The ensemble nature of allostery

Motlagh, Hesam N.; Wrabl, James O.; Li, Jing; Hilser, Vincent J.

doi:10.1038/nature13001

Cited by 1,084 publications

(1,215 citation statements)

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“…Whereas the allosteric behavior of PANK3 is most easily understood in light of the Monod, Wyman, and Changeux model for cooperativity that posits that the ligandfree protein exists in two structurally coupled conformational states (25,26), we have no specific structural data that directly support the existence of two distinct ligand-free states. Instead, the ligand-free state may be more dynamic with one or more intermediate state(s) where localized unfolding may exist (27)(28)(29).…”

Section: Discussionmentioning

confidence: 99%

Allosteric Regulation of Mammalian Pantothenate Kinase

Subramanian

Yun²,

Yao

et al. 2016

Journal of Biological Chemistry

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Pantothenate kinase catalyzes the key regulatory step in CoA biosynthesis in bacteria and mammals (1-3). In mammals, there are four distinct kinases that exhibit tissue-specific expression as follows: PANK1␣ and PANK1␤ are splice variants of the PANK1 gene, and PANK2 and PANK3 are encoded by the PANK2 and PANK3 genes, respectively (4, 5). The kinase isoforms possess almost identical catalytic cores but differ in their amino termini that direct the enzymes to different subcellular compartments (6). Isoform 1␣ is targeted to the nucleus, whereas isoform 1␤ is associated with endosomes in humans and mice. Isoform 2 of mice is cytosolic, but the PANK2 gene in humans encodes a protein with both nuclear localization and mitochondrial targeting sequences. Isoform 3 is cytosolic in both species. All pantothenate kinases operate by a compulsory ordered mechanism with ATP⅐Mg 2ϩ as the leading substrate followed by pantothenate ( Fig. 1) (7). The principal mechanism for controlling mammalian pantothenate kinase activity is through feedback inhibition by acetyl-CoA, and the isoforms differ in their sensitivity to this regulator ( Fig. 1) (4, 8, 9). The 1␣ and 1␤ isoforms are least sensitive to inhibition, whereas isoforms 2 and 3 are more potently inhibited by acetyl-CoA. Acetyl-CoA inhibition is competitive with ATP⅐Mg 2ϩ , but acetyl-CoA binds far more tightly than ATP (10). Acyl-carnitines antagonize the inhibition of pantothenate kinases by acetyl-CoA (8).The importance of pantothenate kinase to mammalian physiology is highlighted by the phenotypes of knock-out mice and their connection to human disease. Isoform 1 is most highly expressed in the liver, and Pank1 Ϫ/Ϫ mice have lower total hepatic CoA and exhibit fatty acid ␤-oxidation and glucose homeostasis defects in the fasted state (11). In addition, Pank1 Ϫ/Ϫ Lep Ϫ/Ϫ mice have dramatically lower blood glucose and insulin levels compared with their diabetic Lep Ϫ/Ϫ counterparts, which highlights the connection between isoform 1 and glucose homeostasis (12). Consistent with this, an association between polymorphisms in the PANK1 gene and insulin levels was uncovered in a cohort of individuals in Finland (13). It has also been shown that the severe neurodegenerative disease pantothenate kinase-associated neurodegeneration arises from mutations in the human PANK2 gene (14). Unfortunately, Pank2 Ϫ/Ϫ mice do not recapitulate the pantothenate kinaseassociated neurodegeneration disease phenotype (15,16), and this may be due either to differences in the levels of isoform expression in mouse and human brains or to the fact that human PANK2 accumulates in the intra-membrane space in mitochondria, whereas mouse isoform 2 is cytosolic (9). Finally, Pank1 Ϫ/Ϫ Pank2 Ϫ/Ϫ double knock-out mice are unable to metabolize fats and ketones resulting in early postnatal death (16), and Pank1 Ϫ/Ϫ Pank3 Ϫ/Ϫ and Pank2 Ϫ/Ϫ Pank3 Ϫ/Ϫ double knock-out mice are both embryonic lethal. A chemical knockout of all pantothenate kinases in adult mice resulted in an 80% reduction in hepatic CoA levels a...

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Section: Discussionmentioning

confidence: 99%

Allosteric Regulation of Mammalian Pantothenate Kinase

Subramanian

Yun²,

Yao

et al. 2016

Journal of Biological Chemistry

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“…The classical model of allosteric conformational effects constitute binding of a ligand to a region or domain of a protein and its effect on conformation of a distal, functional region of the protein. 73,74 An emerging view of protein allostery includes a dynamic continuum in which protein-protein or protein-ligand interactions result in propagation of a signal through changes in protein dynamics, either with or without large scale conformational changes. 73,74 Such alterations in protein dynamics as part of allosteric regulation of proteins are sometimes referred to as propagation of an "allosteric wave."…”

Section: Hx-ms Mapping Of Distant Dynamic Effects On Other Regions Ofmentioning

confidence: 99%

“…73,74 An emerging view of protein allostery includes a dynamic continuum in which protein-protein or protein-ligand interactions result in propagation of a signal through changes in protein dynamics, either with or without large scale conformational changes. 73,74 Such alterations in protein dynamics as part of allosteric regulation of proteins are sometimes referred to as propagation of an "allosteric wave." 75 Examples of such flexibility shifts within single protein molecule upon ligand binding or protein-protein interaction have been reported.…”

