protein Phosphorylation, 29–33. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-75142-4_3.

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7

Scaramozzino, Domenico, Giuseppe Lacidogna, and Alberto Carpinteri. "Exploring Protein Vibrations Experimentally: Raman and THz-TDS." In Waves in Biomechanics, 59–72. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-02614-0_5.

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8

Fayer, M. D., and Dana D. Dlott. "Vibrational Echo Studies of Heme-Protein Dynamics." In ACS Symposium Series, 324–37. Washington, DC: American Chemical Society, 1997. http://dx.doi.org/10.1021/bk-1997-0676.ch023.

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9

Hamm, P. "Ultrafast Peptide and Protein Dynamics by Vibrational Spectroscopy." In Biological and Medical Physics, Biomedical Engineering, 77–94. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-73566-3_4.

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Hochstrasser, R. M., B. R. Cowen, P. L. Dutton, C. Galli, S. LeCours, S. Maiti, C. C. Moser, et al. "Vibrational Dynamics in Condensed Phases and Proteins." In Springer Proceedings in Physics, 191–98. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-642-85060-8_48.

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Тези доповідей конференцій з теми "Protein vibration"

1

Непершина, О. П. "Deviation of indicators of blood plasma protein composition in vibration disease." In The second international youth Forum "OCCUPATION AND HEALTH". PT "ARIAL", 2018. http://dx.doi.org/10.31089/978-5-907032-51-4-2018-1-188-195.

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2

Kawaji, Masahiro. "Studies of Vibration-Induced Multi-Phase Fluid Phenomena and Pulsating Heat Pipe Performance Under Microgravity." In ASME/JSME 2003 4th Joint Fluids Summer Engineering Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/fedsm2003-45664.

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High quality semi-conductor and protein crystals can be grown in space by utilizing the microgravity environment in which natural convection and sedimentation effects are suppressed. But some vibrations exist on space platforms such as Space Shuttle and International Space Station that can induce crystal and fluid motions, affecting the quality of the crystals grown in space. Since the effects of small vibrations (called g-jitter) on crystal growth are not yet precisely known in space, experimental and theoretical investigations are being conducted to better understand the vibration effects on the motion of protein crystals and solid particles in liquid-filled cells. Another topic under investigation is the operation of pulsating heat pipes under microgravity. A recent experiment performed on a parabolic airplane has shown the positive effect of reduced gravity on the pulsating motion of vapour-liquid two-phase flow and heat transport in pulsating heat pipes.
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3

Yeh, Po-Ying, Mu Chiao, and Jayachandran N. Kizhakkedathu. "An Investigation on a Vibration-Based Active Protein Desorption Mechanism for Implantable MEMS-Based Biosensor Applications." In TRANSDUCERS '07 & Eurosensors XXI. 2007 14th International Conference on Solid-State Sensors, Actuators and Microsystems. IEEE, 2007. http://dx.doi.org/10.1109/sensor.2007.4300255.

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4

Shiraishi, Toshihiko, Tetsuo Shikata, Shin Morishita, and Ryohei Takeuchi. "Investigation of Promotion of Bone Matrices in Cultured Osteoblasts by Mechanical Vibration." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11131.

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This paper describes effects of mechanical vibration on osteoblasts. Their bone mass generation was investigated when sinusoidal inertia force was applied to the cells. After the cells were cultured in culture plates in a CO2 incubator for one day and adhered on the cultured plane, vibration group of the culture plate was set on an aluminum plate attached to a exciter and cultured under sinusoidal excitation of 0.5 G and 25 Hz for 24 hours a day in another incubator separated from non-vibration group during 28 days of culture. Gene expression of alkaline phosphatase (ALP) was measured by a real-time reverse transcription polymerase chain reaction method. ALP activity was measured by Azo-dye method. Calcium salts generated by the cells were observed by being stained with alizarin red S solution. As a result, it is found that the mechanical vibration accelerates the gene expression and protein generation of ALP, and the calcium salt generation.
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5

Shi, Caleb, Robert Chang, and Donna Leonardi. "The Effects of Mechanical Vibration on Cellular Health in Differentiated Neuroblastoma Cells." In ASME 2018 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/detc2018-86280.

