Relevant bibliographies by topics / Protein design

Contents

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

Academic literature on the topic 'Protein design'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 September 2023

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Journal articles on the topic "Protein design"

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Porebski, Benjamin T., and Ashley M. Buckle. "Consensus protein design." Protein Engineering Design and Selection 29, no. 7 (June 5, 2016): 245–51. http://dx.doi.org/10.1093/protein/gzw015.

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Sawyer, Nicholas, Elizabeth B. Speltz, and Lynne Regan. "NextGen protein design." Biochemical Society Transactions 41, no. 5 (September 23, 2013): 1131–36. http://dx.doi.org/10.1042/bst20130112.

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Protein engineering is at an exciting stage because designed protein–protein interactions are being used in many applications. For instance, three designed proteins are now in clinical trials. Although there have been many successes over the last decade, protein engineering still faces numerous challenges. Often, designs do not work as anticipated and they still require substantial redesign. The present review focuses on the successes, the challenges and the limitations of rational protein design today.
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Pierce, Niles A., and Erik Winfree. "Protein Design is NP-hard." Protein Engineering, Design and Selection 15, no. 10 (October 2002): 779–82. http://dx.doi.org/10.1093/protein/15.10.779.

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Regan, Lynne. "Protein design." Current Opinion in Biotechnology 2, no. 4 (August 1991): 544–50. http://dx.doi.org/10.1016/0958-1669(91)90079-k.

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Libertini, Giacinto, and Alberto Di Donato. "Computer-aided gene design." "Protein Engineering, Design and Selection" 5, no. 8 (1992): 821–25. http://dx.doi.org/10.1093/protein/5.8.821.

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Kuroda, D., H. Shirai, M. P. Jacobson, and H. Nakamura. "Computer-aided antibody design." Protein Engineering Design and Selection 25, no. 10 (June 2, 2012): 507–22. http://dx.doi.org/10.1093/protein/gzs024.

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Arnold, Frances H. "Protein design for non-aqueous solvents." "Protein Engineering, Design and Selection" 2, no. 1 (1988): 21–25. http://dx.doi.org/10.1093/protein/2.1.21.

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Gutte, B., and S. Klauser. "Design of catalytic polypeptides and proteins." Protein Engineering, Design and Selection 31, no. 12 (December 1, 2018): 457–70. http://dx.doi.org/10.1093/protein/gzz009.

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Abstract The first part of this review article lists examples of complete, empirical de novo design that made important contributions to the development of the field and initiated challenging projects. The second part of this article deals with computational design of novel enzymes in native protein scaffolds; active designs were refined through random and site-directed mutagenesis producing artificial enzymes with nearly native enzyme- like activities against a number of non-natural substrates. Combining aspects of de novo design and biological evolution of nature’s enzymes has started and will accelerate the development of novel enzyme activities.
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Sawyer, Nicholas, Danielle M. Williams, and Lynne Regan. "Protein goldendoodles: Designing new proteins." Biochemist 36, no. 1 (February 1, 2014): 28–33. http://dx.doi.org/10.1042/bio03601028.

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The goldendoodle (Figure 1) is a breed of dog created to combine the desirable features of the golden retriever (calm personality, good with people and an excellent service dog) with those of the poodle (low shedding and hypoallergenic). The result surpasses expectations: not only does the goldendoodle have a great personality and low shedding, but also the animal is exceedingly cute and in great demand. Protein design, the creation of novel proteins either de novo or by extensive mutagenesis of natural proteins, has likewise produced many ‘goldendoodle-esque’ proteins whose unprecedented combination of stability and function have revolutionized academic and clinical research. Here, we discuss the history of protein design and highlight some particularly successful protein designs of this type.
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Kim, Peter S. "Passing the first milestone in protein design." "Protein Engineering, Design and Selection" 2, no. 4 (1988): 249–50. http://dx.doi.org/10.1093/protein/2.4.249.

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Dissertations / Theses on the topic "Protein design"

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Park, Changmoon Goddard William A. "Protein design and simulation Part I. Protein design. Part II. Protein simulation /." Diss., Pasadena, Calif. : California Institute of Technology, 1993. http://resolver.caltech.edu/CaltechTHESIS:11112009-114142428.

