Relevant bibliographies by topics / Protein Folding; Protein Conformation

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Protein Folding; Protein Conformation'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 February 2022

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Journal articles on the topic "Protein Folding; Protein Conformation"

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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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Li, Yanru, Ying Zhang, and Jun Lv. "An Effective Cumulative Torsion Angles Model for Prediction of Protein Folding Rates." Protein & Peptide Letters 27, no. 4 (March 17, 2020): 321–28. http://dx.doi.org/10.2174/0929866526666191014152207.

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Background: Protein folding rate is mainly determined by the size of the conformational space to search, which in turn is dictated by factors such as size, structure and amino-acid sequence in a protein. It is important to integrate these factors effectively to form a more precisely description of conformation space. But there is no general paradigm to answer this question except some intuitions and empirical rules. Therefore, at the present stage, predictions of the folding rate can be improved through finding new factors, and some insights are given to the above question. Objective: Its purpose is to propose a new parameter that can describe the size of the conformational space to improve the prediction accuracy of protein folding rate. Method: Based on the optimal set of amino acids in a protein, an effective cumulative backbone torsion angles (CBTAeff) was proposed to describe the size of the conformational space. Linear regression model was used to predict protein folding rate with CBTAeff as a parameter. The degree of correlation was described by the coefficient of determination and the mean absolute error MAE between the predicted folding rates and experimental observations. Results: It achieved a high correlation (with the coefficient of determination of 0.70 and MAE of 1.88) between the logarithm of folding rates and the (CBTAeff)0.5 with experimental over 112 twoand multi-state folding proteins. Conclusion: The remarkable performance of our simplistic model demonstrates that CBTA based on optimal set was the major determinants of the conformation space of natural proteins.
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Dyson, H. Jane, and Peter E. Wright. "Peptide conformation and protein folding." Current Opinion in Structural Biology 3, no. 1 (February 1993): 60–65. http://dx.doi.org/10.1016/0959-440x(93)90203-w.

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GUYEUX, CHRISTOPHE, NATHALIE M. L. CÔTÉ, JACQUES M. BAHI, and WOJCIECH BIENIA. "IS PROTEIN FOLDING PROBLEM REALLY A NP-COMPLETE ONE? FIRST INVESTIGATIONS." Journal of Bioinformatics and Computational Biology 12, no. 01 (January 28, 2014): 1350017. http://dx.doi.org/10.1142/s0219720013500170.

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To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D conformations, they tend to choose the ones that minimize their free energy. To find the 3D conformation of a protein knowing its amino acid sequence, bioinformaticians use various models of different resolutions and artificial intelligence tools, as the protein folding prediction problem is a NP complete one. More precisely, to determine the backbone structure of the protein using the low resolution models (2D HP square and 3D HP cubic), by finding the conformation that minimizes free energy, is intractable exactly. Both proofs of NP-completeness and the 2D prediction consider that acceptable conformations have to satisfy a self-avoiding walk (SAW) requirement, as two different amino acids cannot occupy a same position in the lattice. It is shown in this document that the SAW requirement considered when proving NP-completeness is different from the SAW requirement used in various prediction programs, and that they are different from the real biological requirement. Indeed, the proof of NP completeness and the predictions in silico consider conformations that are not possible in practice. Consequences of this fact are investigated in this research work.
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CHEN, HU, CHAN GHEE KOH, CHIH YOUNG LIAW, and XIN ZHOU. "ACCESSIBILITY OF COMPACT STRUCTURES AND PRION-LIKE PROTEIN FOLDING PROPERTY." Modern Physics Letters B 19, no. 25 (November 10, 2005): 1241–52. http://dx.doi.org/10.1142/s0217984905009183.

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Based on two-dimensional Gō model of proteins and Monte Carlo simulation method, it is found that different compact conformations have different accessibility, i.e., some are easy to reach in the Monte Carlo simulation from a random conformation, while others are not. The logarithm of folding time is approximately a linear function of the contact order of the native conformation, which is consistent with published experimental results. Transition barrier is the main factor to determine the folding time at low temperature when proteins are stable. To fold to native structure with bigger contact order, higher barrier needs to be overcome. To study the folding properties of some prion-like proteins which have two possible conformations, the normal Gō model is extended to double-Gō model with two native states. In folding simulations, the native state with high accessibility is reached with much higher probability than the other. The accessibility of compact structures determines which structure is easy to reach in folding process.
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Gelman, Hannah, and Martin Gruebele. "Fast protein folding kinetics." Quarterly Reviews of Biophysics 47, no. 2 (March 18, 2014): 95–142. http://dx.doi.org/10.1017/s003358351400002x.

