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Jaipuria G, Shet D, Malik S, Swain M, Atreya HS, Galea CA, Slomiany MG, Rosenzweig SA, Forbes BE, Norton RS, Mondal S. IGF-dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2. Proteins 2022; 90:1732-1743. [PMID: 35443068 PMCID: PMC9357107 DOI: 10.1002/prot.26350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/22/2022] [Indexed: 12/29/2022]
Abstract
Functional regulation via conformational dynamics is well known in structured proteins but less well characterized in intrinsically disordered proteins and their complexes. Using NMR spectroscopy, we have identified a dynamic regulatory mechanism in the human insulin-like growth factor (IGF) system involving the central, intrinsically disordered linker domain of human IGF-binding protein-2 (hIGFBP2). The bioavailability of IGFs is regulated by the proteolysis of IGF-binding proteins. In the case of hIGFBP2, the linker domain (L-hIGFBP2) retains its intrinsic disorder upon binding IGF-1, but its dynamics are significantly altered, both in the IGF binding region and distantly located protease cleavage sites. The increase in flexibility of the linker domain upon IGF-1 binding may explain the IGF-dependent modulation of proteolysis of IGFBP2 in this domain. As IGF homeostasis is important for cell growth and function, and its dysregulation is a key contributor to several cancers, our findings open up new avenues for the design of IGFBP analogs inhibiting IGF-dependent tumors.
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Affiliation(s)
- Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Divya Shet
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India,Nanobiophysics lab, Raman Research Institute, Sadashivnagar, Bangalore-80, India
| | - Shahid Malik
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Monalisa Swain
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India,Frederick National Laboratory for Cancer Research, Maryland-21701, USA
| | | | - Charles A. Galea
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville 3052, Australia
| | - Mark G. Slomiany
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston SC 29425, USA
| | - Steven A. Rosenzweig
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston SC 29425, USA
| | - Briony E. Forbes
- Flinders Health and Medical Research Institute, Flinders University, SA 5042, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville 3052, Australia,ARC Centre for Fragment-Based Design, Monash University, Parkville 3052, Australia
| | - Somnath Mondal
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India,Univ. Bordeaux, Institut Européen de Chimie et Biologie and INSERM U1212, ARNA Laboratory, 2 rue Robert Escarpit, 33607 Pessac Cedex, Bordeaux, France
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2
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Abstract
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Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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3
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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Tiwari VP, Pandit S, Vallurupalli P. Exchangeable deuterons introduce artifacts in amide 15N CEST experiments used to study protein conformational exchange. JOURNAL OF BIOMOLECULAR NMR 2019; 73:43-48. [PMID: 30661150 DOI: 10.1007/s10858-018-00223-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/27/2018] [Indexed: 06/09/2023]
Abstract
Protein molecules sample different conformations in solution and characterizing these conformations is crucial to understanding protein function. 15N CEST experiments are now routinely used to study slow conformational exchange of protein molecules between a 'visible' major state and 'invisible' minor states. These experiments have also been adapted to measure the solvent exchange rates of amide protons by exploiting the one bond deuterium isotope effect on the amide 15N chemical shifts. However at moderately high temperatures (~ 50 °C) that are sometimes required to populate protein minor conformers to levels (~ 1%) that can be detected by CEST experiments solvent H/D exchange can lead to 'dips' in low B115N CEST profiles that can be wrongly assigned to the conformational exchange process being characterized. This is demonstrated in the case of ~ 18 kDa T4 Lysozyme (T4L) at 50 °C and the ~ 11 kDa E. coli hibernation promoting factor (HPF) at 52 °C. This problem is trivially solved by eliminating the exchangeable deuterons in the solvent by using either an external D2O lock or by using a small amount (~ 1-3%) of a molecule like d6-DMSO that does not contain exchangeable deuterons to lock the spectrometer.
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Affiliation(s)
- Ved Prakash Tiwari
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana, 500107, India
| | - Subhendu Pandit
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana, 500107, India
| | - Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana, 500107, India.
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5
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Nikitin K, O'Gara R. Mechanisms and Beyond: Elucidation of Fluxional Dynamics by Exchange NMR Spectroscopy. Chemistry 2019; 25:4551-4589. [PMID: 30421834 DOI: 10.1002/chem.201804123] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 12/31/2022]
Abstract
Detailed mechanistic information is crucial to our understanding of reaction pathways and selectivity. Dynamic exchange NMR techniques, in particular 2D exchange spectroscopy (EXSY) and its modifications, provide indispensable intricate information on the mechanisms of organic and inorganic reactions and other phenomena, for example, the dynamics of interfacial processes. In this Review, key results from exchange NMR studies of small molecules over the last few decades are systemised and discussed. After a brief introduction to the theory, the key types of dynamic processes are identified and fundamental examples given of intra- and intermolecular reactions, which, in turn, could involve, or not, bond-making and bond-breaking events. Following that logic, internal molecular rotation, intramolecular stereomutation and molecular recognition will first be considered because they do not typically involve bond breaking. Then, rearrangements, substitution-type reactions, cyclisations, additions and other processes affecting chemical bonds will be discussed. Finally, interfacial molecular dynamics and unexpected combinations of different types of fluxional processes will also be highlighted. How exchange NMR spectroscopy helps to identify conformational changes, coordination and molecular recognition processes as well as quantify reaction energy barriers and extract detailed mechanistic information by using reaction rate theory in conjunction with computational techniques will be shown.