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Thesis (Ph. D.)--California Institute of Technology, 1993. UM #93-25,374.
Advisor names found in the Acknowledgements pages of the thesis. Title from home page. Viewed 01/15/2010. Includes bibliographical references.
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Kwan, Ann H. Y. "Protein design based on a PHD scaffold." Connect to full text, 2004. http://setis.library.usyd.edu.au/adt/public_html/adt-NU/public/adt-NU20041202.102526/index.html.

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Thesis (Ph. D.)--School of Molecular and Microbial Biosciences, Faculty of Science, University of Sydney, 2004.
Chapter headings on separately inserted unnumbered cream coloured leaves. Bibliography: leaves 122-135.
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Baas, Tracey Lynn. "The design, synthesis, and characterization of template assembled synthetic proteins /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/11561.

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Barua, Bipasha. "Design and study of Trp-cage miniproteins /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/8533.

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Dantas, Gautam. "In silico protein evolution by intelligent design : creating new and improved protein structures /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9236.

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Badger, David B. "Design and Synthesis of Protein-Protein Interaction Inhibitor Scaffolds." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/3964.

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Many currently relevant diseases such as cancer arise from altered biological pathways that rely on protein-protein interactions. The proteins involved in these interactions contain certain functional domains that are responsible for the protein's biological activities. These domains consist of secondary structural elements such as α-helices and Β-sheets which are at the heart of the protein's biological activity. Therefore, designing drugs that inhibit protein-protein interactions by binding to these key secondary structural elements should provide an effective treatment for many diseases. Presented in this dissertation are the designs, syntheses, and biological evaluations for both novel α-helix and novel Β-sheet mimics. The α-helix mimics were designed to inhibit the interactions between the tumor suppressor protein p53 and its inhibitor protein, MDM2. We also targeted the interactions between the Bak/Bcl-xL proteins. Using the knowledge gained from Hamilton's 1,4-terphenylene scaffold, we designed our inhibitors to be non-peptidic small molecule α-helix mimics. These molecules were designed to bind to the NH2-terminal domain of MDM2 protein thus preventing it from binding to the p53 protein thereby allowing p53 to induce apoptosis. The α-helix mimetic scaffold is designed around a central functionalized pyridazine ring while maintaining the appropriate distances between the ith, ith+4, and ith+7 positions of a natural alpha helix. The Β-sheet mimics were designed as inhibitors for the integrin mediated extracellular matrix cell adhesion found in Multiple Myeloma. We have designed, synthesized, and incorporated novel Β-turns to induce the formation of Β-hairpins as well as to cyclize the peptides in order to increase their binding affinities and reduce proteolytic cleavage. Given that many protein-protein interactions occur through hydrophobic interactions; our primary Β-turn promoter was designed with the ability to alter the Β-hairpin's hydrophobicity depending on the sulfonyl group used in the turn. The synthesis of several different sulfonyl chlorides for use in our Β-turn promoter is included in this section. We have also provided a detailed structural analysis and characterization of these new cyclic peptides via NMR and CD spectrometry. Using standard 2D NMR methods, we have elucidated the 3D conformation of several peptides in solution. We have also studied the structure activity relationships (SAR) for these cyclic peptides and then correlated these results with those obtained from the NMR studies.
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Datta, Deepshikha Goddard William A. "Protein-ligand interactions : docking, design and protein conformational change /." Diss., Pasadena, Calif. : California Institute of Technology, 2003. http://resolver.caltech.edu/CaltechETD:etd-03242003-111426.

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Bazzoli, A. "Protein structure prediction and protein design with evolutionary algorithms." Doctoral thesis, Università degli Studi di Milano, 2009. http://hdl.handle.net/2434/64478.

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Campbell, Sean Thomas. "Protein Engineering for Biochemical Interrogation and System Design." Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/560940.

