scholarly journals Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Tiffany Wu ◽  
Liskin Swint-Kruse ◽  
Aron W. Fenton
Keyword(s):  
Binding Sites ◽  
Functional Outcomes ◽  
Human Liver ◽  
Full Range ◽  
Allosteric Coupling ◽  
Multiple Parameters ◽  
Wide Range ◽  
Allosteric Binding Sites ◽  
Fructose 1,6 Bisphosphate ◽  
Effector Binding

AbstractFor protein mutagenesis, a common expectation is that important positions will behave like on/off “toggle” switches (i.e., a few substitutions act like wildtype, most abolish function). However, there exists another class of important positions that manifests a wide range of functional outcomes upon substitution: “rheostat” positions. Previously, we evaluated rheostat positions located near the allosteric binding sites for inhibitor alanine (Ala) and activator fructose-1,6-bisphosphate (Fru-1,6-BP) in human liver pyruvate kinase. When substituted with multiple amino acids, many positions demonstrated moderate rheostatic effects on allosteric coupling between effector binding and phosphoenolpyruvate (PEP) binding in the active site. Nonetheless, the combined outcomes of all positions sampled the full range of possible allosteric coupling (full tunability). However, that study only evaluated allosteric tunability of “local” positions, i.e., positions were located near the binding sites of the allosteric ligand being assessed. Here, we evaluated tunability of allosteric coupling when mutated sites were distant from the allosterically-coupled binding sites. Positions near the Ala binding site had rheostatic outcomes on allosteric coupling between Fru-1,6-BP and PEP binding. In contrast, positions in the Fru-1,6-BP site exhibited modest effects on coupling between Ala and PEP binding. Analyzed in aggregate, both PEP/Ala and PEP/Fru-1,6-BP coupling were again fully tunable by amino acid substitutions at this limited set of distant positions. Furthermore, some positions exhibited rheostatic control over multiple parameters and others exhibited rheostatic effects on one parameter and toggle control over a second. These findings highlight challenges in efforts to both predict/interpret mutational outcomes and engineer functions into proteins.

scholarly journals Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites

2019 ◽  
Author(s):  
Tiffany Wu ◽  
Liskin Swint-Kruse ◽  
Aron W. Fenton
Keyword(s):  
Binding Sites ◽  
Functional Outcomes ◽  
Human Liver ◽  
Full Range ◽  
Allosteric Coupling ◽  
Multiple Parameters ◽  
Wide Range ◽  
Allosteric Binding Sites ◽  
Fructose 1,6 Bisphosphate ◽  
Effector Binding

AbstractFor protein mutagenesis, a common expectation is that important positions will behave like on/off “toggle” switches (i.e., a few substitutions act like wildtype, most abolish function). However, there exists another class of important positions that manifests a wide range of functional outcomes upon substitution: “rheostat” positions. Previously, we evaluated rheostat positions located near the allosteric binding sites for inhibitor alanine (Ala) and activator fructose-1,6-bisphosphate (Fru-1,6-BP) in human liver pyruvate kinase. When substituted with multiple amino acids, many positions demonstrated moderate rheostat effects on allosteric coupling between effector binding and phosphoenolpyruvate (PEP) binding in the active site. Nonetheless, the combined outcomes of all positions sampled the full range of possible allosteric coupling (full tunability). However, that study only evaluated allosteric tunability of “local” positions, i.e., positions were located near the binding sites of the allosteric ligand being assessed. Here, we evaluated tunability of allosteric coupling when mutated sites were distant from the allosterically-coupled binding sites. Positions near the Ala binding site had rheostat outcomes on allosteric coupling between Fru-1,6-BP and PEP binding. In contrast, positions in the Fru-1,6-BP site exhibited modest effects on coupling between Ala and PEP binding. Analyzed in aggregate, both PEP/Ala and PEP/Fru-1,6-BP coupling were again fully tunable by amino acid substitutions at this limited set of distant positions. Furthermore, some positions exhibited rheostatic control over multiple parameters and others exhibited rheostatic effects on one parameter and toggle control over a second. These findings highlight challenges in efforts to both predict/interpret mutational outcomes and engineer functions into proteins.

scholarly journals Two Populations of Glucocorticoid Receptor-Binding Sites in the Male Rat Hippocampal Genome