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Affiliation(s)
- Kirill Nikitin
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Ryan O'Gara
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
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6
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Yuwen T, Bah A, Brady JP, Ferrage F, Bouvignies G, Kay LE. Measuring Solvent Hydrogen Exchange Rates by Multifrequency Excitation 15N CEST: Application to Protein Phase Separation. J Phys Chem B 2018; 122:11206-11217. [DOI: 10.1021/acs.jpcb.8b06820] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Alaji Bah
- Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Lewis E. Kay
- Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
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7
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Sternisha SM, Liu P, Marshall AG, Miller BG. Mechanistic Origins of Enzyme Activation in Human Glucokinase Variants Associated with Congenital Hyperinsulinism. Biochemistry 2018; 57:1632-1639. [PMID: 29425029 DOI: 10.1021/acs.biochem.8b00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human glucokinase (GCK) acts as the body's primary glucose sensor and plays a critical role in glucose homeostatic maintenance. Gain-of-function mutations in gck produce hyperactive enzyme variants that cause congenital hyperinsulinism. Prior biochemical and biophysical studies suggest that activated disease variants can be segregated into two mechanistically distinct classes, termed α-type and β-type. Steady-state viscosity variation studies indicate that the kcat values of wild-type GCK and an α-type variant are partially diffusion-limited, whereas the kcat value of a β-type variant is viscosity-independent. Transient-state chemical quench-flow analyses demonstrate that wild-type GCK and the α-type variant display burst kinetics, whereas the β-type variant lacks a burst phase. Comparative hydrogen-deuterium exchange mass spectrometry of unliganded enzymes demonstrates that a disordered active site loop, which folds upon binding of glucose, is protected from exchange in the α-type variant. The α-type variant also displays an increased level of exchange within a β-strand located near the enzyme's hinge region, which becomes more solvent-exposed upon glucose binding. In contrast, β-type activation causes no substantial difference in global or local exchange relative to that of unliganded, wild-type GCK. Together, these results demonstrate that α-type activation results from a shift in the conformational ensemble of unliganded GCK toward a state resembling the glucose-bound conformation, whereas β-type activation is attributable to an accelerated rate of product release. This work elucidates the molecular basis of naturally occurring, activated GCK disease variants and provides insight into the structural and dynamic origins of GCK's unique kinetic cooperativity.
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Affiliation(s)
- Shawn M Sternisha
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Peilu Liu
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Alan G Marshall
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program , The National High Magnetic Field Laboratory , Tallahassee , Florida 32310 , United States
| | - Brian G Miller
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
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8
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McKenzie RH, Athokpam B, Ramesh SG. Isotopic fractionation in proteins as a measure of hydrogen bond length. J Chem Phys 2015; 143:044309. [DOI: 10.1063/1.4927391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Ross H. McKenzie
- School of Mathematics and Physics, University of Queensland, Brisbane 4072, Australia
| | - Bijyalaxmi Athokpam
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sai G. Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
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9
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Felli IC, Pierattelli R. Novel methods based on (13)C detection to study intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:115-25. [PMID: 24656084 DOI: 10.1016/j.jmr.2013.10.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 05/23/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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10
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Yao S, Keizer DW. Nutation frequency modulation on NMR signal of nuclear spins in chemical exchange with solvent water under the BEST conditions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:190-194. [PMID: 24459096 DOI: 10.1002/mrc.4045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/16/2013] [Accepted: 01/03/2014] [Indexed: 06/03/2023]
Abstract
Solvent exchange properties of protein backbone amide protons provide valuable residue-specific information on protein solvent accessibility, structure stability and flexibility and hence are of significant interest in structural biology. NMR has served as a unique means for the characterization of chemical exchange including proton amide exchange with solvent water at residue-specific levels across a broad range of exchange rates. One of the methods used for the characterization of protein backbone amide exchange by NMR involves the use of progressive selective irradiation of the water resonance. Here, we report the experimental observation of the nutation frequency (strength of RF field used for the irradiation of water resonance) modulation on amide proton signals for those in exchange with the solvent water under the band-selective excitation short transient (BEST) conditions. Compared with conventional saturation transfer of water magnetization experiments, this nutation frequency modulation observed on signal of nuclear spins under the BEST conditions potentially offers a quick identification of protein backbone amides in rapid exchange with solvent water.
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Affiliation(s)
- Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia
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11
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Bermel W, Felli IC, Gonnelli L, Koźmiński W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A. High-dimensionality 13C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:353-61. [PMID: 24203099 DOI: 10.1007/s10858-013-9793-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/23/2013] [Indexed: 05/13/2023]
Abstract
We present three novel exclusively heteronuclear 5D (13)C direct-detected NMR experiments, namely (H(N-flip)N)CONCACON, (HCA)CONCACON and (H)CACON(CA)CON, designed for easy sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The experiments proposed have been optimized to overcome the drawbacks which may dramatically complicate the characterization of IDPs by NMR, namely the small dispersion of chemical shifts and the fast exchange of the amide protons with the solvent. A fast and reliable automatic assignment of α-synuclein chemical shifts was obtained with the Tool for SMFT-based Assignment of Resonances (TSAR) program based on the information provided by these experiments.
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Affiliation(s)
- Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287, Rheinstetten, Germany
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