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Proteins are intimately involved in almost every cellular phenomenon, from life to death. Understanding the interactions of proteins with each other and other macromolecules and the ability to rationally redesign them to improve their activities or control their function are of considerable current interest. Split-protein methodologies provide an avenue for achieving many of these goals. Since the original discovery of conditionally activated split-ubiquitin, the field has grown exponentially to include the activities of over a dozen different proteins. The flexibility of the systems has resulted in their use across a wide spectrum, both literally and figuratively, to primarily screen, visualize and quantitate macromolecular interactions in a variety of biological systems. In another arena, there is significant interest the apoptosis-regulating proteins: the Bcl-2 family. These proteins are found in many cell types and control, through expression levels as well as other mechanisms, the apoptotic state of a protein as governed by intrinsic death signals generated from such sources as DNA damage and viral infection. The apoptotic function of these proteins are mainly governed by a single type of interaction: the helix:receptor binding of the BH3-Only helices to the anti-apoptotic receptor proteins. While this often promiscuous helix:receptor interaction has received much scrutiny, the nature of the anti-apoptotic binding pocket, especially with regard to the specific residues that govern the interaction, has been lacking. With the high sensitivity and rapid analysis platform afforded by the cell-free split-luciferase analysis methodology, we devised and carried out the first systematic and large scale alanine mutagenesis of all five major anti-apoptotic members of the Bcl-2 family, validated these results both with biophysical methods as well as correlation with previous studies. Our results help explain how different receptors can bind a wide range of helices and also uncovered details regarding binding that are not possible with structural or computational analysis alone. In a second area of research, we have utilized the interaction of BH3 helices and their receptors for designing small molecule controlled protein kinases and phosphatases. In this protein design area, BH3-Only helices were inserted using a knowledge based approach into particular loops within both a protein kinase and a protein phosphatase. The BH3-Only helix interaction with added receptors, such as Bcl-xL provided an allosteric switch for turning-off the activity of the helix-inserted enzymes. The activity of the enzymes could then be turned-on by the addition of a cell-permeable small molecule that is known to bind the receptor. This plug-and-play design was demonstrated to be successful for two very different enzyme classes and likely provides a general and tunable biological element for controlling the activity of one or more proteins and enzymes in a biochemical networks.
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Rege, Nischay Kiran. "THE UN-DESIGN AND DESIGN OF INSULIN: STRUCTURAL EVOLUTIONWITH APPLICATION TO THERAPEUTIC DESIGN." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1531429783955495.

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Books on the topic "Protein design"

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Raphael, Guerois, and de la Paz Manuela López. Protein Design. New Jersey: Humana Press, 2006. http://dx.doi.org/10.1385/1597451169.

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Köhler, Valentin, ed. Protein Design. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1486-9.

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J, Park Sheldon, and Cochran Jennifer R, eds. Protein engineering and design. Boca Raton: CRC Press, 2010.

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Hogue, Angeletti Ruth, ed. Proteins: Analysis and design. San Diego: Academic Press, 1998.

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Raphael, Guerois, and Lopez de la Paz, Manuela., eds. Protein design: Methods and applications. Totowa, N.J: Humana Press, 2006.

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Thermostable proteins: Structural stability and design. Boca Raton: Taylor & Francis, 2012.

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R, Carey Paul, ed. Protein engineering and design. San Diego, Calif: Academic Press, 1996.

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M, Hatano, ed. Protein structural analysis, folding, and design. Tokyo: Japan Scientific Societies Press, 1990.

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Samish, Ilan, ed. Computational Protein Design. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6637-0.

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Hamilton, Arnold Frances, ed. Evolutionary protein design. San Diego: Academic Press, 2001.

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Book chapters on the topic "Protein design"

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Poluri, Krishna Mohan, Khushboo Gulati, Deepak Kumar Tripathi, and Nupur Nagar. "Drug Design Methods to Regulate Protein–Protein Interactions." In Protein-Protein Interactions, 265–341. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-2423-3_6.

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Saven, Jeffery G. "Computational Protein Design." In Protein Engineering Handbook, 325–42. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527634026.ch12.

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Contreras, Marinela, Sara Artigas-Jerónimo, Juan J. Pastor Comín, and José de la Fuente. "A Quantum Vaccinomics Approach Based on Protein–Protein Interactions." In Vaccine Design, 287–305. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1888-2_17.

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Shifman, Julia, and Anamika Singh. "Computational Protein Design." In Encyclopedia of Biophysics, 1–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_10084-1.

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Carey, Robert I., Karl-Heinz Altmann, and Manfred Mutter. "Protein Design: Template-Assembled Synthetic Proteins." In Novartis Foundation Symposia, 187–212. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514085.ch13.

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Kangueane, Pandjassarame, and Christina Nilofer. "HLA-Peptide Interaction to Short Peptide Vaccine Design." In Protein-Protein and Domain-Domain Interactions, 169–78. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7347-2_15.

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Briem, H. "De Novo Design Methods." In Small Molecule — Protein Interactions, 153–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_10.

