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Bychkova VE, Dolgikh DA, Balobanov VA, Finkelstein AV. The Molten Globule State of a Globular Protein in a Cell Is More or Less Frequent Case Rather than an Exception. Molecules 2022; 27:molecules27144361. [PMID: 35889244 PMCID: PMC9319461 DOI: 10.3390/molecules27144361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/01/2023] Open
Abstract
Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn’s hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners.
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Affiliation(s)
- Valentina E. Bychkova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117871 Moscow, Russia;
| | - Vitalii A. Balobanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
- Correspondence:
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
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2
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Markin CJ, Mokhtari DA, Sunden F, Appel MJ, Akiva E, Longwell SA, Sabatti C, Herschlag D, Fordyce PM. Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics. Science 2021; 373:373/6553/eabf8761. [PMID: 34437092 DOI: 10.1126/science.abf8761] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Systematic and extensive investigation of enzymes is needed to understand their extraordinary efficiency and meet current challenges in medicine and engineering. We present HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a microfluidic platform for high-throughput expression, purification, and characterization of more than 1500 enzyme variants per experiment. For 1036 mutants of the alkaline phosphatase PafA (phosphate-irrepressible alkaline phosphatase of Flavobacterium), we performed more than 670,000 reactions and determined more than 5000 kinetic and physical constants for multiple substrates and inhibitors. We uncovered extensive kinetic partitioning to a misfolded state and isolated catalytic effects, revealing spatially contiguous regions of residues linked to particular aspects of function. Regions included active-site proximal residues but extended to the enzyme surface, providing a map of underlying architecture not possible to derive from existing approaches. HT-MEK has applications that range from understanding molecular mechanisms to medicine, engineering, and design.
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Affiliation(s)
- C J Markin
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - D A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - F Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - M J Appel
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - E Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - S A Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - C Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - D Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - P M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub; San Francisco, CA 94110, USA
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Elia F, Cantini F, Chiti F, Dobson CM, Bemporad F. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies. Biophys J 2017; 112:2540-2551. [PMID: 28636911 PMCID: PMC5479110 DOI: 10.1016/j.bpj.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/29/2023] Open
Abstract
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state.
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Affiliation(s)
- Francesco Elia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | - Francesca Cantini
- Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | | | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy.
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4
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Fisher AB. Peroxiredoxin 6 in the repair of peroxidized cell membranes and cell signaling. Arch Biochem Biophys 2017; 617:68-83. [PMID: 27932289 PMCID: PMC5810417 DOI: 10.1016/j.abb.2016.12.003] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/02/2016] [Accepted: 12/03/2016] [Indexed: 12/12/2022]
Abstract
Peroxiredoxin 6 represents a widely distributed group of peroxiredoxins that contain a single conserved cysteine in the protein monomer (1-cys Prdx). The cys when oxidized to the sulfenic form is reduced with glutathione (GSH) catalyzed by the π isoform of GSH-S-transferase. Three enzymatic activities of the protein have been described:1) peroxidase with H2O2, short chain hydroperoxides, and phospholipid hydroperoxides as substrates; 2) phospholipase A2 (PLA2); and 3) lysophosphatidylcholine acyl transferase (LPCAT). These activities have important physiological roles in antioxidant defense, turnover of cellular phospholipids, and the generation of superoxide anion via initiation of the signaling cascade for activation of NADPH oxidase (type 2). The ability of Prdx6 to reduce peroxidized cell membrane phospholipids (peroxidase activity) and also to replace the oxidized sn-2 fatty acyl group through hydrolysis/reacylation (PLA2 and LPCAT activities) provides a complete system for the repair of peroxidized cell membranes.
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Affiliation(s)
- Aron B Fisher
- Institute for Environmental Medicine of the Department of Physiology, University of Pennsylvania, 3620 Hamilton Walk, 1 John Morgan Building, Philadelphia, PA, United States.
