Relevant bibliographies by topics / Protein flexibility

Academic literature on the topic 'Protein flexibility'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 September 2023

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Journal articles on the topic "Protein flexibility"

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Ragone, R., F. Facchiano, A. Facchiano, A. M. Facchiano, and G. Colonna. "Flexibility plot of proteins." "Protein Engineering, Design and Selection" 2, no. 7 (1989): 497–504. http://dx.doi.org/10.1093/protein/2.7.497.

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Vihinen, Mauno. "Relationship of protein flexibility to thermostability." "Protein Engineering, Design and Selection" 1, no. 6 (1987): 477–80. http://dx.doi.org/10.1093/protein/1.6.477.

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Cioni, Patrizia, and Giovanni B. Strambini. "Pressure Effects on Protein Flexibility Monomeric Proteins." Journal of Molecular Biology 242, no. 3 (September 1994): 291–301. http://dx.doi.org/10.1006/jmbi.1994.1579.

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Wang, Chu, Philip Bradley, and David Baker. "Protein–Protein Docking with Backbone Flexibility." Journal of Molecular Biology 373, no. 2 (October 2007): 503–19. http://dx.doi.org/10.1016/j.jmb.2007.07.050.

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Greene, Lesley H., Jay A. Grobler, Vladimir A. Malinovskii, Jie Tian, K. Ravi Acharya, and Keith Brew. "Stability, activity and flexibility in α-lactalbumin." Protein Engineering, Design and Selection 12, no. 7 (July 1999): 581–87. http://dx.doi.org/10.1093/protein/12.7.581.

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Teplyakov, Alexey, Thomas J. Malia, Galina Obmolova, Steven A. Jacobs, Karyn T. O'Neil, and Gary L. Gilliland. "Conformational flexibility of an anti-IL-13 DARPin†." Protein Engineering, Design and Selection 30, no. 1 (December 15, 2016): 31–37. http://dx.doi.org/10.1093/protein/gzw059.

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Abstract Designed ankyrin repeat proteins (DARPin®) are artificial non-immunoglobulin binding proteins with potential applications as therapeutic molecules. DARPin 6G9 binds interleukin-13 with high affinity and blocks the signaling pathway and as such is promising for the treatment of asthma and other atopic diseases. The crystal structures of DARPin 6G9 in the unbound form and in complex with IL-13 were determined at high resolution. The DARPin competes for the same epitope as the IL-13 receptor chain 13Rα1 but does not interfere with the binding of the other receptor chain, IL-4Rα. Analysis of multiple copies of the DARPin molecule in the crystal indicates the conformational instability in the N-terminal cap that was predicted from molecular dynamics simulations. Comparison of the DARPin structures in the free state and in complex with IL-13 reveals a concerted movement of the ankyrin repeats upon binding resulted in the opening of the binding site. The induced-fit mode of binding employed by DARPin 6G9 is very unusual for DARPins since they were designed as particularly stable and rigid molecules. This finding shows that DARPins can operate by various binding mechanisms and suggests that some flexibility in the scaffold may be an advantage.
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Berynskyy, Mykhaylo, and Rebecca C. Wade. "Treating Conformational Flexibility in Protein-Protein Docking." Current Physical Chemistry 3, no. 1 (January 1, 2013): 27–35. http://dx.doi.org/10.2174/1877946811303010006.

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Fayos, Rosa, Giuseppe Melacini, Marceen G. Newlon, Lora Burns, John D. Scott, and Patricia A. Jennings. "Induction of Flexibility through Protein-Protein Interactions." Journal of Biological Chemistry 278, no. 20 (February 25, 2003): 18581–87. http://dx.doi.org/10.1074/jbc.m300866200.

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Vasilache, Simina, Nazanin Mirshahi, Soo-Yeon Ji, James Mottonen, Donald J. Jacobs, and Kayvan Najarian. "A Signal Processing Method to Explore Similarity in Protein Flexibility." Advances in Bioinformatics 2010 (December 20, 2010): 1–8. http://dx.doi.org/10.1155/2010/454671.

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Understanding mechanisms of protein flexibility is of great importance to structural biology. The ability to detect similarities between proteins and their patterns is vital in discovering new information about unknown protein functions. A Distance Constraint Model (DCM) provides a means to generate a variety of flexibility measures based on a given protein structure. Although information about mechanical properties of flexibility is critical for understanding protein function for a given protein, the question of whether certain characteristics are shared across homologous proteins is difficult to assess. For a proper assessment, a quantified measure of similarity is necessary. This paper begins to explore image processing techniques to quantify similarities in signals and images that characterize protein flexibility. The dataset considered here consists of three different families of proteins, with three proteins in each family. The similarities and differences found within flexibility measures across homologous proteins do not align with sequence-based evolutionary methods.
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Ehrlich, Lutz P., Michael Nilges, and Rebecca C. Wade. "The impact of protein flexibility on protein-protein docking." Proteins: Structure, Function, and Bioinformatics 58, no. 1 (October 28, 2004): 126–33. http://dx.doi.org/10.1002/prot.20272.