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Narad, Priyanka, Romasha Gupta, Isha Gupta, and Abhishek Sengupta. "Protein Engineering Methods to Design Protein Therapeutics." In Protein-based Therapeutics, 49–100. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-8249-1_3.

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Kaiser, E. T. "Design and Construction of Biologically Active Peptides and Proteins Including Enzymes." In Protein Structure and Protein Engineering, 109–12. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-74173-9_12.

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Shukla, Rohit, and Timir Tripathi. "Molecular Dynamics Simulation of Protein and Protein–Ligand Complexes." In Computer-Aided Drug Design, 133–61. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-6815-2_7.

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Conference papers on the topic "Protein design"

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Chen, Lingyun. "Structural design of plant protein gel networks for food applications." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/wnsz2802.

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Gelation is one of the most important functional properties of proteins as it provides texture and structure in foods. Gelatin, egg white and whey proteins are widely used as gelling agents in the food industry. Plant proteins are considered inferior to animal proteins in gelling properties. With the recent surge in demand led by sustainability and health considerations, plant-based food products have taken a center stage in food product innovation. This trend has spurred academic and industrial interest to explore the opportunity of developing gelling ingredients from diversified plant protein sources, replacing animal protein based gels. This presentation will introduce the recent research efforts in our group to develop gelling properties from emerging sources of plant proteins (e.g. pea, lentil and oat). The structural design approaches (e.g. pH-shifting, protein aggregates to build gel network) and novel technologies (e.g. cold plasma, high pressure) that have potential to increase gel performances from plant proteins will be highlighted. The gel rheological properties and mechanical strength as impacted by the protein composition, conformation and aggregation will be discussed. The food application of plant protein based gels will be illustrated.
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Yun-yuan, Dong, Yang Jun, Liu Qi-jun, and Wang Zheng-hua. "The topological features of nonessential-nonhub proteins in the protein-protein interaction network." In 2012 3rd International Conference on System Science, Engineering Design and Manufacturing Informatization (ICSEM). IEEE, 2012. http://dx.doi.org/10.1109/icssem.2012.6340764.

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "On Hydrogen Bonds and Mobility of Protein Molecules." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-87470.

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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. In this paper we explore the pivotal role of Hydrogen bonds in determining the structure and function of the proteins from the point of view of mechanical mobility. The existing geometric criteria on the formation of Hydrogen bonds are reviewed and a new set of geometric criteria are proposed. We show that the new criteria better correlate the number of predicted Hydrogen bonds with those established by biological principles than other existing criteria. Furthermore, we employ established tools in kinematics mobility analysis to evaluate the internal mobility of protein molecules, and to identify the rigid and flexible segments of the proteins. Our results show that the developed procedure significantly reduces the DOF of the protein models, with an average reduction of 94%. Such a dramatic reduction in the number of DOF can have has enormous computational implications in protein folding simulations.
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Kuo, Huang-Cheng, Ping-Lin Ong, Jia-Jie Li, and Jen-Peng Huang. "Predicting Protein-Protein Recognition Using Feature Vector." In 2008 Eighth International Conference on Intelligent Systems Design and Applications (ISDA). IEEE, 2008. http://dx.doi.org/10.1109/isda.2008.149.

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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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Arikawa, Keisuke. "A Computational Framework for Predicting the Motions of a Protein System From a Robot Kinematics Viewpoint." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-12527.

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There is an analogy between the kinematic structures of proteins and robotic mechanisms. On the basis of this analogy, we have so far developed some methods for predicting the internal motions of proteins from their three-dimensional structural data in protein data bank (PDB). However, these methods are basically applicable to a single protein molecule. In this study, we extended these methods to apply them to systems that consist of multiple molecules including proteins (protein systems), and developed a computational framework for predicting the motions of the molecules. The model used in this method is a type of elastic network model. In particular, proteins are modeled as a robot manipulator constrained by the springs (the dihedral angles on the main chains correspond to the joint angles). The interactions between molecules are also modeled as springs. The basic concept for predicting the motions is based on the analysis of structural compliance. By applying statically balanced forces to the model in various directions, we extracted those motions with larger structural compliance. To reduce the computational time, we formulated the method with the prospect of efficient computation including parallel computation. In addition, we developed a preparatory computer program implementing the proposed algorithms, and analyzed some protein systems. The results showed that the proposed computational framework can efficiently analyze large protein systems.
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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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Arikawa, Keisuke. "Investigation of Algorithms for Analyzing Protein Internal Motion From Viewpoint of Robot Kinematics." In ASME 2010 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/detc2010-28551.