Endocrinology ◽  
2013 ◽  
Vol 154 (5) ◽  
pp. 1832-1844 ◽  
Author(s):  
J. Annelies E. Polman ◽  
E. Ronald de Kloet ◽  
Nicole A. Datson
Keyword(s):  
Receptor Binding ◽  
Binding Sites ◽  
Glucocorticoid Receptors ◽  
Full Range ◽  
Male Rat ◽  
Motif Analysis ◽  
Wide Range ◽  
Neuronal Processes ◽  
Almost All

Abstract In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 μg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 μg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome.

scholarly journals Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria

2013 ◽  
Vol 288 (29) ◽  
pp. 21295-21306 ◽  
Author(s):  
Anna Feldman-Salit ◽  
Silvio Hering ◽  
Hanan L. Messiha ◽  
Nadine Veith ◽  
Vlad Cojocaru ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Ionic Strength ◽  
Lactic Acid Bacteria ◽  
Binding Sites ◽  
Binding Affinities ◽  
Nacl Concentration ◽  
Allosteric Binding Sites ◽  
Regulatory Effects ◽  
Fructose 1,6 Bisphosphate ◽  
Lactate Dehydrogenases

Despite high similarity in sequence and catalytic properties, the l-lactate dehydrogenases (LDHs) in lactic acid bacteria (LAB) display differences in their regulation that may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose 1,6-bisphosphate (FBP), phosphate (Pi), and ionic strength (NaCl concentration) on six LDHs from four LABs studied at pH 6 and pH 7. We found that 1) the extent of activation by FBP (Kact) differs. Lactobacillus plantarum LDH is not regulated by FBP, but the other LDHs are activated with increasing sensitivity in the following order: Enterococcus faecalis LDH2 ≤ Lactococcus lactis LDH2 < E. faecalis LDH1 < L. lactis LDH1 ≤ Streptococcus pyogenes LDH. This trend reflects the electrostatic properties in the allosteric binding site of the LDH enzymes. 2) For L. plantarum, S. pyogenes, and E. faecalis, the effects of Pi are distinguishable from the effect of changing ionic strength by adding NaCl. 3) Addition of Pi inhibits E. faecalis LDH2, whereas in the absence of FBP, Pi is an activator of S. pyogenes LDH, E. faecalis LDH1, and L. lactis LDH1 and LDH2 at pH 6. These effects can be interpreted by considering the computed binding affinities of Pi to the catalytic and allosteric binding sites of the enzymes modeled in protonation states corresponding to pH 6 and pH 7. Overall, the results show a subtle interplay among the effects of Pi, FBP, and pH that results in different regulatory effects on the LDHs of different LABs.

scholarly journals Identification of biochemically neutral positions in liver pyruvate kinase

2019 ◽  
Author(s):  
Tyler A. Martin ◽  
Tiffany Wu ◽  
Qingling Tang ◽  
Larissa L. Dougherty ◽  
Daniel J. Parente ◽  
...  
Keyword(s):  
Pyruvate Kinase ◽  
Protein Function ◽  
Functional Outcomes ◽  
High Surface ◽  
Experimental Studies ◽  
Substitution Effects ◽  
Evolutionary Patterns ◽  
Allosteric Coupling ◽  
Allosteric Binding Sites ◽  
Residue Position

AbstractUnderstanding how each residue position contributes to protein function has been a long-standing goal in protein science. Substitution studies have historically focused on conserved protein positions. However, substitutions of nonconserved positions can also modify function. Indeed, we recently identified nonconserved positions that have large substitution effects in human liver pyruvate kinase (hLPYK), including altered allosteric coupling. To facilitate a comparison of which characteristics determine when a nonconserved position does vs. does not contribute to function, the goal of the current work was to identify neutral positions in hLPYK. However, existing hLPYK data showed that three features commonly associated with neutral positions – high sequence entropy, high surface exposure, and alanine scanning – lacked the sensitivity needed to guide experimental studies. We used multiple evolutionary patterns identified in a sequence alignment of the PYK family to identify which positions were least patterned, reasoning that these were most likely to be neutral. Nine positions were tested with a total of 117 amino acid substitutions. Although exploring all potential functions is not feasible for any protein, five parameters associated with substrate/effector affinities and allosteric coupling were measured for hLPYK variants. For each position, the aggregate functional outcomes of all variants were used to quantify a “neutrality” score. Three positions showed perfect neutral scores for all five parameters. Furthermore, the nine positions showed larger neutral scores than 17 positions located near allosteric binding sites. Thus, our strategy successfully enriched the dataset for positions with neutral and modest substitutions.