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The effects of mechanical impact forces on neurological health is a critical concern, likely due to issues of traumatic brain injury (TBI) in sports and brain damage stemming from the potential of “sonic terrorism.” The quantitative analysis and evaluation of such forces on brain tissue function is very difficult. To address this issue, this research proposes a novel approach of using a cellular model subjected to mechanical vibration for analysis. Here, neuron-like differentiated neuroblastoma cells were subjected to vibration at frequencies of 20, 200, 2000, and 20000 Hz for a period of 24 hours at constant amplitude. Cell proliferation and inflammatory cytokine production, including IL-6, IL-1β, and TGF-β1, was measured as response of the cells and indicators of cellular health after vibrational treatment. Cell proliferation was found to increase after 20, 200, and 20000 Hz treatments; p<0.05) and decrease after 2000 Hz treatment (p<0.05). IL-6 production was found to decrease after 200 and 20000 Hz treatments (p<0.01) and increase after 20 and 2000 Hz treatments (p<0.01). IL-1β protein production was found to decrease after 20 Hz and increase after 200 Hz treatments (p<0.001), while TGF-β1 was found to decrease after 200 Hz treatment (p<0.001). The results suggest that cell proliferation and cytokine production serve as a sensitive measure to external impact forces applied to the cells. In addition, it is suggested that inflammatory mechanisms exhibit inhibitory “cross-talk” between IL-6 and IL-1β signaling pathways at 20 and 200 Hz. Inflammatory cytokine data suggest frequency-specific responses, which can be used not only to better understand the mechanism of vibration induced cellular damage, but also to unveil the cellular signaling processes.
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6

Shiraishi, Toshihiko, and Akitoshi Nishijima. "A Study of a Mechanism of Cell Proliferation Promotion of Cultured Osteoblasts by Mechanical Vibration." In ASME 2018 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/imece2018-87364.

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This paper describes a mechanism of cell proliferation promotion of cultured osteoblasts by mechanical vibration focusing on β-catenin. 12.5 Hz and 0.5 G mechanical vibration was reported to promote the cell proliferation of cultured osteoblasts in plane culture. That is because the mechanical vibration weakens cell-cell adhesion, promotes to pile up cells, and allows cells to form multilayer structure. However, it has not been clarified why cells continue cell division after their monolayer confluent state. Here we show that mechanical vibration not only weakens cell-cell adhesion bound by β-catenin but also promotes to move β-catenin from the cytoplasm to the nuclei, where β-catenin associates with DNA-binding members of the Tcf/LEF family and other associated transcription factors including cell division. After osteoblastic cells were cultured under 12.5 Hz and 0.5 G mechanical vibration, cells were fractionated into nuclear and cytoplasmic fractions using a centrifugation method. β-catenin in each fraction was detected by a western blot experiment. The protein bands from western blot films were quantified with an image processing and analysis software, ImageJ. As a result, the vibration group gave higher expression of β-catenin in nuclear fraction than the non-vibration group just after the vibration group reached the saturated cell density. It indicates that 12.5 Hz and 0.5 G mechanical vibration may promote to move β-catenin into the nuclei and the cell division.
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7

Henry, E., W. A. Eaton, and R. M. Hochstrasser. "Dynamics of Vibrational Populations in Optically Pumped Hemeproteins." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1986. http://dx.doi.org/10.1364/up.1986.wb7.

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Although proteins are disordered materials they can be crystallized and an equilibrium distribution of atomic coordinates can be determined using X-ray diffraction. Thus in contrast to liquids and glasses, the relaxation processes that are induced by the medium can be evaluated in terms of a known equilibrium structure. We report here molecular dynamics simulations of the influence of the surrounding protein on the vibrational energy content of the heme (iron porphyrin) typical of that introduced by absorption of the energy of a visible photon.
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8

Kholodenko, Yuriy, Martin Volk, Ed Gooding, and Robin M. Hochstrasser. "New Features in the Ultrafast Ligand Dynamics and Energy Dissipation in Myoglobin." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/up.1996.tue.23.