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AbstractFast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well <1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even ‘slow’ folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.
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Xu, Jinbo. "Distance-based protein folding powered by deep learning." Proceedings of the National Academy of Sciences 116, no. 34 (August 9, 2019): 16856–65. http://dx.doi.org/10.1073/pnas.1821309116.

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Direct coupling analysis (DCA) for protein folding has made very good progress, but it is not effective for proteins that lack many sequence homologs, even coupled with time-consuming conformation sampling with fragments. We show that we can accurately predict interresidue distance distribution of a protein by deep learning, even for proteins with ∼60 sequence homologs. Using only the geometric constraints given by the resulting distance matrix we may construct 3D models without involving extensive conformation sampling. Our method successfully folded 21 of the 37 CASP12 hard targets with a median family size of 58 effective sequence homologs within 4 h on a Linux computer of 20 central processing units. In contrast, DCA-predicted contacts cannot be used to fold any of these hard targets in the absence of extensive conformation sampling, and the best CASP12 group folded only 11 of them by integrating DCA-predicted contacts into fragment-based conformation sampling. Rigorous experimental validation in CASP13 shows that our distance-based folding server successfully folded 17 of 32 hard targets (with a median family size of 36 sequence homologs) and obtained 70% precision on the top L/5 long-range predicted contacts. The latest experimental validation in CAMEO shows that our server predicted correct folds for 2 membrane proteins while all of the other servers failed. These results demonstrate that it is now feasible to predict correct fold for many more proteins lack of similar structures in the Protein Data Bank even on a personal computer.
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JANUAR, M., A. SULAIMAN, and L. T. HANDOKO. "NONLINEAR CONFORMATION OF SECONDARY PROTEIN FOLDING." International Journal of Modern Physics: Conference Series 09 (January 2012): 127–32. http://dx.doi.org/10.1142/s2010194512005181.

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A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially assumed to be nonlinear and represented by the Sine-Gordon equation, while the nonlinear external bosonic sources is represented by ϕ4 interaction. It is argued that the nonlinear source induces the folding pathway in a different way than the previous work with initially linear backbone. Also, the nonlinearity of protein backbone decreases the folding speed.
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Luo, Liaofu. "Conformation-transitional rate in protein folding." International Journal of Quantum Chemistry 54, no. 4 (May 15, 1995): 243–47. http://dx.doi.org/10.1002/qua.560540407.

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Reid, J., R. Betney, K. Watt, and I. J. McEwan. "The androgen receptor transactivation domain: the interplay between protein conformation and protein–protein interactions." Biochemical Society Transactions 31, no. 5 (October 1, 2003): 1042–46. http://dx.doi.org/10.1042/bst0311042.

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The AR (androgen receptor) belongs to the nuclear receptor superfamily and directly regulates patterns of gene expression in response to the steroids testosterone and dihydrotestosterone. Sequences within the large N-terminal domain of the receptor have been shown to be important for transactivation and protein–protein interactions; however, little is known about the structure and folding of this region. Folding of the AR transactivation domain was observed in the presence of the helix-stabilizing solvent trifluorethanol and the natural osmolyte TMAO (trimethylamine N-oxide). TMAO resulted in the movement of two tryptophan residues to a less solvent-exposed environment and the formation of a protease-resistant conformation. Critically, binding to a target protein, the RAP74 subunit of the general transcription factor TFIIF, resulted in a similar resistance to protease digestion, consistent with induced folding of the receptor transactivation domain. Our current hypothesis is that the folding of the transactivation domain in response to specific protein–protein interactions creates a platform for subsequent interactions, resulting in the formation of a competent transcriptional activation complex.
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Dissertations / Theses on the topic "Protein Folding; Protein Conformation"

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Simons, Kim T. "Deciphering the protein folding code : ab initio prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9234.