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Dissertations / Theses on the topic "Protein flexibility"

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Mitchell, Felicity. "Modelling protein flexibility using molecular simulation methods." Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525167.

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Broadhead, Richard Ian. "Metabolic flexibility in Escherichia coli." Thesis, University of Aberdeen, 1998. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU104201.

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This study of the relationship between heterologous protein production and bacterial growth has shown that foreign protein can account for as much as 30% of the total cell protein without the specific growth rate being affected. Higher levels of foreign protein production are achieved at lower growth rates. Foreign protein is synthesised without any increase in ribosome number or ribosome activity occurring in the recombinant cells relative to their parent strain, i.e. the capacity of parental and recombinant cells to synthesise protein is the same. These observations are explained in terms of a model in which Escherichia coli proteins are be divided into two types. Type I proteins are involved in the processes of transcription and translation. Type 2 proteins are those which serve other purposes. The model suggests that the synthesis of type 2 proteins will be decreased in order to accommodate foreign protein production. This implies that some Escherichia coli proteins are overproduced relative to the amount of that protein that is essential to the cell to maintain growth. Two dimensional electrophoresis showed that there was a decrease in some host cell protein levels between parental and recombinant cells. An increase in the levels of molecular chaperone proteins in recombinant cells grown under some conditions was observed. These data are explained in terms of our current understanding of the regulation of molecular chaperone production. The data obtained are discussed in relation to our current understanding of the growth of bacteria and the reported effects of high levels of foreign protein production on bacterial physiology.
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Magnusson, Ulrika. "Structural Studies of Binding Proteins: Investigations of Flexibility, Specificity and Stability." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3640.

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Zöllner, Frank G. "Enhancing protein-protein docking by new approaches to protein flexibility and scoring of docking hypotheses." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972854142.

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Dobbins, Sara E. "Computational Studies of Protein Flexibility using Normal Mode Analysis." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.508940.

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Koch, Kerstin. "Statistical analysis of amino acid side chain flexibility for 1:n protein protein docking." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968919413.

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Sánchez, Martínez Melchor. "Protein Flexibility: From local to global motions. A computational study." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/288044.

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Proteins are flexible entities, and thus move. Its function is closely related to the flexibility. To carry out any function is necessary a conformational change. As protein motions imply an exchange of conformations, protein dynamics is also known as Protein Conformational Dynamics. The fluctuations between the different proteic configurations can be classified according to the length-scale, the time-scale and the amplitude and directionality of them. The movement could be local movement, involving only the rearrangement of a few amino- acid side chains or even backbone, or it may be a large, global movement, modulating the allostery or the conformational transitions, and even involve folding of the entire protein. Generally local motions are also fast and small amplitude motions whereas global motions are associated with slow and large amplitude motions. All these motions encompassed into protein dynamics are governed by the features of the underlying energy landscape. To fully describe a protein, a multidimensional and rugged energy landscape defining the relative probabilities of the conformational states (thermodynamics) and the energy barriers between them (kinetics) is required. To understand proteins in action, the fourth dimension, time, must be added. As these motions are important for the proteic function a deep understanding is required. To do that in this thesis we have tried to answer several questions related to these dynamical phenomena. Concretely we have performed local studies, related to enzyme catalysis and protein damage, and globally, with the determination and analysis of protein conformational ensembles. These studies have been developed using methods of computational chemistry, computational biochemistry and computational biophysics, which have proven to be very useful tools when studying the protein dynamics. Computational methods are an efficient and useful tool to characterize protein motions. However the current computational approaches present limitations and to solve them the incorporation of experimental data and its correct interpretation is crucial. This necessity of be complemented comes from different sides: 1) from experiments to computations and 2) from computations to experiments. The convergence of experimental and computational techniques to the same point is key to achieve a deep understanding of protein dynamics.
La presente tesis se centra en el estudio computacional de la dinámica de las proteínas. Las proteínas son entidades flexibles y como tales se mueven. Este movimiento es indispensable y esta directamente relacionado con su función. La dinámica de las proteínas se puede dividir en dos grandes bloques conceptuales según el número de átomos involucrados, la escala de tiempo en que tiene lugar y la amplitud y dirección de la misma. Debido a la importancia de estos fenómenos, emerge la necesidad de tener un conocimiento profundo sobre los mismos. Debido a ello, en esta tesis doctoral se ha tratado de dar respuesta a varios fenómenos observados en relación directa con la dinámica de las proteínas. Concretamente, hemos realizado estudios a nivel local, de 'centro activo', relacionados con la catálisis enzimática y el daño proteico, así como a nivel global, con la determinación y el análisis de conjuntos conformacionales de proteínas. Estos estudios, se han desarrollado usando métodos propios de la química, la bioquímica y la biofísica computacionales, los cuales se han mostrado como herramientas muy útiles a la hora de estudiar la dinámica. De todos ellos, de forma general, podemos concluir que los métodos computacionales son una herramienta eficaz y util para caracterizar la dinámica de las proteínas. Sin embargo, los métodos computacionales actuales presentan limitaciones y para resolverlos la incorporación de datos experimentales as como su correcta interpretación es crucial. Pero aunque los metodos computacionales necesitan de los experimentales, esta necesidad también se da de manera opuesta. La convergencia de los métodos experimentales y computacionales es clave para poder profundizar en el conocimiento de la dinámica de las proteínas.
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Salmaso, Veronica. "Exploring protein flexibility during docking to investigate ligand-target recognition." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421817.

