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Relevant bibliographies by topics / Protein conformation

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Academic literature on the topic 'Protein conformation'

Author: Grafiati

Published: 4 June 2021

Last updated: 28 July 2024

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Journal articles on the topic "Protein conformation"

1

Cresti, Julianna R., Abramo J. Manfredonia, Christopher E. Bragança, Joseph A. Boscia, Christina M. Hurley, Mary D. Cundiff, and Daniel A. Kraut. "Proteasomal conformation controls unfolding ability." Proceedings of the National Academy of Sciences 118, no. 25 (June 14, 2021): e2101004118. http://dx.doi.org/10.1073/pnas.2101004118.

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The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome’s various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome’s ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome’s conformational state and its unfolding ability.

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Ohhashi, Yumiko, Yoshiki Yamaguchi, Hiroshi Kurahashi, Yuji O. Kamatari, Shinju Sugiyama, Boran Uluca, Timo Piechatzek, et al. "Molecular basis for diversification of yeast prion strain conformation." Proceedings of the National Academy of Sciences 115, no. 10 (February 21, 2018): 2389–94. http://dx.doi.org/10.1073/pnas.1715483115.

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Self-propagating β-sheet–rich fibrillar protein aggregates, amyloid fibers, are often associated with cellular dysfunction and disease. Distinct amyloid conformations dictate different physiological consequences, such as cellular toxicity. However, the origin of the diversity of amyloid conformation remains unknown. Here, we suggest that altered conformational equilibrium in natively disordered monomeric proteins leads to the adaptation of alternate amyloid conformations that have different phenotypic effects. We performed a comprehensive high-resolution structural analysis of Sup35NM, an N-terminal fragment of the Sup35 yeast prion protein, and found that monomeric Sup35NM harbored latent local compact structures despite its overall disordered conformation. When the hidden local microstructures were relaxed by genetic mutations or solvent conditions, Sup35NM adopted a strikingly different amyloid conformation, which redirected chaperone-mediated fiber fragmentation and modulated prion strain phenotypes. Thus, dynamic conformational fluctuations in natively disordered monomeric proteins represent a posttranslational mechanism for diversification of aggregate structures and cellular phenotypes.

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Cretin, Gabriel, Tatiana Galochkina, Alexandre G. de Brevern, and Jean-Christophe Gelly. "PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction." International Journal of Molecular Sciences 22, no. 16 (August 17, 2021): 8831. http://dx.doi.org/10.3390/ijms22168831.

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Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids. The representation of complex protein 3D structures as 1D PB sequences was previously successfully applied to protein structure alignment and protein structure prediction. In the current study, we present a new model, PYTHIA (predicting any conformation at high accuracy), for the prediction of the protein local conformations in terms of PBs directly from the amino acid sequence. PYTHIA is based on a deep residual inception-inside-inception neural network with convolutional block attention modules, predicting 1 of 16 PB classes from evolutionary information combined to physicochemical properties of individual amino acids. PYTHIA clearly outperforms the LOCUSTRA reference method for all PB classes and demonstrates great performance for PB prediction on particularly challenging proteins from the CASP14 free modelling category.

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Seo, Udeok, Ku-Jin Kim, and Beom Kang. "An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel." Molecules 23, no. 10 (September 26, 2018): 2459. http://dx.doi.org/10.3390/molecules23102459.

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In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.

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Merski, Matthew, Marcus Fischer, Trent E. Balius, Oliv Eidam, and Brian K. Shoichet. "Homologous ligands accommodated by discrete conformations of a buried cavity." Proceedings of the National Academy of Sciences 112, no. 16 (April 6, 2015): 5039–44. http://dx.doi.org/10.1073/pnas.1500806112.

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Conformational change in protein–ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design.

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Giri Rao, V. V. Hemanth, and Shachi Gosavi. "On the folding of a structurally complex protein to its metastable active state." Proceedings of the National Academy of Sciences 115, no. 9 (January 17, 2018): 1998–2003. http://dx.doi.org/10.1073/pnas.1708173115.