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Sapsaman, Temsiri. "An energy landscaping approach to the protein folding problem." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31637.

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Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2010.
Committee Chair: Harvey Lipkin; Committee Member: Joel S. Sokol; Committee Member: Michael J. Leamy; Committee Member: Nader Sadegh; Committee Member: Stephen C. Harvey. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Kim, Junghwa. "Roles of intermediate conformation and transient disulfide bonding on native folding of P22 tailspike protein." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.50 Mb., 176 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3220719.

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Duan, Jianxin. "Protein folding, stability and recognition /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-098-2/.

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Lundell, Sandra J. "Quantum Mechanical Studies of N-H···N Hydrogen Bonding in Acetamide Derivatives and Amino Acids." DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7309.

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Proteins are made of vast chains of amino acids that twist and fold into intricate designs. These structures are held in place by networks of noncovalent interactions. One of these, the hydrogen bond, forms bridges between adjacent pieces of the protein chain and is one of the most important contributors to the shape and stability of proteins. Hydrogen bonds come in all shapes and sizes and a full understanding of these not only aids in our understanding of proteins in general but can bridge the gap to finding cures to many protein-related diseases, such as sickle-cell anemia. The primary aim of this thesis is to discover if a specific type of hydrogen bond, the N-H···N bond, occurs within proteins and if so, if it contributes to the structure and stability of proteins.
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English, William R. "Effects of calcium on conformation and stability of porcine pancreatic phospholipase A←2." Thesis, University of Kent, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285981.

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Phan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer." Scholarly Commons, 2013. https://scholarlycommons.pacific.edu/uop_etds/859.

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Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.
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Phan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer : a thesis." Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/859.

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Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.
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Devlin, Glyn L. "The mechanisms of serpin misfolding and its inhibition." Monash University, Dept. of Biochemistry and Molecular Biology, 2003. http://arrow.monash.edu.au/hdl/1959.1/9469.

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Chen, Chong. "Investigating Nonnative Contacts in Protein Folding." University of Akron / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880.

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Books on the topic "Protein Folding; Protein Conformation"

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

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

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Protein aggregation. Hauppauge, N.Y: Nova Science Publishers, 2010.

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NATO, Advanced Research Workshop on Statistical Mechanics Protein Structure and Protein Substrate Interactions (1993 Cargèse Corsica France). Statistical mechanics, protein structure, and protein substrate interactions: [proceedings of a NATO Research Workshop on Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, Held June 1-5, 1993, in Cargèse, Corsica, France]. New York: Plenum Press in cooperation with NATO Scientific Affairs Division, 1994.

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Fuzziness: Structural disorder in protein complexes. Austin, TX: Landes Bioscience, 2011.

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Protein folding, misfolding, and disease: Methods and protocols. New York: Humana, 2011.

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Leopoldina, Symposium on the Structure Self-organization and Stability of Proteins (2000 Wittenberg Germany). Structure, Self-organization and Stability of Proteins: Experiments and models : Faltertage 2000 : Leopoldina Symposium : Leucorea in Wittenberg, Germany, September 21, 2000 to September 23, 2000. Halle: Deutsche Akademie der Naturforscher Leopoldina, 2001.

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Wendt, Hans. Leucine zipper peptides as models for protein folding. Konstanz: Hartung-Gorre, 1995.

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Coleman, Thomas F. Parallel continuation-based global optimization for molecular conformation and protein folding. Ithaca, N.Y: Cornell Theory Center, Cornell University, 1994.

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Tompa, Peter. Structure and function of intrinsically disordered proteins. Boca Raton, FL: Chapman & Hall/CRC Press, 2009.

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Book chapters on the topic "Protein Folding; Protein Conformation"

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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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Nölting, Bengt. "High structural resolution of transient protein conformations." In Protein Folding Kinetics, 95–123. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-662-03966-3_8.

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Levitt, M. "A Calculated Conformation for the Folding Transition State of Bovine Pancreatic Trypsin Inhibitor." In Protein Structure and Protein Engineering, 45–50. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-74173-9_5.