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5
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Kasper JR, Park C. Ligand binding to a high-energy partially unfolded protein. Protein Sci 2014; 24:129-37. [PMID: 25367157 DOI: 10.1002/pro.2596] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 11/05/2022]
Abstract
The conformational energy landscape of a protein determines populations of all possible conformations of the protein and also determines the kinetics of the conversion between the conformations. Interaction with ligands influences the conformational energy landscapes of proteins and shifts populations of proteins in different conformational states. To investigate the effect of ligand binding on partial unfolding of a protein, we use Escherichia coli dihydrofolate reductase (DHFR) and its functional ligand NADP(+) as a model system. We previously identified a partially unfolded form of DHFR that is populated under native conditions. In this report, we determined the free energy for partial unfolding of DHFR at varying concentrations of NADP(+) and found that NADP(+) binds to the partially unfolded form as well as the native form. DHFR unfolds partially without releasing the ligand, though the binding affinity for NADP(+) is diminished upon partial unfolding. Based on known crystallographic structures of NADP(+) -bound DHFR and the model of the partially unfolded protein we previously determined, we propose that the adenosine-binding domain of DHFR remains folded in the partially unfolded form and interacts with the adenosine moiety of NADP(+) . Our result demonstrates that ligand binding may affect the conformational free energy of not only native forms but also high-energy non-native forms.
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Affiliation(s)
- Joseph R Kasper
- Department of Medicinal Chemistry and Molecular Pharmacology, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, 47907
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6
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Bardwell JCA, Jakob U. Conditional disorder in chaperone action. Trends Biochem Sci 2012; 37:517-25. [PMID: 23018052 DOI: 10.1016/j.tibs.2012.08.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/17/2012] [Accepted: 08/29/2012] [Indexed: 11/18/2022]
Abstract
Protein disorder remains an intrinsically fuzzy concept. Its role in protein function is difficult to conceptualize and its experimental study is challenging. Although a wide variety of roles for protein disorder have been proposed, establishing that disorder is functionally important, particularly in vivo, is not a trivial task. Several molecular chaperones have now been identified as conditionally disordered proteins; fully folded and chaperone-inactive under non-stress conditions, they adopt a partially disordered conformation upon exposure to distinct stress conditions. This disorder appears to be vital for their ability to bind multiple aggregation-sensitive client proteins and to protect cells against the stressors. The study of these conditionally disordered chaperones should prove useful in understanding the functional role for protein disorder in molecular recognition.
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Affiliation(s)
- James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Rahaman H, Zhou S, Dodia C, Feinstein SI, Huang S, Speicher D, Fisher AB. Increased phospholipase A2 activity with phosphorylation of peroxiredoxin 6 requires a conformational change in the protein. Biochemistry 2012; 51:5521-30. [PMID: 22663767 DOI: 10.1021/bi300380h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We have shown previously and confirmed in this study that the phospholipase A(2) (PLA(2)) activity of peroxiredoxin 6 (Prdx6) is markedly increased by phosphorylation. This report evaluates the conformation and thermodynamic stability of Prdx6 protein after phosphorylation to understand the physical basis for increased activity. Phosphorylation resulted in decreased negative far-UV CD, strengthened ANS binding, and a lack of rigid tertiary structure, compatible with a change in conformation to that of a molten globule. The ΔG°(D) was 3.3 ± 0.3 kcal mol(-1) for Prdx6 and 1.7 ± 0.7 kcal mol(-1) for pPrdx6, suggesting that phosphorylation destabilizes the protein. Phosphorylation of Prdx6 changed the conformation of the N-terminal domain exposing Trp 33, as determined by tryptophan fluorescence and NaI fluorescence quenching. The kinetics of interaction of proteins with unilamellar liposomes (50:25:15:10 DPPC:egg PC:cholesterol:PG molar ratio) were evaluated with tryptophan fluorescence. pPrdx6 bound to liposomes with a higher affinity (K(d) = 5.6 ± 1.2 μM) than Prdx6 (K(d) = 24.9 ± 4.5 μM). By isothermal titration calorimetry, pPrdx6 bound to liposomes with a large exothermic heat loss (ΔH = -31.49 ± 0.22 kcal mol(-1)). Correlating our conformational studies with the published crystal structure of oxidized Prdx6 suggests that phosphorylation results in exposure of hydrophobic residues, thereby providing accessibility to the sites for liposome binding. Because binding of the enzyme to the phospholipid substrate interface is a requirement for PLA(2) activity, these results indicate that a change in the conformation of Prdx6 upon its phosphorylation is the basis for enhancement of PLA(2) enzymatic activity.