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We investigate various algorithms for analyzing the characteristics of the internal motion of proteins based on the analogies between their kinematic structures and robotic mechanisms. First, we introduce an artificial simple protein model, planar main chain (PMC), composed of a planar serial link mechanism to investigate the algorithms. Then, we develop algorithms for analyzing the conformational fluctuations by applying the manipulability analysis of robot manipulators and control strategies for redundant manipulators. Next, we develop algorithms for analyzing the conformational deformation caused by the external forces and to evaluate the compliances of the specified parts of proteins. Finally, we show that the proposed algorithms developed by using PMC models are applicable for the three dimensional main chain structures of real proteins, and may be used to analyze their characteristics of the internal motion. We also reveal some preliminary simulation results of the analysis of a real protein.
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Caffrey, Martin. "Lipid Phase Behavior: Databases, Rational Design and Membrane Protein Crystallization." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-192724.

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The relationship that exists between structure and function is a unifying theme in my varied biomembrane-based research activities. It applies equally well to the lipid as to the protein component of membranes. With a view to exploiting information that has been and that is currently being generated in my laboratory, as well as that which exists in the literature, a number of web-accessible, relational databases have been established over the years. These include databases dealing with lipids, detergents and membrane proteins. Those catering to lipids include i) LIPIDAT, a database of thermodynamic information on lipid phases and phase transitions, ii) LIPIDAG, a database of phase diagrams concerning lipid miscibility, and iii) LMSD, a lipid molecular structures database. CMCD is the detergent-based database. It houses critical micelle concentration information on a wide assortment of surfactants under different conditions. The membrane protein data bank (MPDB) was established to provide convenient access to the 3-D structure and related properties of membrane proteins and peptides. The utility and current status of these assorted databases will be described and recommendations will be made for extending their range and usefulness.
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Belure, Sandeep V., Ofer M. Shir, and Vikas Nanda. "Protein design by multiobjective optimization." In GECCO '17: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3071178.3071268.

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Reports on the topic "Protein design"

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Bramson, H. N. A Modular Approach to Protein Design. Fort Belvoir, VA: Defense Technical Information Center, July 1991. http://dx.doi.org/10.21236/ada239041.

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Bramson, H. N. A Modular Approach to Protein Design. Fort Belvoir, VA: Defense Technical Information Center, April 1990. http://dx.doi.org/10.21236/ada220926.

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Sapiro, Guillermo. New Forcefields and Algorithms for Computational Protein Design. Fort Belvoir, VA: Defense Technical Information Center, January 2003. http://dx.doi.org/10.21236/ada428012.

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Avdjieva, Irena, Ivan Terziyski, Gergana Zahmanova, Anelia Nisheva, and Dimitar Vassilev. Fusion Protein Design with Computational Homologybased Structure Prediction. "Prof. Marin Drinov" Publishing House of Bulgarian Academy of Sciences, July 2021. http://dx.doi.org/10.7546/crabs.2021.07.07.

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Herman, Eliot D., Gad Galili, and Alan Bennett. Recognition and Disposal of Misfolded Seed Proteins. United States Department of Agriculture, August 1994. http://dx.doi.org/10.32747/1994.7568791.bard.

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This project was directed at determining mechanisms involved in storage of intrinsic and foreign storage proteins in seeds. Seeds constitute the majority of direct and indirect food. Understanding how seeds store proteins is important to design approaches to improve the quality of seed proteins through biotechnology. In the Israeli part of this project we have conducted investigations to elucidate the mechanisms involved in assembling wheat storage proteins into ER-derived protein bodies. The results obtained have shown how domains of storage protein molecules are critical in the assembly of protein bodies. In the US side of this project the fate of foreign and engineered proteins expressed in seeds has been investigated. Engineering seed proteins offers the prospect of improving the quality of crops. Many foreign proteins are unstable when expressed in transgenic seeds. The results obtained have demonstrated that sequestering foreign proteins in the ER or ER-derived protein bodies stabilizes the proteins permitting their accumulation. The collaboration conducted in this project has advanced the understanding how protein bodies are assembled and the potential to use the ER and protein bodies to store engineered proteins that can enhance the composition of seeds.
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Matthews, Lisa, Guanming Wu, Robin Haw, Timothy Brunson, Nasim Sanati, Solomon Shorser, Deidre Beavers, Patrick Conley, Lincoln Stein, and Peter D'Eustachio. Illuminating Dark Proteins using Reactome Pathways. Reactome, October 2022. http://dx.doi.org/10.3180/poster/20221027matthews.