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Numerous transformations in heme proteins can be triggered upon photoexcitation, providing perfect model systems for the study of protein dynamics. In particular, the recombination of CO after photodissociation has been investigated in great detail. It was found to occur on the ns time scale. In contrast, the geminate recombination of NO proceeds much faster, within several 100 ps, i.e. on the same time scale as the relaxation of the protein to its unligated structure [1]. Furthermore, the recombination of NO was found to be nonexponential. Several mechanisms have been suggested to explain this behavior: (i) distribution of the barrier to rebinding due to different protein substates (inhomogeneous model), (ii) time dependence of the barrier due to protein/heme relaxation to the unligated structure or (iii) dissociation of the ligand to different intermediate sites in the protein. We are investigating these possibilities by time resolved IR measurements of the NO recombination. Furthermore, the comparison of native heme proteins with specially designed mutants will discriminate between the different mechanisms. We have also investigated the effect of the amount of excess energy in the precursor state on the resulting dynamics. The question is whether a higher excitation energy leads to the release of a ligand with higher kinetic energy, and thereby results in different intermediate protein sites, or whether the excess energy simply leads to hotter heme product which then undergoes vibrational cooling.
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9

Dyer, R. Brian, and Timothy P. Causgrove. "Ultrafast Protein Relaxation: Time-Resolved Infrared Studies of Protein Dynamics Triggered by CO Photodissociation from CO Myoglobin." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/up.1994.tub.4.

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A critical feature of the biological function of heme proteins is the direct coupling of protein motion to the process of binding exogenous ligands to the heme. In carbonmonoxymyoglobin (MbCO), a substantial, specific conformational relaxation is associated with the transition from the ligated to the unligated form of the protein. The analogous tertiary structural changes of the monomer heme subunits of hemoglobin ultimately lead to the R→T quaternary structural transition, the allosteric control mechanism of O2 binding efficiency [1]. We have studied these processes on the earliest timescales, using picosecond, time-resolved infrared (TRIR) spectroscopy. It has long been known that infrared spectra in the amide region are sensitive to protein secondary conformation [2]. Recent advances in equipment and techniques have permitted researchers to quantitatively predict secondary structures from infrared spectra [3,4], particularly in the amide I region [4]. Therefore, it is now possible to study protein motion in time-resolved experiments on dynamics and function. The ligation reactions of small molecules such as CO with the heme site of Mb exemplify the mechanisms available to O2. CO is an ideal candidate for initial time-resolved IR experiments in the amide I region because it is easily photolyzed, little geminate recombination [5], and the structure of both MbCO and unligated Mb have been studied by crystallographic methods [6]. TRIR has already been applied to the stretching vibrations of the bound and free CO ligand [7,8]; dynamics of the protein, however, have yet to be probed by TRIR spectroscopy of the protein vibrations. Here we report results on the motions of the protein in response to ligation reactions, probed in the amide I region centered about 1650 cm-1.
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10

Hochstrasser, R. M. "Femtosecond Infrared Spectroscopic Studies of Protein Dynamics." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.wa1.

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Ultrafast methods of interrogating the molecular vibrational spectrum in the infrared have advanced significantly in the past few years (1). Experiments in the regime 1200 cm–1 to 3500 cm–1 are now demonstrated and IR pulses as short as 280 fs have been used in experiments near 5 µ. Because infrared spectroscopy is universally applicable and structurally sharp, it is a particularly powerful tool with which to investigate complex systems such as proteins. In this paper some recent results in which transient IR spectroscopy was used to explore changes in the vibrational spectrum that result from optical triggering of protein structural changes will be discussed.
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Звіти організацій з теми "Protein vibration"

1

Barbara, Paul F., Gilbert C. Walker, and Terrance P. Smith. Vibrational Modes and the Dynamic Solvent Effect in Electron and Proton Transfer. Fort Belvoir, VA: Defense Technical Information Center, May 1992. http://dx.doi.org/10.21236/ada250727.

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2

Holinga IV, George Joseph. Sum Frequency Generation Vibrational Spectroscopy of Adsorbed Amino Acids, Peptides and Proteins of Hydrophilic and Hydrophobic Solid-Water Interfaces. Office of Scientific and Technical Information (OSTI), September 2010. http://dx.doi.org/10.2172/988994.

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3

Schwartz, Benjamin Joel. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation. Office of Scientific and Technical Information (OSTI), November 1992. http://dx.doi.org/10.2172/10131752.

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4

Schwartz, B. J. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation. [Spiropyrans]. Office of Scientific and Technical Information (OSTI), November 1992. http://dx.doi.org/10.2172/6666275.

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5

Koffas, Telly Stelianos. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy. Office of Scientific and Technical Information (OSTI), January 2004. http://dx.doi.org/10.2172/825532.

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