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Ligand-protein binding models have experienced an evolution during time: from the lock-key model to induced-fit and conformational selection, the role of protein flexibility has become more and more relevant. Understanding binding mechanism is of great importance in drug-discovery, because it could help to rationalize the activity of known binders and to optimize them. The application of computational techniques to drug-discovery has been reported since the 1980s, with the advent computer-aided drug design. During the years several techniques have been developed to address the protein flexibility issue. The present work proposes a strategy to consider protein structure variability in molecular docking, through a ligand-based/structure-based integrated approach and through the development of a fully automatic cross-docking benchmark pipeline. Moreover, a full exploration of protein flexibility during the binding process is proposed through the Supervised Molecular Dynamics. The application of a tabu-like algorithm to classical molecular dynamics accelerates the binding process from the micro-millisecond to the nanosecond timescales. In the present work, an implementation of this algorithm has been performed to study peptide-protein recognition processes.
I modelli di riconoscimento ligando-proteina si sono evoluti nel corso degli anni: dal modello chiave-serratura a quello di fit-indotto e selezione conformazionale, il ruolo della flessibilità proteica è diventato via via più importante. Capire il meccanismo di riconoscimento è di grande importanza nella progettazione di nuovi farmaci, perchè può dare la possibilità di razionalizzare l’attività di ligandi noti e di ottimizzarli. L’applicazione di tecniche computazionali alla scoperta di nuovi farmaci risale agli anni ‘80, con l’avvento del cosiddetto “Computer-Aided Drug Design”, o, tradotto, progettazione di farmaci aiutata dal computer. Negli anni sono state sviluppate molte tecniche che hanno affrontato il problema della flessibilità proteica. Questo lavoro propone una strategia per considerare la variabilità delle strutture proteiche nel docking, attraverso un approccio combinato ligand-based/structure-based e attraverso lo sviluppo di una procedura completamente automatizzata di docking incrociato. In aggiunta, viene proposta una piena esplorazione della flessibilità proteica durante il processo di legame attraverso la Dinamica Molecolare Supervisionata. L’applicazione di un algoritmo simil-tabu alla dinamica molecolare classica accelera il processo di riconoscimento dalla scala dei micro-millisecondi a quella dei nanosecondi. Nel presente lavoro è stata fatta un’implementazione di questa algoritmica per studiare il processo di riconoscimento peptide-proteina.
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Cobb, Andrew Martin. "Resolving the flexibility and intricacy of DNA repair protein-DNA interactions." Thesis, University of East Anglia, 2010. https://ueaeprints.uea.ac.uk/10586/.