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For successful protease inhibition, the reactive center loop (RCL) of the two-domain serine protease inhibitor, α1-antitrypsin (α1-AT), needs to remain exposed in a metastable active conformation. The α1-AT RCL is sequestered in a β-sheet in the stable latent conformation. Thus, to be functional, α1-AT must always fold to a metastable conformation while avoiding folding to a stable conformation. We explore the structural basis of this choice using folding simulations of coarse-grained structure-based models of the two α1-AT conformations. Our simulations capture the key features of folding experiments performed on both conformations. The simulations also show that the free energy barrier to fold to the latent conformation is much larger than the barrier to fold to the active conformation. An entropically stabilized on-pathway intermediate lowers the barrier for folding to the active conformation. In this intermediate, the RCL is in an exposed configuration, and only one of the two α1-AT domains is folded. In contrast, early conversion of the RCL into a β-strand increases the coupling between the two α1-AT domains in the transition state and creates a larger barrier for folding to the latent conformation. Thus, unlike what happens in several proteins, where separate regions promote folding and function, the structure of the RCL, formed early during folding, determines both the conformational and the functional fate of α1-AT. Further, the short 12-residue RCL modulates the free energy barrier and the folding cooperativity of the large 370-residue α1-AT. Finally, we suggest experiments to test the predicted folding mechanism for the latent state.

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DOWNING, Donald T., and N. D. LAZO. "Molecular modelling indicates that the pathological conformations of prion proteins might be β-helical." Biochemical Journal 343, no. 2 (October 8, 1999): 453–60. http://dx.doi.org/10.1042/bj3430453.

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Creutzfeldt-Jakob disease, kuru, scrapie and bovine spongiform encephalopathy are diseases of the mammalian central nervous system that involve the conversion of a cellular protein into an insoluble extracellular isoform. Spectroscopic studies have shown that the precursor protein contains mainly α-helical and random-coil conformations, whereas the prion isoform is largely in the β conformation. The pathogenic prion is resistant to denaturation and protease digestion and can promote the conversion of the precursor protein to the pathogenic form. These properties have yet to be explained in terms of the structural conformations of the proteins. In the present study, molecular modelling showed that prion proteins could adopt the β-helical conformation, which has been established for a number of fibrous proteins and has been suggested previously as the basis of amyloid fibrils. The β-helical conformation provides explanations for the biophysical and biochemical stability of prions, their ability to form templates for the transmission of pathological conformation, and the existence of phenotypical strains of the prion diseases.

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Avdeev, P. A., V. A. Ignatenko, Yu V. Kornoushenko, and L. A. Evtuhova. "EFFECT OF DIFFERENT CONCENTRATIONS OF UREA AND PH ON THE FLUORESCENCE PARAMETERS OF BOVINE SERUM ALBUMIN." Health and Ecology Issues, no. 1 (March 28, 2011): 106–10. http://dx.doi.org/10.51523/2708-6011.2011-8-1-20.

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Urea is a chemical effect on the conformation of bovine serum albumin, causing a partial unfolding of the protein globule its exit to the surface of hydrophobic amino acids. Changing the pH of the solution in which the protein also affects the state of the protein, so there are multiple conformational states in which urea as a chemical effect on the conformation of bovine serum albumin, causing a partial unfolding of the protein globule of its exit to the surface of hydrophobic amino acids. Changing the pH of the solution in which the protein also affects the state of the protein, so there are multiple conformational states into which the serum albumin. The objective of our research was to study the effect of different protein concentrations and pH on the conformation of serum albumin. Very sensitive method for studying protein conformation are their own methods and probe fluorescence. The dependence of the effect of various factors on the fluorescence can be with a certain degree of probability suggest conformational transitions in proteins.

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Lamichhane, Rajan, Jeffrey J. Liu, Goran Pljevaljcic, Kate L. White, Edwin van der Schans, Vsevolod Katritch, Raymond C. Stevens, Kurt Wüthrich, and David P. Millar. "Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β2AR." Proceedings of the National Academy of Sciences 112, no. 46 (November 2, 2015): 14254–59. http://dx.doi.org/10.1073/pnas.1519626112.

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Binding of extracellular ligands to G protein-coupled receptors (GPCRs) initiates transmembrane signaling by inducing conformational changes on the cytoplasmic receptor surface. Knowledge of this process provides a platform for the development of GPCR-targeting drugs. Here, using a site-specific Cy3 fluorescence probe in the human β2-adrenergic receptor (β2AR), we observed that individual receptor molecules in the native-like environment of phospholipid nanodiscs undergo spontaneous transitions between two distinct conformational states. These states are assigned to inactive and active-like receptor conformations. Individual receptor molecules in the apo form repeatedly sample both conformations, with a bias toward the inactive conformation. Experiments in the presence of drug ligands show that binding of the full agonist formoterol shifts the conformational distribution in favor of the active-like conformation, whereas binding of the inverse agonist ICI-118,551 favors the inactive conformation. Analysis of single-molecule dwell-time distributions for each state reveals that formoterol increases the frequency of activation transitions, while also reducing the frequency of deactivation events. In contrast, the inverse agonist increases the frequency of deactivation transitions. Our observations account for the high level of basal activity of this receptor and provide insights that help to rationalize, on the molecular level, the widely documented variability of the pharmacological efficacies among GPCR-targeting drugs.