The Major Transitions in Evolution

1997 ◽  
Author(s):  
John Maynard Smith ◽  
Eors Szathmary
Keyword(s):  
Full Range ◽  
Evolution Of Cooperation ◽  
Major Transitions ◽  
Insect Societies ◽  
Wide Range ◽  
Major Transition ◽  
Life Itself ◽  
History Of ◽  
Emergence Of Cooperation ◽  
Multicellular Organisms

Over the history of life there have been several major changes in the way genetic information is organized and transmitted from one generation to the next. These transitions include the origin of life itself, the first eukaryotic cells, reproduction by sexual means, the appearance of multicellular plants and animals, the emergence of cooperation and of animal societies, and the unique language ability of humans. This ambitious book provides the first unified discussion of the full range of these transitions. The authors highlight the similarities between different transitions--between the union of replicating molecules to form chromosomes and of cells to form multicellular organisms, for example--and show how understanding one transition sheds light on others. They trace a common theme throughout the history of evolution: after a major transition some entities lose the ability to replicate independently, becoming able to reproduce only as part of a larger whole. The authors investigate this pattern and why selection between entities at a lower level does not disrupt selection at more complex levels. Their explanation encompasses a compelling theory of the evolution of cooperation at all levels of complexity. Engagingly written and filled with numerous illustrations, this book can be read with enjoyment by anyone with an undergraduate training in biology. It is ideal for advanced discussion groups on evolution and includes accessible discussions of a wide range of topics, from molecular biology and linguistics to insect societies.

Oxford Studies in Medieval Philosophy Volume 7

2019 ◽  
Keyword(s):  
Late Antiquity ◽  
Full Range ◽  
Current Work ◽  
Medieval Philosophy ◽  
Original Essays ◽  
Wide Range ◽  
Extended Review

Oxford Studies in Medieval Philosophy annually collects the best current work in the field of medieval philosophy. The various volumes print original essays, reviews, critical discussions, and editions of texts. The aim is to contribute to an understanding of the full range of themes and problems in all aspects of the field, from late antiquity into the Renaissance, and extending over the Jewish, Islamic, and Christian traditions. Volume 6 includes work on a wide range of topics, including Davlat Dadikhuda on Avicenna, Christopher Martin on Abelard’s ontology, Jeremy Skrzypek and Gloria Frost on Aquinas’s ontology, Jean‐Luc Solère on instrumental causality, Peter John Hartman on Durand of St.‐Pourçain, and Kamil Majcherek on Chatton’s rejection of final causality. The volume also includes an extended review of Thomas Williams of a new book on Aquinas’s ethics by Colleen McCluskey.

Compressor Performance and Operability in Swirl Distortion

2010 ◽  
Author(s):  
Yogi Sheoran ◽  
Bruce Bouldin ◽  
P. Murali Krishnan
Keyword(s):  
Gas Turbine ◽  
Complex Geometry ◽  
Full Range ◽  
Axial Compressor ◽  
Cfd Model ◽  
Generator System ◽  
Sliding Mesh ◽  
Wide Range ◽  
Compressor Performance ◽  
The Impact

Inlet swirl distortion has become a major area of concern in the gas turbine engine community. Gas turbine engines are increasingly installed with more complicated and tortuous inlet systems, like those found on embedded installations on Unmanned Aerial Vehicles (UAVs). These inlet systems can produce complex swirl patterns in addition to total pressure distortion. The effect of swirl distortion on engine or compressor performance and operability must be evaluated. The gas turbine community is developing methodologies to measure and characterize swirl distortion. There is a strong need to develop a database containing the impact of a range of swirl distortion patterns on a compressor performance and operability. A recent paper presented by the authors described a versatile swirl distortion generator system that produced a wide range of swirl distortion patterns of a prescribed strength, including bulk swirl, twin swirl and offset swirl. The design of these swirl generators greatly improved the understanding of the formation of swirl. The next step of this process is to understand the effect of swirl on compressor performance. A previously published paper by the authors used parallel compressor analysis to map out different speed lines that resulted from different types of swirl distortion. For the study described in this paper, a computational fluid dynamics (CFD) model is used to couple upstream swirl generator geometry to a single stage of an axial compressor in order to generate a family of compressor speed lines. The complex geometry of the analyzed swirl generators requires that the full 360° compressor be included in the CFD model. A full compressor can be modeled several ways in a CFD analysis, including sliding mesh and frozen rotor techniques. For a single operating condition, a study was conducted using both of these techniques to determine the best method given the large size of the CFD model and the number of data points that needed to be run to generate speed lines. This study compared the CFD results for the undistorted compressor at 100% speed to comparable test data. Results of this study indicated that the frozen rotor approach provided just as accurate results as the sliding mesh but with a greatly reduced cycle time. Once the CFD approach was calibrated, the same techniques were used to determine compressor performance and operability when a full range of swirl distortion patterns were generated by upstream swirl generators. The compressor speed line shift due to co-rotating and counter-rotating bulk swirl resulted in a predictable performance and operability shift. Of particular importance is the compressor performance and operability resulting from an exposure to a set of paired swirl distortions. The CFD generated speed lines follow similar trends to those produced by parallel compressor analysis.