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Within all cells, complex molecular systems exist that are responsible for maintaining genome stability by detecting and repairing dangerous alterations in DNA. Ensuring the accurate and efficient functioning of such systems is necessary for the preservation of DNA integrity and avoidance of disease. The flexible and diverse modes of DNA-binding exhibited by human p53 permits this ‘guardian of the genome’ to elicit versatile cellular activities that are crucial in monitoring threats to genome dynamics and conducting appropriate responses. In conjunction with its sequence-specific DNA-binding activity that is essential to target gene transactivation, p53 can bind to unusual DNA structures independent of DNA sequence and it has been proposed this activity may allow p53 to interact with detrimental secondary structures that arise in unstable genomic regions. To provide further insight into p53-DNA interactions, an in vitro DNA binding assay was developed that was used to characterise binding properties towards several DNA molecules to allow comparison of non-specific, sequence-specific and structurespecific binding. It was determined that unusual structures in DNA significantly enhanced p53 binding in non-sequence specific DNA and that the presence of internal hairpin regions induced binding comparable to sequence-specific binding. In vivo p53-DNA interactions were also quantified using chromatin immunoprecipitation and variations in preference to different response element sequences was ascertained. DNA binding is also central to the ability of Ku proteins to function as essential components of non-homologous end joining and telomere maintenance in eukaryotes. Prokaryotic homologues of Ku proteins that function as homodimers in two-component repair systems have also been identified. Recently, 3 Ku homologues in Streptomyces coelicolor were reported, but very little is currently known regarding their biological activity. It was discovered that all 3 Ku proteins exhibited varied independent DNA-binding properties that were influenced by DNA topology, size and end-structure. Unusually for Ku, it was found 1 of these proteins exhibited strong binding to single-stranded DNA. Precipitation assays determined that these proteins may act as DNA end synapsis mediators during the DNA endjoining process and ligation experiments revealed Ku was responsible for rigidifying DNAs or completely inhibiting ligation activity, probably via DNA end-protection activity. Experimental evidence indicated that specific interactions could occur between S. coelicolor Ku suggesting these proteins form both homodimers and heterodimers.
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Yu, Hongtao. "Water in Protein Cavities: Free Energy, Entropy, Enthalpy, and its Influences on Protein Structure and Flexibility." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/341.

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Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistantto novobiocin as well as those with a decreased affinity for novobiocin over clorobiocinboth involve a less favorable entropy of binding, which more than compensates for amore favorable enthalpy, and additional water molecules at the proteinligandinterface.Free energy, enthalpy, and entropy for these water molecules were calculated by thermodynamicintegration computer simulations. The calculations show that addition of thewater molecules is entropically unfavorable, with values that are comparable to the measuredentropy differences. The free energies and entropies correlate with the change inthe number of hydrogen bonds due to the addition of water molecules.To examine the wide variety of cavities available to water molecules inside proteins,a model of the protein cavities is developed with the local environment treated at atomicdetail and the nonlocal environment treated approximately. The cavities are then changedto vary in size and in the number of hydrogen bonds available to a water molecule insidethe cavity. The free energy, entropy, and enthalpy change for the transfer of a watermolecule to the cavity from the bulk liquid is calculated from thermodynamic integration.The results of the model are close to those of similar cavities calculated using the fullprotein and solvent environment. As the number of hydrogen bonds resulting from theaddition of the water molecule increases, the free energy decreases, as the enthalpic gainof making a hydrogen bond outweighs the entropic cost. Changing the volume of thecavity has a smaller effect on the thermodynamics. Once the hydrogen bond contributionis taken into account, the volume dependence on free energy, entropy, and enthalpy issmall and roughly the same for a hydrophobic cavity as a hydrophilic cavity.The influences of bound water on protein structure and influences are also evaluatedby performing molecular dynamics simulation for proteins with and without boundwater. Four proteins are simulated, the wildtypebovine pancreatic trypsin inhibitor(BPTI), the wildtypehen egg white lysozyme (HEWL), and two variants of the wildtypeStaphylococcal nuclease (SNase), PHS and PHS/V66E. The simulation reveals that allthese four proteins suffer structural changes upon the removing of bound water molecules,as indicating by their increased RMSD values with respect to the crystal structures. Threeout of the four proteins, BPTI, HEWL, and the PHS mutant of SNase have increased flexibility,while no apparent flexibility change is seen in the PHS/V66E variant of SNase.
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Books on the topic "Protein flexibility"

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A, Kuhn Leslie, and Thorpe M. F, eds. Protein flexibility and folding. Amsterdam: Elsevier, 2001.

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Solvent-dependent flexibility of proteins and principles of their function. Dordrecht: D. Reidel, 1985.

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Käiväräinen, Alex I., ed. Solvent-Dependent Flexibility of Proteins and Principles of Their Function. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-5197-6.

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GOVERNMENT, US. An Act to Provide Tax Relief for Small Businesses, to Protect Jobs, to Create Opportunities, to Increase the Take Home Pay of Workers, to Amend the Portal-to-Portal Act of 1947 Relating to the Payment of Wages to Employees Who Use Employer Owned Vehicles, and to Amend the Fair Labor Standards Act of 1938 to Increase the Minimum Wage Rate and to Prevent Job Loss by Providing Flexibility to Employers in Complying with Minimum Wage and Overtime Requirements under that Act. [Washington, D.C.?: U.S. G.P.O., 1996.

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Kuhn, L. A. Protein Flexibility and Folding. Elsevier Science & Technology Books, 2001.

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Käiväräinen, Alex I. Solvent-Dependent Flexibility of Proteins and Principles of Their Function. Springer, 2012.

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Käiväräinen, Alex I. Solvent-Dependent Flexibility of Proteins and Principles of Their Function. Springer, 2011.

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Solvent-Dependent Flexibility of Proteins and Principles of Their Function. Springer, 2012.