Section: Hx-ms Mapping Of Distant Dynamic Effects On Other Regions Ofmentioning

confidence: 99%

“…75 Although the distant dynamic coupling effects we observed within mAb-C upon extensive RSA may lack any biological consequences, the molecular mechanism of alterations in local backbone flexibility upon protein-protein interactions are "allosteric-like" in that they resemble the molecular mechanisms of protein dynamic allostery. 73,74,78 The observed localized changes in backbone dynamics upon RSA may potentially have important implications in terms of pharmaceutical properties of a mAb including storage stability, manufacturability, and syringeability. Since HX-MS provides increased resolution for characterizing RSA directly at high protein concentrations, this information could be used to design superior next-generation mAb molecules with lower propensity for RSA.…”

Section: Hx-ms Mapping Of Distant Dynamic Effects On Other Regions Ofmentioning

confidence: 99%

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Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody

Arora

Hickey

Majumdar

et al. 2015

mAbs

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Volkin (2015) Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody, mAbs, 7:3, 525-539, DOI: 10.1080DOI: 10. /19420862.2015 To link to this article: https://doi.org/10. 1080/19420862.2015 There is a need for new analytical approaches to better characterize the nature of the concentration-dependent, reversible self-association (RSA) of monoclonal antibodies (mAbs) directly, and with high resolution, when these proteins are formulated as highly concentrated solutions. In the work reported here, hydrogen exchange mass spectrometry (HX-MS) was used to define the concentration-dependent RSA interface, and to characterize the effects of association on the backbone dynamics of an IgG1 mAb (mAb-C). Dynamic light scattering, chemical cross-linking, and solution viscosity measurements were used to determine conditions that caused the RSA of mAb-C. A novel HX-MS experimental approach was then applied to directly monitor differences in local flexibility of mAb-C due to RSA at different protein concentrations in deuterated buffers. First, a stable formulation containing lyoprotectants that permitted freeze-drying of mAb-C at both 5 and 60 mg/mL was identified. Upon reconstitution with RSA-promoting deuterated solutions, the low vs. high protein concentration samples displayed different levels of solution viscosity (i.e., approx. 1 to 75 mPa.s). The reconstituted mAb-C samples were then analyzed by HX-MS. Two specific sequences covering complementarity-determining regions CDR2H and CDR2L (in the variable heavy and light chains, respectively) showed significant protection against deuterium uptake (i.e., decreased hydrogen exchange). These results define the major protein-protein interfaces associated with the concentration-dependent RSA of mAb-C. Surprisingly, certain peptide segments in the V H domain, the constant domain (C H 2), and the hinge region (C H 1-C H 2 interface) concomitantly showed significant increases in local flexibility at high vs. low protein concentrations. These results indicate the presence of longer-range, distant dynamic coupling effects within mAb-C occurring upon RSA.

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“…in glutamate dehydrogenase (51). Recent models of allosteric communication suggest that there are many different structural forms of the enzyme present (possibly including some intrinsically disordered states) (33).…”

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confidence: 99%

Modulating Mobility: a Paradigm for Protein Engineering?

McAuley

Timson

2016

Appl Biochem Biotechnol

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Additional Information:Question ResponsePlease select a section/category for your manuscript.Biocatalysis for organic synthesis -Novel and significant advances in biocatalysis for organic synthesis, including chemo-, regio-and enantioselective biotransformation, screening and engineering of novel enzymes for biocatalysis, biocatalyst immobilization, and nonaqueous biocatalysis.Abstract: Proteins are highly mobile structures. In addition to gross conformational changes occurring on, for example, ligand binding, they are also subject to constant thermal motion. The mobility of the protein varies through its structure and can be modulated by ligand binding and other events. It is becoming increasingly clear that this mobility plays an important role in key functions of proteins including catalysis, allostery, cooperativity and regulation. Thus, in addition to an optimum structure, proteins most likely also require an optimal dynamic state. Alteration of this dynamic state through protein engineering will affect protein function. A dramatic example of this is seen in some inherited metabolic diseases where alternation of residues distant from the active site affects the mobility of the protein and impairs function. We postulate that using molecular dynamics simulations, experimental data or a combination of the two it should be possible to engineer the mobility of active sites. This may be useful in, for example, increasing the promiscuity of enzymes. Thus, a paradigm for protein engineering is suggested in which the mobility of the active site is rationally modified. This might be combined with more "traditional" approaches such as altering functional groups in the active site. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Manuscript #ABAB-D-16-00805 Modulating mobility: a paradigm for protein engineering? Margaret McAuley and David J. TimsonReviewer: Flexibility of protein plays an important role in protein functions such as activity and stability. Up to now, a number of studies strategized for engineering the protein towards desirable properties are published. The manuscript has a great summary of recent studies based on modulating mobility of protein especially in activity aspect. I recommend its publication after addressing the following issue.Response: We thank the reviewer for his/her support and encouraging remarks.There are also many reports about the improvement of stability of protein by modulating the flexibility of protein. Such as, "Park.H.J et al, Computational approach for designing thermostable Candidaantarctica lipase B by molecular dynamics simulation; Zhu, F., et al, Rational substitution of surface acidic residues for enhancing the thermostability of thermolysin; Chen, J et al, Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions, and so on". It would be attractive if the authors could incorporate some examples that explain the relationship between activity and stability modulated by flexibility of prote...

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The ensemble nature of allostery

Cited by 1,084 publications

References 106 publications

Allosteric Regulation of Mammalian Pantothenate Kinase

Allosteric Regulation of Mammalian Pantothenate Kinase

Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody

Modulating Mobility: a Paradigm for Protein Engineering?

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