scholarly journals State of the Science in Dried Blood Spots

2018 ◽  
Vol 64 (4) ◽  
pp. 656-679 ◽  
Author(s):  
Jeffrey D Freeman ◽  
Lori M Rosman ◽  
Jeremy D Ratcliff ◽  
Paul T Strickland ◽  
David R Graham ◽  
...  
Keyword(s):  
Systematic Approach ◽  
Full Range ◽  
Dried Blood Spots ◽  
Blood Spots ◽  
Highly Sensitive ◽  
Wide Range ◽  
Potential Applications ◽  
Review Of Reviews ◽  
Near Term ◽  
State Of The Science

Abstract BACKGROUND Advancements in the quality and availability of highly sensitive analytical instrumentation and methodologies have led to increased interest in the use of microsamples. Among microsamples, dried blood spots (DBS) are the most well-known. Although there have been a variety of review papers published on DBS, there has been no attempt at describing the full range of analytes measurable in DBS, or any systematic approach published for characterizing the strengths and weaknesses associated with adoption of DBS analyses. CONTENT A scoping review of reviews methodology was used for characterizing the state of the science in DBS. We identified 2018 analytes measured in DBS and found every common analytic method applied to traditional liquid samples had been applied to DBS samples. Analytes covered a broad range of biomarkers that included genes, transcripts, proteins, and metabolites. Strengths of DBS enable its application in most clinical and laboratory settings, and the removal of phlebotomy and the need for refrigeration have expanded biosampling to hard-to-reach and vulnerable populations. Weaknesses may limit adoption in the near term because DBS is a nontraditional sample often requiring conversion of measurements to plasma or serum values. Opportunities presented by novel methodologies may obviate many of the current limitations, but threats around the ethical use of residual samples must be considered by potential adopters. SUMMARY DBS provide a wide range of potential applications that extend beyond the reach of traditional samples. Current limitations are serious but not intractable. Technological advancements will likely continue to minimize constraints around DBS adoption.

Précis ofUnified theories of cognition

1992 ◽  
Vol 15 (3) ◽  
pp. 425-437 ◽  
Author(s):  
Allen Newell
Keyword(s):  
Cognitive Science ◽  
Full Range ◽  
Cognitive Architecture ◽  
Convincing Evidence ◽  
Syllogistic Reasoning ◽  
Human Cognition ◽  
Unified Theory ◽  
Theoretical Concepts ◽  
Wide Range ◽  
Unified Theories

AbstractThe book presents the case that cognitive science should turn its attention to developing theories of human cognition that cover the full range of human perceptual, cognitive, and action phenomena. Cognitive science has now produced a massive number of high-quality regularities with many microtheories that reveal important mechanisms. The need for integration is pressing and will continue to increase. Equally important, cognitive science now has the theoretical concepts and tools to support serious attempts at unified theories. The argument is made entirely by presenting an exemplar unified theory of cognition both to show what a real unified theory would be like and to provide convincing evidence that such theories are feasible. The exemplar is SOAR, a cognitive architecture, which is realized as a software system. After a detailed discussion of the architecture and its properties, with its relation to the constraints on cognition in the real world and to existing ideas in cognitive science, SOAR is used as theory for a wide range of cognitive phenomena: immediate responses (stimulus-response compatibility and the Sternberg phenomena); discrete motor skills (transcription typing); memory and learning (episodic memory and the acquisition of skill through practice); problem solving (cryptarithmetic puzzles and syllogistic reasoning); language (sentence verification and taking instructions); and development (transitions in the balance beam task). The treatments vary in depth and adequacy, but they clearly reveal a single, highly specific, operational theory that works over the entire range of human cognition, SOAR is presented as an exemplar unified theory, not as the sole candidate. Cognitive science is not ready yet for a single theory – there must be multiple attempts. But cognitive science must begin to work toward such unified theories.

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