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Kellaway, Roy, and Tim Harrington. Feeding Concentrates. CSIRO Publishing, 2004. http://dx.doi.org/10.1071/9780643091047.

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This book presents strategies for feeding energy and protein supplements to pasture-fed dairy cows and examines the potential economic benefits. Effective supplementary feeding of concentrates is critical to the success of all dairy farms. This book is a substantially revised edition of 'Feeding Concentrates: Supplements for Dairy Cows' DRDC 1993. It focuses on feeding concentrates to pasture fed cows to achieve high milk production per cow per hectare, and will assist farmers to decide which supplements give the best results in their particular situation. The benefits that arise from supplementary feeding include higher stocking rates, promotion of growth in heifers and young cows; better body condition score and increased lactation length when pasture is less available; improved pasture use; reduced cost per tonne of pasture eaten; flexibility to increase milk production when milk prices are high; and increased milk protein content when the energy content in pasture is low. This edition has thoroughly reviewed the issues and clearly documents the results of research particularly for grains supplementation. The summaries and recommendations in each chapter will be particularly helpful to dairy farmers in making best management decisions relating to concentrate feeding.
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Käiväräinen, Alex I. Solvent-Dependent Flexibility of Proteins and Principles of Their Function (Advances in Inclusion Science). Springer, 1985.

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Book chapters on the topic "Protein flexibility"

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Roberts, G. C. K. "Conformational Flexibility and Protein Specificity." In Novartis Foundation Symposia, 169–86. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470514085.ch12.

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Blow, D. M. "Flexibility and Rigidity in Protein Crystals." In Novartis Foundation Symposia, 55–61. Chichester, UK: John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470720424.ch4.

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Verma, Deeptak, Jun-tao Guo, Donald J. Jacobs, and Dennis R. Livesay. "Towards Comprehensive Analysis of Protein Family Quantitative Stability–Flexibility Relationships Using Homology Models." In Protein Dynamics, 239–54. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-658-0_13.

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Lukman, Suryani, Chandra S. Verma, and Gloria Fuentes. "Exploiting Protein Intrinsic Flexibility in Drug Design." In Advances in Experimental Medicine and Biology, 245–69. Cham: Springer International Publishing, 2013. http://dx.doi.org/10.1007/978-3-319-02970-2_11.

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Kaslik, Gyula, András Patthy, Miklós Bálint, and László Gráf. "Trypsin Complexed with α1-Proteinase Inhibitor Has an Increased Structural Flexibility." In Protein Structure — Function Relationship, 81–89. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-0359-6_9.

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Brown, Matthew C., Deeptak Verma, Christian Russell, Donald J. Jacobs, and Dennis R. Livesay. "A Case Study Comparing Quantitative Stability–Flexibility Relationships Across Five Metallo-β-Lactamases Highlighting Differences Within NDM-1." In Protein Dynamics, 227–38. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-658-0_12.

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Punekar, N. S. "Structure and Catalysis: Conformational Flexibility and Protein Motion." In ENZYMES: Catalysis, Kinetics and Mechanisms, 75–82. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-0785-0_8.

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Hernández, Griselda, Janet S. Anderson, and David M. LeMaster. "Electrostatics of Hydrogen Exchange for Analyzing Protein Flexibility." In Methods in Molecular Biology, 369–405. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-480-3_20.

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Pires, Douglas E. V., Carlos H. M. Rodrigues, Amanda T. S. Albanaz, Malancha Karmakar, Yoochan Myung, Joicymara Xavier, Eleni-Maria Michanetzi, Stephanie Portelli, and David B. Ascher. "Exploring Protein Supersecondary Structure Through Changes in Protein Folding, Stability, and Flexibility." In Methods in Molecular Biology, 173–85. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9161-7_9.

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Sljoka, Adnan. "Structural and Functional Analysis of Proteins Using Rigidity Theory." In Sublinear Computation Paradigm, 337–67. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-4095-7_14.