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Mizutani, Tadashi, and Shigeyuki Yagi. "Linear tetrapyrroles as functional pigments in chemistry and biology." Journal of Porphyrins and Phthalocyanines 08, no. 03 (March 2004): 226–37. http://dx.doi.org/10.1142/s1088424604000210.

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1,19,21,24-tetrahydro-1,19-bilindione is the framework of pigments frequently found in nature, which includes biliverdin IX α, phytochromobilin and phycocyanobilin. 1,19-bilindiones have unique features such as (1) photochemical and thermal cis-trans isomerization, (2) excited energy transfer, (3) chiroptical properties due to the cyclic helical conformation, (4) redox activity, (5) coordination to various metals, and (6) reconstitution to proteins. 1,19-bilindione can adopt a number of conformations since it has exocyclic three double bonds and three single bonds that are rotatable thermally and photochemically. In solution, biliverdin and phycocyanobilin adopt a cyclic helical ZZZ, syn, syn, syn conformation, but other conformations are stabilized depending on the experimental conditions and substituents on the bilin framework. The conformational changes in 1,19-bilindiones are related to the biological functions of a photoreceptor protein, phytochrome. Structural and conformational studies of bilindiones are summarized both in solution and in protein. The conformational changes of bilins can be used for other functions such as a chirality sensor. The bilindiones and the zinc complexes of bilindiones can be employed as a chirality sensor due to the helically chiral structure and the dynamics of racemization of enantiomers. In this paper, we discuss the conformational equilibria and dynamics of bilindiones and its implications in photobiology and materials science.

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Dissertations / Theses on the topic "Protein conformation"

1

Link, Justin J. "Ultrafast Protein Conformation Dynamics." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1230584570.

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Wang, Chu. "Improved conformational sampling for protein-protein docking /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9194.

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Billsten, Peter. "Studies on the conformation of adsorbed proteins." Lund : Göteborg University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39776983.html.

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Florane, H. "Exploring protein conformation with mass spectrometry." Thesis, University of Edinburgh, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.650980.

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The first part of this thesis describes the development and viability of a phase I screening system for obtaining a rank order of affinity of novel ligands against the immunophilin, Cyclophilin A (CypA). The naturally occurring inhibitor Cyclosporin A (CsA) was used as a positive control to validate a method for calculating the dissociation constant (K_d). An HPLC autosampler and pumping system was used as a high throughput on-line electrospray ionisation (ESI)-MS sampling system. Optimised ESI conditions were then used to screen novel ligands from 3 combinatorial libraries and approaches for data analysis is discussed. Hydrogen/deuterium exchange (HDX) can be used directly and indirectly as a means for studying protein conformations. Melittin, the major component of honey bee venom is taken here as a model system for studying secondary structure in solution and the gas phase. Comprising a 26 amino acid polypeptide, melittin occupies a random coil in aqueous conditions which can be transformed into an α-helix under increasingly hydrophobic conditions. A variety of HDX techniques were utilised: i) comparing rats of deuterium (d-) uptake by direct infusion – ESI at different pDs and methanol concentrations; ii) PLIMSTEX (protein-ligand interactions by mass spectrometry, titration and HDX) at high and low salt concentrations with varying pDs; iii) gas phase exchange in an LCQ ion trap using He/d-methanol as the bath gas. Melittin was pre-incubated in a variety of methanol concentrations. Comparing results from these different approaches, α-helical retention has been shown to exist in the N-terminal half of the peptide. All the afore-mentioned techniques developed using melittin were adapted for CypA. Comparisons of d-uptake in the presence and absence of CsA shows the ligand to have a stabilising affect on the protein.

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Nicholls, Robert Adam. "Conformation-independent comparison of protein structures." Thesis, University of York, 2011. http://etheses.whiterose.ac.uk/2120/.