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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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Wilson, Stephen R., and Weili Cui. "Conformation Searching Using Simulated Annealing." In The Protein Folding Problem and Tertiary Structure Prediction, 43–70. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4684-6831-1_2.

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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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Sali, Andrej, Eugene Shakhnovich, and Martin Karplus. "Thermodynamics and kinetics of protein folding." In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 199–213. Providence, Rhode Island: American Mathematical Society, 1995. http://dx.doi.org/10.1090/dimacs/023/13.

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Blundell, Tom L. "Comparative Analysis of Protein Three-Dimensional Structures and an Approach to the Inverse Folding Problem." In Ciba Foundation Symposium 161 - Protein Conformation, 28–51. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514146.ch3.

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Bruccoleri, Robert E. "Conformational Search and Protein Folding." In The Protein Folding Problem and Tertiary Structure Prediction, 125–63. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4684-6831-1_5.

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Byrd, Richard, Elizabeth Eskow, Andre Van der Hoek, Robert Schnabel, Chung-Shang Shao, and Zhihong Zou. "Global optimization methods for protein folding problems." In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 29–39. Providence, Rhode Island: American Mathematical Society, 1995. http://dx.doi.org/10.1090/dimacs/023/03.

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Conference papers on the topic "Protein Folding; Protein Conformation"

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "Protein Molecules as Natural Nano Bio Devices: Mobility Analysis." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13021.

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Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.
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JANUAR, M., A. SULAIMAN, and L. T. HANDOKO. "CONFORMATION CHANGES AND PROTEIN FOLDING INDUCED BY ϕ4 INTERACTION." In Quantum Mechanics, Elementary Particles, Quantum Cosmology and Complexity. WORLD SCIENTIFIC, 2010. http://dx.doi.org/10.1142/9789814335614_0047.

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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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Asher, S., B. Sharma, L. Ma, S. Bykov, N. Myshakina, Z. Hong, K. Xiong, P. M. Champion, and L. D. Ziegler. "UV Resonance Raman Investigations of Peptide∕Protein Conformation and Folding." In XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY. AIP, 2010. http://dx.doi.org/10.1063/1.3482445.

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Kullman, Lisen. "Functional Sub-Conformations in Protein Folding: Evidence from Single-Channel Experiments." In UNSOLVED PROBLEMS OF NOISE AND FLUCTUATIONS: UPoN 2005: Fourth International Conference on Unsolved Problems of Noise and Fluctuations in Physics, Biology, and High Technology. AIP, 2005. http://dx.doi.org/10.1063/1.2138635.

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Shimp, Samuel K., Christopher M. Reilly, and Marissa Nichole Rylander. "Empirical Modeling the Effect of Hsp90 Inhibition on Cytokines Associated With Impaired Biotransport of Apoptotic Debris." In ASME 2010 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2010. http://dx.doi.org/10.1115/sbc2010-19572.

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Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disorder that can affect nearly every organ in the body. A link has been established between abnormal biotransport of apoptotic cell debris and pathogenesis of SLE [1]. Lupus mice are hyper-responsive to immune stimulation and overproduce inflammatory mediators including IL-6, IL-12, and nitric oxide (NO) [2]. Extracellular expression and transport of inflammatory cytokines are thought to be involved with the inhibited clearance of cellular debris [1]. Hsp90 has a prominent role in folding and conformational regulation of several client proteins, including proteins involved with production of inflammatory mediators [3]. Hsp90 readily binds ATP at the amino (N-) terminal domain. This binding event causes a conformational change in Hsp90 making it “clamp down” on its client protein [3]. Geldanamycin (Geld) is a known inhibitor of Hsp90 that out competes ATP binding at the N-terminal. This prevents chaperone capability and ultimately leads to client protein deactivation, destabilization, and degradation [3]. Hsp90 inhibitors have been shown to suppress immune stimulated release of interleukin 6 (IL-6), IL-12, tumor necrosis factor alpha (TNF-α), and nitric oxide (NO) [4].
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Piccoli, Vinicius, and Leandro Martínez. "Solvation of different folding states of ubiquitin by EMIMDCA: a study using minimum distance distribution functions." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol202043.