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Affiliation(s)
- Hamidur Rahaman
- Institute for Environmental Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6068, United States
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Structural and kinetic mapping of side-chain exposure onto the protein energy landscape. Proc Natl Acad Sci U S A 2011; 108:10532-7. [PMID: 21670244 DOI: 10.1073/pnas.1103629108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.
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Suskiewicz MJ, Sussman JL, Silman I, Shaul Y. Context-dependent resistance to proteolysis of intrinsically disordered proteins. Protein Sci 2011; 20:1285-97. [PMID: 21574196 DOI: 10.1002/pro.657] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 05/05/2011] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins (IDPs), also known as intrinsically unstructured proteins (IUPs), lack a well-defined 3D structure in vitro and, in some cases, also in vivo. Here, we discuss the question of proteolytic sensitivity of IDPs, with a view to better explaining their in vivo characteristics. After an initial assessment of the status of IDPs in vivo, we briefly survey the intracellular proteolytic systems. Subsequently, we discuss the evidence for IDPs being inherently sensitive to proteolysis. Such sensitivity would not, however, result in enhanced degradation if the protease-sensitive sites were sequestered. Accordingly, IDP access to and degradation by the proteasome, the major proteolytic complex within eukaryotic cells, are discussed in detail. The emerging picture appears to be that IDPs are inherently sensitive to proteasomal degradation along the lines of the "degradation by default" model. However, available data sets of intracellular protein half-lives suggest that intrinsic disorder does not imply a significantly shorter half-life. We assess the power of available systemic half-life measurements, but also discuss possible mechanisms that could protect IDPs from intracellular degradation. Finally, we discuss the relevance of the proteolytic sensitivity of IDPs to their function and evolution.
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Affiliation(s)
- Marcin J Suskiewicz
- The Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
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Shaw WJ, Ferris K. Structure, orientation, and dynamics of the C-terminal hexapeptide of LRAP determined using solid-state NMR. J Phys Chem B 2008; 112:16975-81. [PMID: 19368031 PMCID: PMC2771880 DOI: 10.1021/jp808012g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amelogenin is the predominant protein found during enamel development and has been shown to be essential to proper enamel formation. Leucine-rich amelogenin peptide (LRAP) is a naturally occurring splice variant that preserves the charged N- and C-termini of full length amelogenin, regions thought to be crucial in interacting with hydroxaypatite. Particularly, the highly charged C-terminal hexapeptide (KREEVD) is thought to be the region most intimately interacting with hydroxyapatite (HAP). The structure of this charged region was investigated, along with the proximity to the surface and the mobility of two of the residues. The structure was found to be consistent with a random coil or more extended structure, as has been seen for more internalized residues in the C-terminus. The backbone K54(13C'), V58(13C'), and V58(15N) were all found to be close to the surface of HAP, approximately 6.0 angstroms from the nearest 31P atom, suggesting a strong interaction and emphasizing the importance of these residues in interacting with HAP. However, both ends of the hexapeptide at residues K54 and V58 experience significant mobility under hydrated conditions, implying that another portion of the protein helps to stabilize the strong LRAP-HAP interaction. Interestingly, the backbone of the C-terminal third of the protein is consistently 6.0 angstroms from the HAP surface, providing a model in this region of the protein lying flat on the surface with no three-dimensional folding. The combination of these features, that is, a random coil structure, a significant mobility, and a lack of three-dimensional folding in this region of the protein, may have an important functional role, possibly allowing maximum crystal inhibition at low protein concentrations.
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Affiliation(s)
- Wendy J Shaw
- Pacific Northwest National Laboratories, Richland, Washington 99354, USA.
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