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The comparative analysis of protein structures is often performed in order to identify and explore similarities/dissimilarities present between target structures. Whilst many tools are available for structural comparison, the development of new tools providing different information is desirable. The work presented here concerns the development of ProSMART (Procrustes Structural Matching Alignment and Restraints Tool), a tool to aid the comparative analysis of protein structures. Primarily, the software is used for conformation-independent pairwise structural alignment, allowing identification of local similarities, and quantification of dissimilarities. Functionality also allows the identification and superposition of rigid substructures, providing output that allows visualisation of local dissimilarities by means of residue-based scoring. The ProSMART pairwise alignment method optimises the net agreement of local structures along the chain, using structural fragments. In order to maintain conformation-independence, the structure-based residue alignment does not enforce global rigidity of chains, nor domains. This feature makes the tool suited to the analysis of domain movement and other conformational changes, as well as for the identification of structural units conserved between seemingly different structures. Given an alignment, ProSMART can be used to generate external restraints on the distances between relatively close atoms, for use in the crystallographic refinement of macromolecules. Using one or more similar structures, the software generates restraints that are intended to help the target protein adopt a conformation that is more reasonable, whilst allowing global flexibility. Such restraints may stabilise refinement in some cases, especially at low resolution where experimental data alone may not be sufficient. We also present a method of Procrustes score normalisation, which allows the consideration of the significance of observed fragment scores. It is suggested that the resulting global scores for the overall pairwise agreement of protein structures may provide an interesting new way of viewing protein fold space.

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Watt, Stephen J. "Use of electrospray ionization mass spectrometry to study protein conformation and protein-protein interactions." Access electronically, 2005. http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20060516.114814/index.html.

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Thesis (Ph.D.)--University of Wollongong, 2005.
Typescript. EMBARGOED-this thesis is subject to a six months embargo (07/09/06) and may only be viewed and copied with the permission of the author. For further information please Contact the Archivist. Includes bibliographical references: leaf 159-194.

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Rashid, Mahmood Abdur. "Heuristic Based Search for Protein Structure Prediction." Thesis, Griffith University, 2014. http://hdl.handle.net/10072/367134.

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Proteins that are essentially sequences of amino acids, adopt specific folded 3-dimensional (3D) structures to perform their specific tasks. However, misfolded proteins cause fatal diseases. Hence, protein structure prediction (PSP) has emerged as an important multi-disciplinary research problem. Given a protein sequence, the PSP problem is to find a 3D structure of the protein such that the total free energy amongst the amino acids in the sequence is minimised. In-vitro laboratory methods are time-consuming, expensive, and failure-prone. Conversely, computational methods are NP-hard even when the models are simplified by using low-resolution energy functions and lattice-based structures.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Institute for Integrated and Intelligent Systems
Science, Environment, Engineering and Technology
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Chivian, Dylan Casey. "Application of information from homologous proteins for the prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9264.

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Hosia, Waltteri. "Molecular mechanisms in amyloid fibril formation /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-976-5.

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Sandin, Sara. "Cryo-electron tomography of individual protein molecules /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-462-7/.

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Books on the topic "Protein conformation"

1

Symposium on Protein Conformation (1991 : Ciba Foundation), ed. Protein conformation. Chichester [England]: Wiley, 1991.

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Hamaguchi, Kōzō. The protein molecule: Conformation, stability, and folding. Tokyo: Japan Scientific Societies Press, 1992.

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Protein folding. Hauppauge, N.Y: Nova Science, 2010.

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A, Shirley Bret, ed. Protein stability and folding: Theory and practice. Totowa, N.J: Humana Press, 1995.

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B, Roswell Linda, ed. Protein conformation: New research. New York: Nova Science Publishers, 2008.

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Joël, Janin, and Wodak Shoshana J, eds. Protein modules and protein-protein interaction. Amsterdam: Academic Press, 2002.

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Siddhartha, Roy, and Biswas B. B, eds. Subcellular biochemistry. New York: Plenum, 1995.

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B, Biswas B., and Roy Siddhartha, eds. Proteins: Structure, function, and engineering. New York: Plenum, 1995.

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E, Sternberg Michael J., ed. Protein structure prediction: A practical approach. Oxford: IRL Press at Oxford University Press, 1996.

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10

D, Fasman Gerald, ed. Prediction of protein structure and the principles of protein confirmation. New York: Plenum, 1989.

