Multisteric Regulation by Structural Disorder in Modular Signaling Proteins: An Extension of the Concept of Allostery

Tompa, Péter

doi:10.1021/cr4005082

Cited by 101 publications

(124 citation statements)

References 180 publications

(506 reference statements)

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“…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%

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

confidence: 99%

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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“…In fact, the accuracy and Matthew's Correlation Coefficients are very low for most prediction methods (between 0.77-0.53 and 0.36-0.05 for Acc and MCC, respectively). Moreover, the variations of the values in Table 4 0.62 (12) 0.33 (16) 0.32 (14) 0.86 (5) 12.71…”

Section: Evaluating Of Disorder Prediction Methodsmentioning

confidence: 99%

“…IUPred_long_io15 0.65 (12) 0.9 (14) 0.32 (20) 0.94 (14) 0.28 (10) 0 (1) 37.81 (17) 205.5 (24) 0.28 (18) 4789 (20) 0.63 (10) 0.32 (14) 0.33 (10) 0.68 (14) 13.86…”

Section: Evaluating Of Disorder Prediction Methodsmentioning

confidence: 99%

“…In multidomain proteins, it gives rise to complex regulatory phenomena [14] by promoting interactions with external partners, and autoregulatory interactions within the protein, both of which are subject to complex input by other partners and modifications. This is clearly the case in TMPs, as demonstrated in several concrete instances, which provide some insight into the role of IDRs in TMPs.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Disordered regions in transmembrane proteins

Tusnády

Dobson

Tompa

2015

Biochimica et Biophysica Acta (BBA) - Biomembranes

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The functions of transmembrane proteins in living cells are widespread; they range from various transport processes to energy production, from cell-cell adhesion to communication. Structurally, they are highly ordered in their membrane-spanning regions, but may contain disordered regions in the cytosolic and extra-cytosolic parts. In this study, we have investigated the disordered regions in transmembrane proteins by a stringent definition of disordered residues on the currently available largest experimental dataset, and show a significant correlation between the spatial distributions of positively charged residues and disordered regions. This finding suggests a new role of disordered regions in transmembrane proteins by providing structural flexibility for stabilizing interactions with negatively charged head groups of the lipid molecules. We also find a preference of structural disorder in the terminal--as opposed to loop--regions in transmembrane proteins, and survey the respective functions involved in recruiting other proteins or mediating allosteric signaling effects. Finally, we critically compare disorder prediction methods on our transmembrane protein set. While there are no major differences between these methods using the usual statistics, such as per residue accuracies, Matthew's correlation coefficients, etc.; substantial differences can be found regarding the spatial distribution of the predicted disordered regions. We conclude that a predictor optimized for transmembrane proteins would be of high value to the field of structural disorder.

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“…The impor-550 tance of this finding is that small molecule not only can bind to a disordered segment of a protein but also can have an allosteric inhibitory effect. Allosteric drugs have a unique flavor of specificity [103], which, in the case of IDPs, also puts emphasis on subtle allosteric long-range communication in IDPs termed 555 multistery [104].…”

Section: Proteins and Proteomics In Structural Disordermentioning

confidence: 99%

The role of structural disorder in cell cycle regulation, related clinical proteomics, disease development and drug targeting

Tantos

Kalmár

Tompa

2015

Expert Review of Proteomics

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Multisteric Regulation by Structural Disorder in Modular Signaling Proteins: An Extension of the Concept of Allostery

Cited by 101 publications

References 180 publications

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

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

Disordered regions in transmembrane proteins

The role of structural disorder in cell cycle regulation, related clinical proteomics, disease development and drug targeting

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