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Ionic liquids are versatile solvents that have been used in various applications: as green solvents, catalysts, and in biotechnological systems. The optimization of ionic liquids use can be achieved by an understanding of its behavior in chemical systems. Here, the interaction between EMIMDCA and four different folding states of the ubiquitin is studied by the computation of minimum-distance distribution functions from molecular dynamics. In all systems presented here, EMIMDCA solvates the protein preferentially for all types of structures simulated, indicating a denaturation behavior in the presence of ubiquitin. The affinity of EMIMDCA to the protein conformations, with more residues exposed to the solvent, is related to the interactions of the ions with, manly, the apolar residues. Hence, we will show that as the protein structure becomes more open, the interactions between the ions and the protein start to have more influence from the dispersive interaction than the hydrogen bonds.
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Hwang, Wonmuk, and Matthew J. Lang. "Mechanism of Force Generation in Kinesin Motility." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-175543.

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Conventional kinesin is a dimeric motor protein that uses adenosine triphosphate (ATP) to walk processively along the microtubule. Although its nucleotide dependent conformational switching and binding of the neck linker (NL) on the motor head are known to be key events in kinesin motility, the basic mechanism by which it amplifies a small conformational change upon ATP binding to generate the force of the walking stroke has not been known. We combined structural analysis with a set of molecular dynamics simulations to identify the 9-residue long N-terminal region, which we named the ‘cover strand’ (CS), as an additional element essential for kinesin’s power stroke. It operates by differentially forming a β-sheet with NL when ATP binds, whereby the ‘cover-neck bundle’ (CNB) has an inherent conformational bias that drives NL into its binding pocket on the motor head. After the initial stroke, the later half of NL, starting with the ‘asparagine latch’ in the middle, forms specific bonds with the motor head to ensure tight binding. We constructed the force map generated by CNB, which showed a forward bias in agreement with single molecule motility measurements. Our result is consistent with other experimental observations, including the estimated stall force and the transverse anisotropy. The novel mechanism of force generation by the dynamic folding of CNB appears to hold in various kinesin families, and elucidates the economy in the design principle of the smallest known processive motor.
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CRUZEIRO-HANSSON, L. "WHAT DRIVES PROTEIN FOLDING AND PROTEIN FUNCTION?" In Proceedings of the Third Conference. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704627_0009.

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Bahi, Jacques M., Nathalie Cote, and Christophe Guyeux. "Chaos of protein folding." In 2011 International Joint Conference on Neural Networks (IJCNN 2011 - San Jose). IEEE, 2011. http://dx.doi.org/10.1109/ijcnn.2011.6033463.

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Reports on the topic "Protein Folding; Protein Conformation"

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Dill, Ken A. Inverse Protein Folding. Fort Belvoir, VA: Defense Technical Information Center, May 1998. http://dx.doi.org/10.21236/ada361002.

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Woodruff, W., R. Callender, T. Causgrove, R. Dyer, and S. Williams. Fast events in protein folding. Office of Scientific and Technical Information (OSTI), April 1996. http://dx.doi.org/10.2172/212494.

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Eliezer, D. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering. Office of Scientific and Technical Information (OSTI), June 1994. http://dx.doi.org/10.2172/10194910.

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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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Harris, R. D. Development of Rules for Folding of Biotechnology Produced Protein. Fort Belvoir, VA: Defense Technical Information Center, July 1992. http://dx.doi.org/10.21236/ada254771.

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Chen, Lingling. Studies of protein structure in solution and protein folding using synchrotron small-angle x-ray scattering. Office of Scientific and Technical Information (OSTI), April 1996. http://dx.doi.org/10.2172/510600.

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Abagyan, Ruben A. Combined approach to the inverse protein folding problem. Final report. Office of Scientific and Technical Information (OSTI), June 2000. http://dx.doi.org/10.2172/761120.

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Bakajin, O. Development of a Fast Microfluidic Mixer for Studies of Protein Folding KineticsFinal Report Cover Page. Office of Scientific and Technical Information (OSTI), February 2005. http://dx.doi.org/10.2172/917494.

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Hart, W. E., and S. Istrail. Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal. Office of Scientific and Technical Information (OSTI), August 1996. http://dx.doi.org/10.2172/425317.

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