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Book chapters on the topic "Protein conformation"

1

Jaenicke, Rainer. "Protein Stability and Protein Folding." In Ciba Foundation Symposium 161 - Protein Conformation, 206–21. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch13.

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Alber, Tom. "Stabilization Energies of Protein Conformation." In Prediction of Protein Structure and the Principles of Protein Conformation, 161–92. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-1571-1_5.

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Duquerroy, Stéphane, Jacqueline Cherfils, and Joël Janin. "Protein-Protein Interaction: An Analysis by Computer Simulation." In Ciba Foundation Symposium 161 - Protein Conformation, 237–59. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch15.

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Na, Hyuntae, and Guang Song. "Ellipsoid-Weighted Protein Conformation Alignment." In Bioinformatics Research and Applications, 273–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-38036-5_27.

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Richardson, Jane S., and David C. Richardson. "Principles and Patterns of Protein Conformation." In Prediction of Protein Structure and the Principles of Protein Conformation, 1–98. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-1571-1_1.

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Taneva, Stefka G., Sonia Bañuelos, and Arturo Muga. "Protein-membrane interaction: Lipid environment modulates protein conformation." In Spectroscopy of Biological Molecules: New Directions, 343–46. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4479-7_152.

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Baldwin, Robert L. "Experimental Studies of Pathways of Protein Folding." In Ciba Foundation Symposium 161 - Protein Conformation, 190–205. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch12.

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Richards, F. M. "Introduction." In Ciba Foundation Symposium 161 - Protein Conformation, 1–7. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch1.

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Gunsteren, W. F. van, P. Gros, A. E. Torda, H. J. C. Berendsent, and R. C. van Schaik. "On Deriving Spatial Protein Structure from NMR or X-Ray Diffraction Data." In Ciba Foundation Symposium 161 - Protein Conformation, 150–66. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch10.

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Dobson, Christopher M. "NMR Spectroscopy and Protein Folding: Studies of Lysozyme and α-Lactalbumin." In Ciba Foundation Symposium 161 - Protein Conformation, 167–89. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch11.

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Conference papers on the topic "Protein conformation"

1

Xu, Yangqing, and Gang Bao. "Protein Conformational Changes Under Applied Forces." In ASME 1999 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1999. http://dx.doi.org/10.1115/imece1999-0408.

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Abstract Recent studies confirm that stresses, including that due to gravity, tension, compression, pressure, and shear influence cell growth, differentiation, secretion, movement, signal transduction, and gene expression. Yet, little is known about how cells sense the mechanical stresses or deformations, and convert these mechanical signals into biological or biochemical responses. A possible mechno-chemical coupling mechanism involves protein conformational changes under mechanical forces. Our hypothesis is that mechanical forces can cause large changes of the conformation of proteins, which in turn can influence receptor-ligand binding. To test this hypothesis, molecular dynamics simulations and biochemical assays are performed.

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Karplus, M. "Internal dynamics of macromolecules : Simulations of motion in proteins." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb1.

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The internal motions of proteins will be discussed. Detailed atom-bases simulations of the native conformation space will be supplemented by simplified models for the full conformation space involved in protein folding.

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Škrhák, Vít, and David Hoksza. "Framework for Protein Structures Conformation Analysis." In 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2023. http://dx.doi.org/10.1109/bibm58861.2023.10385905.

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Kazerounian, Kazem, Khalid Latif, Kimberly Rodriguez, and Carlos Alvarado. "ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57243.

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Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this paper, we present the methods utilized in the kinematics notion and kinematics analysis of protein molecules. The kinematics portion of ProtoFold incorporates the Zero-Position Analysis Method and draws upon other recent advances in robot manipulation theories. We claim that the methodology presented is a computationally superior and more stable alternative to traditional molecular dynamics simulation techniques.

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Kumar, Sugam, I. Yadav, V. K. Aswal, and J. Kohlbrecher. "Modifications in nanoparticle-protein interactions by varying the protein conformation." In DAE SOLID STATE PHYSICS SYMPOSIUM 2016. Author(s), 2017. http://dx.doi.org/10.1063/1.4980309.

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Koh, Sung K., and G. K. Ananthasuresh. "Design of HP Models of Proteins by Energy Gap Criterion Using Continuous Modeling and Optimization." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57598.