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AbstractOver the past two decades, we have witnessed an unprecedented explosion in available biological data. In the age of big data, large biological datasets have created an urgent need for the development of bioinformatics methods and innovative fast algorithms. Bioinformatics tools can enable data-driven hypothesis and interpretation of complex biological data that can advance biological and medicinal knowledge discovery. Advances in structural biology and computational modelling have led to the characterization of atomistic structures of many biomolecular components of cells. Proteins in particular are the most fundamental biomolecules and the key constituent elements of all living organisms, as they are necessary for cellular functions. Proteins play crucial roles in immunity, catalysis, metabolism and the majority of biological processes, and hence there is significant interest to understand how these macromolecules carry out their complex functions. The mechanical heterogeneity of protein structures and a delicate mix of rigidity and flexibility, which dictates their dynamic nature, is linked to their highly diverse biological functions. Mathematical rigidity theory and related algorithms have opened up many exciting opportunities to accurately analyse protein dynamics and probe various biological enigmas at a molecular level. Importantly, rigidity theoretical algorithms and methods run in almost linear time complexity, which makes it suitable for high-throughput and big-data style analysis. In this chapter, we discuss the importance of protein flexibility and dynamics and review concepts in mathematical rigidity theory for analysing stability and the dynamics of protein structures. We then review some recent breakthrough studies, where we designed rigidity theory methods to understand complex biological events, such as allosteric communication, large-scale analysis of immune system antibody proteins, the highly complex dynamics of intrinsically disordered proteins and the validation of Nuclear Magnetic Resonance (NMR) solved protein structures.
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Conference papers on the topic "Protein flexibility"

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Hui, Liu, Lin Feng, Yang Jianli, and Liu Xiu-Ling. "Side-chain flexibility in protein docking." In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2015. http://dx.doi.org/10.1109/cibcb.2015.7300315.

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Flynn, Emily, Filip Jagodzinski, Sharon Pamela Santana, and Ileana Streinu. "Rigidity and flexibility of protein-nucleic acid complexes." In 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2013. http://dx.doi.org/10.1109/iccabs.2013.6629213.

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BRACKEN, CLAY, MALIN M. YOUNG, and KEITH DUNKER. "DISORDER AND FLEXIBILITY IN PROTEIN STRUCTURE AND FUNCTION." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2000. http://dx.doi.org/10.1142/9789814447362_0007.

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Teodoro, Miguel L., George N. Phillips, and Lydia E. Kavraki. "A dimensionality reduction approach to modeling protein flexibility." In the sixth annual international conference. New York, New York, USA: ACM Press, 2002. http://dx.doi.org/10.1145/565196.565235.

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Barlowe, Scott, Jing Yang, Donald J. Jacobs, Dennis R. Livesay, Jamal Alsakran, Ye Zhao, Deeptak Verma, and James Mottonen. "A visual analytics approach to exploring protein flexibility subspaces." In 2013 IEEE Pacific Visualization Symposium (PacificVis). IEEE, 2013. http://dx.doi.org/10.1109/pacificvis.2013.6596145.

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Sharma, Akansha, Deepu George, and Andrea Markelz. "Biomolecular Flexibility Characterization Using Solution Phase THz Protein Dynamical Transition." In 2020 45th International Conference on Infrared, Millimeter and Terahertz Waves (IRMMW-THz). IEEE, 2020. http://dx.doi.org/10.1109/irmmw-thz46771.2020.9370687.

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Sljoka, Adnan, and Nobuyuki Tsuchimura. "Exploring Protein Flexibility and Allosteric Signalling Mechanism with Rigidity Theory." In 2016 3rd Asia-Pacific World Congress on Computer Science and Engineering (APWC on CSE). IEEE, 2016. http://dx.doi.org/10.1109/apwc-on-cse.2016.047.

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Lillian, Todd D. "An Elastic Rod Representation for the LacI-DNA Loop Complex." In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/detc2011-47407.

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The well-recognized Lac repressor protein (LacI) regulates transcription by bending DNA into a loop. In addition to the known role of DNA flexibility, there is accumulating evidence suggesting that the flexibility of LacI also plays a role in this gene regulation. Here we extend our elastic rod model for DNA (previously used to model DNA only) to represent LacI. Specifically, we represent sites of concentrated flexibility in the protein with flexible elastic rod domains; and we represent relatively rigid domains of the protein with stiff elastic rod domains. Our analysis shows the sensitivity of looping energetics to the degree of flexibility within the protein over a large range of DNA lengths. In addition, we show that the predicted energetically dominant binding topology (A) remains upon introducing protein flexibility.
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Metlicka, Magdalena, Mojtaba Nouri Bygi, and Ileana Streinu. "Repairing gaps in Kinari-2 for large scale protein and flexibility analysis applications." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217714.

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Schulze, Bernd, Adnan Sljoka, Walter Whiteley, Ilias Kotsireas, Roderick Melnik, and Brian West. "Protein Flexibility of Dimers: Do Symmetric Motions Play a Role in Allosteric Interactions?" In ADVANCES IN MATHEMATICAL AND COMPUTATIONAL METHODS: ADDRESSING MODERN CHALLENGES OF SCIENCE, TECHNOLOGY, AND SOCIETY. AIP, 2011. http://dx.doi.org/10.1063/1.3663478.

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Reports on the topic "Protein flexibility"

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Ori, Naomi, and Mark Estelle. Role of GOBLET and Auxin in Controlling Organ Development and Patterning. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697122.bard.