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Diseases are often the consequence of proteins or protein complexes that are non-functional or that function improperly. An active area of research has focused on the identification of molecules that can interact with defective proteins and restore their function. While 22% percent of human proteins are estimated to be druggable, less than fifteen percent are targeted by FDA-approved drugs, and the vast majority of untargeted proteins are understudied or so-called "dark" proteins. Elucidation of the function of these dark proteins, particularly those in commonly drug-targeted protein families, may offer therapeutic opportunities for many diseases. Reactome is the most comprehensive, open-access pathway knowledgebase covering 2585 pathways and including 14246 reactions, 11088 proteins, 13984 complexes, and 1093 drugs. Placing dark proteins in the context of Reactome pathways provides a framework of reference for these proteins facilitating the generation of hypotheses for experimental biologists to develop targeted experiments, unravel the potential functions of these proteins, and then design drugs to manipulate them. To this end, we have trained a random forest with 106 protein/gene pairwise features collected from multiple resources to predict functional interactions between dark proteins and proteins annotated in Reactome and then developed three scores to measure the interactions between dark proteins and Reactome pathways based on enrichment analysis and fuzzy logic simulations. Literature evidence via manual checking and systematic NLP-based analysis support predicted interacting pathways for dark proteins. To visualize dark proteins in the context of Reactome pathways, we have also developed a new website, idg.reactome.org, by extending the Reactome web application with new features illustrating these proteins together with tissue-specific protein and gene expression levels and drug interactions.
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Banai, Menachem, and Gary Splitter. Molecular Characterization and Function of Brucella Immunodominant Proteins. United States Department of Agriculture, July 1993. http://dx.doi.org/10.32747/1993.7568100.bard.

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The BARD project was a continuation of a previous BARD funded research project. It was aimed at characterization of the 12kDa immunodominant protein and subsequently the cloning and expression of the gene in E. coli. Additional immunodominant proteins were sought among genomic B. abortus expression library clones using T-lymphocyte proliferation assay as a screening method. The 12kDa protein was identified as the L7/L12 ribosomal protein demonstrating in the first time the role a structural protein may play in the development of the host's immunity against the organism. The gene was cloned from B. abortus (USA) and B. melitensis (Israel) showing identity of the oligonucleotide sequence between the two species. Further subcloning allowed expression of the protein in E. coli. While the native protein was shown to have DTH antigenicity its recombinant analog lacked this activity. In contrast the two proteins elicited lymphocyte proliferation in experimental murine brucellosis. CD4+ cells of the Th1 subset predominantly responded to this protein demonstrating the development of protective immunity (g-IFN, and IL-2) in the host. Similar results were obtained with bovine Brucella primed lymphocytes. UvrA, GroE1 and GroEs were additional Brucella immunodominant proteins that demonstrated MHC class II antigenicity. The role cytotoxic cells are playing in the clearance of brucella cells was shown using knock out mice defective either in their CD4+ or CD8+ cells. CD4+ defective mice were able to clear brucella as fast as did normal mice. In contrast mice which were defective in their CD8+ cells could not clear the organisms effectively proving the importance of this subtype cell line in development of protective immunity. The understanding of the host's immune response and the expansion of the panel of Brucella immunodominant proteins opened new avenues in vaccine design. It is now feasible to selectively use immunodominant proteins either as subunit vaccine to fortify immunity of older animals or as diagnostic reagents for the serological survaillance.
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Maestrini, Bernardo. Better informed decision making in consumers' food choice, breeders' crop design and protein transition : subproject 2 (parbars). Wageningen: Wageningen Plant Research, 2022. http://dx.doi.org/10.18174/577255.

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Nellis, David, Rashmi Rawat, Gunnar Malmquist, Kavita Aiyer, Fabien Rousset, and Isabelle Leqeux. BioPhorum approach to the registration of innovative raw materials using quality by design principles – Appendix 2: Protein A resins. BioPhorum, January 2023. http://dx.doi.org/10.46220/2023ds001.

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