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The sequence of 20 types of amino acid residues in a heteropolymer chain of a protein is believed to be the basis for the 3-D conformation (folded structure) that a protein assumes to serve its functions. We present a deterministic optimization method to design the sequence of a simplified model of proteins for a desired conformation. A design methodology developed for the topology optimization of compliant mechanisms is adapted here by converting the discrete combinatorial problem of protein sequence design to a continuous optimization problem. It builds upon our recent work which used a minimum energy criterion on a deterministic approach to protein design using continuous models. This paper focuses on the energy gap criterion, which is argued to be one of the most important characteristics determining the stable folding of a protein chain. The concepts, methodology, and illustrative examples are presented using HP models of proteins where only two types (H: hydrophobic and P: polar) of monomers are considered instead of 20. The highlight of the method presented in this paper is the drastic reduction in computational costs.

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Buzdalov, Maxim, Sergey Knyazev, and Yury Porozov. "Protein Conformation Motion Modeling Using Sep-CMA-ES." In 2014 13th International Conference on Machine Learning and Applications (ICMLA). IEEE, 2014. http://dx.doi.org/10.1109/icmla.2014.12.

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Sapin, Emmanuel, Kenneth De Jong, and Amarda Shehu. "Evolving Conformation Paths to Model Protein Structural Transitions." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3107411.3107498.

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Taylor, Kimberly, and Daniel W. van der Weide. "Microwave assay for detecting protein conformation in solution." In Environmental and Industrial Sensing, edited by James O. Jensen and Robert L. Spellicy. SPIE, 2002. http://dx.doi.org/10.1117/12.455151.

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Kapralova, A. V., and A. S. Pogodin. "Protein conformation change induced by THz laser radiation." In Lasers, Applications, and Technologies, edited by Vladislav Panchenko, Gérard Mourou, and Aleksei M. Zheltikov. SPIE, 2010. http://dx.doi.org/10.1117/12.880335.

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Reports on the topic "Protein conformation"

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Zhu, Xiaoyang. Controlling Protein Conformation and Activities on Block-Copolymer Nanopatterns. Fort Belvoir, VA: Defense Technical Information Center, October 2013. http://dx.doi.org/10.21236/ada607976.

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Zhu, Xiaoyang, and Tim P. Lodge. Controlling Protein Conformation & Activities on Block-Copolymer Nanopatterns. Fort Belvoir, VA: Defense Technical Information Center, November 2009. http://dx.doi.org/10.21236/ada520626.

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Hanke, Andreas. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding. Fort Belvoir, VA: Defense Technical Information Center, July 2008. http://dx.doi.org/10.21236/ada483440.

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Lu, Hong P. Controlling Protein Conformations to Explore Unprecedented Material Properties by Single-Molecule Surgery. Fort Belvoir, VA: Defense Technical Information Center, August 2012. http://dx.doi.org/10.21236/ada584676.

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Schubert, David R., Yuanbin Liu, and Roland Riek. The Antemortem Detection and Conformational Switches of Prion Proteins. Fort Belvoir, VA: Defense Technical Information Center, July 2005. http://dx.doi.org/10.21236/ada446422.

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Beck, Thomas, Nimal Wijesekera, David Rogers, and Roman Petrenko. Multiscale Modeling of Complex Systems Conformational Transitions in Proteins. Fort Belvoir, VA: Defense Technical Information Center, October 2006. http://dx.doi.org/10.21236/ada482296.

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McGuirl, Michele A. Elucidation of Prion Protein Conformational Changes Associated With Infectivity by Fluorescence Spectroscopy. Fort Belvoir, VA: Defense Technical Information Center, June 2004. http://dx.doi.org/10.21236/ada426340.

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McGuirl, Michele A., and Jessica Gilbert. Elucidation of Prion Protein Conformational Changes Associated with Infectivity by Fluorescence Spectroscopy. Fort Belvoir, VA: Defense Technical Information Center, June 2007. http://dx.doi.org/10.21236/ada575958.

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McGuirl, Michele. Elucidation of Prion Protein Conformational Changes Associated with Infectivity by Fluorescence Spectroscopy. Fort Belvoir, VA: Defense Technical Information Center, June 2006. http://dx.doi.org/10.21236/ada462868.

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Kim, Sangtae. Microstructural Models of Interactions That Govern Protein Conformations: Algorithms for High Performance Computer Architectures. Fort Belvoir, VA: Defense Technical Information Center, January 1998. http://dx.doi.org/10.21236/ada360981.

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