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The size and shape of plant leaves are extremely diverse within and among species, and are also sensitive to growth conditions. Compound leaves, such as those of tomato, maintain morphogenetic activity during early stages of their development, enabling them to elaborate lateral appendages such as leaflets. The aim of the research project was to understand the interaction between the plant hormone auxin, the putative auxin response inhibitor ENTIRE (E, SlIAA9) and the NAM/CUC transcription factor GOBLET (GOB) in compound-leaf development in tomato (Solanum lycopersicum). The specific aims of the project were: 1. Investigation of the role of GOB in compound-leaf development. 2. Characterization of E function in auxin signaling. 3. Characterization of the role of auxin in compound-leaf development. 4. Investigation of the genetic and molecular interaction between E and GOB. 5. Investigate the role of these factors in fruit development. There were no major changes in these objectives. GOB was shown to mark and promote the boundaries between the leaf and initiating leaflets. Its accurate distribution was found to be required for proper leaflet initiation and separation. E was found to interact with the TIR1 and AFB6 proteins in an auxin-dependant manner, indicating that these are functional auxin receptors that mediate E degradation in the presence of auxin. This was further supported by the stabilization of E by a mutation in domain II of the protein, which is thought to mediate its auxin-dependant degradation. Over expression of this stabilized form in tomato leaves and characterization of the e mutant phenotype and the E expression domain indicated that E acts between initiating leaflets to inhibit auxin response and lamina growth. Generation and analysis of tomato plants expressing the auxin response reporter DR5::VENUS, and analysis of the effect of auxin microapplication or overexpression of an auxin biosynthesis gene, indicated that auxin marks the sites of leaflet initiation and promotes lamina growth. Investigation of the molecular and genetic interaction between auxin, GOB and E revealed a complex network of mutual regulation that is utilized to precisely pattern the leaf margin in a manner that enables the combination of tight control and flexibility. E, auxin and GOB were shown to affect fruit development and fruit set, and in an extension of the project are currently utilized to identify new players that affect these processes. The research project yielded enhanced understanding of the mechanisms of compound leaf patterning and provided tools that will enable the manipulation of leaf shape and fruit set.
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Hodges, Thomas K., and David Gidoni. Regulated Expression of Yeast FLP Recombinase in Plant Cells. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7574341.bard.

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Research activities in both our laboratories were directed toward development of control of the FLP/frt recombination system for plants. As described in the text of the research proposal, the US lab has been engaged in developing regulatory strategies such as tissue-specific promoters and the steroid-inducible activation of the FLP enzyme while the main research activities in Israel have been directed toward the development and testing of a copper-regulated expression of flp recombinase in tobacco (this is an example of a promoter activation by metal ions). The Israeli lab hat additionally completed experiments of previous studies regarding factors affecting the efficiency of recombinase activity using both a gain-of-function assay (excisional-activation of a gusA marker) and loss of function assay (excision of a rolC marker) in tobacco. Site-specific recombinase systems, in particular the FLP/frt and R/RS systems of yeast and the Cre/lox system of bacteriophage P1, have become an essential component of targeted genetic transformation procedures both in animal and plant organisms. To provide more flexibility in transgene excisions by the recombinase systems as well as gene targeting, and to widen possible applications, the development of controlled or regulated recombination systems is highly desirable and was therefore the subject of this research proposal. There are a few possible mechanisms to regulate expression of a recombinase system. They include: 1) control of the recombination system by having the target sites (e.g. frt) in one plant and the flp recombinase gene in another, and bringing the two together by cross fertilization. 2) regulation of promoter activities by external stimuli such as temperature, chemicals, metal ions, etc. 3) regulation of promoter activities by internal signals, i.e. cell- or tissue-specific, or developmental regulation. 4) regulation of enzyme activity by providing cofactors essential for biochemical reactions to take place such as steroid molecules in conjunction with a steroid ligand-binding protein (domains). During the course of this research our major emphasis have been focused toward studying the feasibility of hybrid seed production in Arabidopsis, using FLP/frt. Male-sterility was induced using the antisence of a pollen- and tapetum-specific gene, bcp1, isolated from Arabidopsis. The sterility inducing gene was flanked by frt sites. Upon cross pollination of flowers of male-sterile plants with pollen from FLP-containing plants, viable seeds were produced, and the progeny hybrid plants developed normally. The major achievement from this work is the first demonstration of using a site-specific recombinase to restore fertility in male-sterile plants (see attached paper, Luo et al., Plant J 2000; 23:423-430). The implication from this finding is that site-specific recombination systems can be applied in crop plants as a useful alternative method for hybrid seed production.
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Delmer, Deborah, Nicholas Carpita, and Abraham Marcus. Induced Plant Cell Wall Modifications: Use of Plant Cells with Altered Walls to Study Wall Structure, Growth and Potential for Genetic Modification. United States Department of Agriculture, May 1995. http://dx.doi.org/10.32747/1995.7613021.bard.

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Our previous work indicated that suspension-cultured plant cells show remarkable flexibility in altering cell wall structure in response either to growth on saline medium or in the presence of the cellulose synthesis inhibitor 2,-6-dichlorobenzonitrile (DCB). We have continued to analyze the structure of these modified cell walls to understand how the changes modify wall strength, porosity, and ability to expand. The major load-bearing network in the walls of DCB-adapted dicot cells that lack a substantial cellulose-xyloglucan network is comprised of Ca2+-bridged pectates; these cells also have an unusual and abundant soluble pectic fraction. By contrast, DCB-adapted barley, a graminaceous monocot achieves extra wall strength by enhanced cross-linking of its non-cellulosic polysaccharide network via phenolic residues. Our results have also shed new light on normal wall stucture: 1) the cellulose-xyloglucan network may be independent of other wall networks in dicot primary walls and accounts for about 70% of the total wall strength; 2) the pectic network in dicot walls is the primary determinant of wall porosity; 3) both wall strength and porosity in graminaceous monocot primary walls is greatly influenced by the degree of phenolic cross-linking between non-cellulosic polysaccharides; and 4) the fact that the monocot cells do not secrete excess glucuronoarabinoxylan and mixed-linked glucan in response to growth on DCB, suggests that these two non-cellulosic polymers do not normally interact with cellulose in a manner similar to xyloglucan. We also attempted to understand the factors which limit cell expansion during growth of cells in saline medium. Analyses of hydrolytic enzyme activities suggest that xyloglucan metabolism is not repressed during growth on NaCl. Unlike non-adapted cells, salt-adapted cells were found to lack pectin methyl esterase, but it is not clear how this difference could relate to alterations in wall expansibility. Salt-adaped cell walls contain reduced hyp and secrete two unique PRPP-related proteins suggesting that high NaCl inhibits the cross-linking of these proteins into the walls, a finding that might relate to their altered expansibility.
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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
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Paterson, Andrew H., Yehoshua Saranga, and Dan Yakir. Improving Productivity of Cotton (Gossypsum spp.) in Arid Region Agriculture: An Integrated Physiological/Genetic Approach. United States Department of Agriculture, December 1999. http://dx.doi.org/10.32747/1999.7573066.bard.

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Objectives: We seek to establish the basis for improving cotton productivity under arid conditions, by studying the water use efficiency - evaporative cooling interrelationship. Specifically, we will test the hypothesis that cotton productivity under arid conditions can be improved by combining high seasonal WUE with efficient evaporative cooling, evaluate whether high WUE and/or evaporative cooling are based on specific physiological factors such as diurnal flexibility in stomatal conductance, stomatal density, photosynthetic capacity, chlorophyll fluorescence, and plant water status. Genes influencing both WUE and evaporative cooling, as well as other parameters such as economic products (lint yield, quality, harvest index) of cotton will also be mapped, in order to evaluate influences of water relations on these parameters. Approach: Carbon isotope ratio will be used to evaluate WUE, accompanied by additional parameters to elucidate the relationship between WUE, evaporative cooling, and cotton productivity. A detailed RFLP map will be used to determine the number, location, and phenotypic effects of genes underlying genetic variation in WUE between cultivated cottons, as well as test associations of these genes with traits of economic importance such as harvest index, lint yield, and lint quality. Major Conclusions: Productivity and quality of cotton grown under well-watered versus water-limited conditions was shown to be partly accounted for by different quantitative trait loci (QTLs). Among a suite of physiological traits often found to differ between genotypes adapted to arid versus well-watered conditions, genetic mapping implicated only reduced plant osmotic potential in improved cotton productivity under arid conditions. Our findings clearly implicate OP as a major component of cotton adaptation to arid conditions. However, testing of further physiological hypotheses is clearly needed to account for additional QTL alleles conferring higher seed-cotton yield under arid conditions, such as three of the five we found. Near-isogenic lines being made for QTLs discovered herein will offer a powerful new tool useful toward identification of the underlying gene(s) by using fine-scale mapping approaches (Paterson et al 1990). Implications: Adaptation to both arid and favorable conditions can be combined into the same genotype. We have identified diagnostic DNA markers that are being applied to creation of such desirable genotypes. Simultaneous improvement of productivity (and/or quality) for both arid and irrigated conditions will require more extensive field testing and the manipulation of larger numbers of genes, reducing the expected rate of genetic gain These difficulties may be at least partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers. Genomic tools and approaches may expedite adaptation of crops to arid cultivation, help to test roles of additional physiological factors, and guide the isolation of the underlying genes that protect crop performance under arid conditions.
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