1
|
Terrell E, Dellon LD, Dufour A, Bartolomei E, Broadbelt LJ, Garcia-Perez M. A Review on Lignin Liquefaction: Advanced Characterization of Structure and Microkinetic Modeling. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b05744] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Evan Terrell
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Lauren D. Dellon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Anthony Dufour
- LRGP, CNRS, Universite de Lorraine, ENSIC, 54000 Nancy, France
| | | | - Linda J. Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Manuel Garcia-Perez
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| |
Collapse
|
2
|
Tischer A, Machha VR, Rösgen J, Auton M. "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams. Biopolymers 2018; 109:e23106. [PMID: 29457634 DOI: 10.1002/bip.23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 11/09/2022]
Abstract
Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how Δ H and the urea m-value interconvert through the slope of cm versus T, ( ∂ c m / ∂ T ) = Δ H / ( m T ) . This relationship permits the calculation of Δ H at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from Δ H obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of Δ H and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall free energy.
Collapse
Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Venkata R Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jörg Rösgen
- Department Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, 17033
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
3
|
Tsoi PS, Choi K, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N‐Terminal Domain of ALS‐Linked TDP‐43 Assembles without Misfolding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Phoebe S. Tsoi
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Kyoung‐Jae Choi
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Paul G. Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function University of Texas MD Anderson Cancer Center Houston TX USA
| | - Antons Sizovs
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Kevin R. MacKenzie
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
- Department of Pathology and Immunology Baylor College of Medicine Houston TX USA
| | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| |
Collapse
|
4
|
Tsoi PS, Choi KJ, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N-Terminal Domain of ALS-Linked TDP-43 Assembles without Misfolding. Angew Chem Int Ed Engl 2017; 56:12590-12593. [PMID: 28833982 DOI: 10.1002/anie.201706769] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/08/2017] [Indexed: 12/28/2022]
Abstract
Transactivation response element (TAR) DNA-binding protein 43 (TDP-43) misfolding is implicated in several neurodegenerative diseases characterized by aggregated protein inclusions. Misfolding is believed to be mediated by both the N- and C-terminus of TDP-43; however, the mechanistic basis of the contribution of individual domains in the process remained elusive. Here, using single-molecule fluorescence and ensemble biophysical techniques, and a wide range of pH and temperature conditions, we show that TDP-43NTD is thermodynamically stable, well-folded and undergoes reversible oligomerization. We propose that, in full-length TDP-43, association between folded N-terminal domains enhances the propensity of the intrinsically unfolded C-terminal domains to drive pathological aggregation.
Collapse
Affiliation(s)
- Phoebe S Tsoi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kyoung-Jae Choi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Paul G Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Antons Sizovs
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin R MacKenzie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
5
|
Ferreon ACM, Ferreon JC, Wright PE, Deniz AA. Modulation of allostery by protein intrinsic disorder. Nature 2013; 498:390-4. [PMID: 23783631 PMCID: PMC3718496 DOI: 10.1038/nature12294] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 05/17/2013] [Indexed: 12/26/2022]
Abstract
Allostery is an intrinsic property of many globular proteins and enzymes that is indispensable for cellular regulatory and feedback mechanisms. Recent theoretical and empirical observations indicate that allostery is also manifest in intrinsically disordered proteins, which account for a substantial proportion of the proteome. Many intrinsically disordered proteins are promiscuous binders that interact with multiple partners and frequently function as molecular hubs in protein interaction networks. The adenovirus early region 1A (E1A) oncoprotein is a prime example of a molecular hub intrinsically disordered protein. E1A can induce marked epigenetic reprogramming of the cell within hours after infection, through interactions with a diverse set of partners that include key host regulators such as the general transcriptional coactivator CREB binding protein (CBP), its paralogue p300, and the retinoblastoma protein (pRb; also called RB1). Little is known about the allosteric effects at play in E1A-CBP-pRb interactions, or more generally in hub intrinsically disordered protein interaction networks. Here we used single-molecule fluorescence resonance energy transfer (smFRET) to study coupled binding and folding processes in the ternary E1A system. The low concentrations used in these high-sensitivity experiments proved to be essential for these studies, which are challenging owing to a combination of E1A aggregation propensity and high-affinity binding interactions. Our data revealed that E1A-CBP-pRb interactions have either positive or negative cooperativity, depending on the available E1A interaction sites. This striking cooperativity switch enables fine-tuning of the thermodynamic accessibility of the ternary versus binary E1A complexes, and may permit a context-specific tuning of associated downstream signalling outputs. Such a modulation of allosteric interactions is probably a common mechanism in molecular hub intrinsically disordered protein function.
Collapse
Affiliation(s)
- Allan Chris M Ferreon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | |
Collapse
|
6
|
Ferreon ACM, Deniz AA. Osmolyte-, binding-, and temperature-induced transitions of intrinsically disordered proteins. Methods Mol Biol 2012; 896:257-66. [PMID: 22821530 DOI: 10.1007/978-1-4614-3704-8_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Structural studies of intrinsically disordered proteins (IDPs) entail unique experimental challenges due in part to the lack of well-defined three-dimensional structures exhibited by this class of proteins. Although IDPs can be studied in their native disordered conformations using a variety of ensemble and single-molecule biophysical techniques, one particularly informative experimental strategy is to probe protein disordered states as part of folding-unfolding transitions. In this chapter, we describe solution methods for probing conformational properties of IDPs (and unfolded proteins, in general), including the use of naturally occurring osmolytes to force protein folding, the quantification of coupled folding and ligand binding of IDPs, and the structural interrogation of solvent- and/or binding-induced folded conformations by thermal perturbations.
Collapse
|
7
|
Abstract
Protein scientists have long used cosolutes to study protein stability. While denaturants, such as urea, have been employed for a long time, the attention became focused more recently on protein stabilizers, including osmolytes. Here, we provide practical experimental instructions for the use of both stabilizing and denaturing osmolytes with proteins, as well as data evaluation strategies. We focus on protein stability in the presence of cosolutes and their mixtures at constant and variable temperature.
Collapse
Affiliation(s)
- Luis Marcelo F Holthauzen
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
| | | | | | | |
Collapse
|
8
|
Permyakov SE, Khokhlova TI, Uversky VN, Permyakov EA. Analysis of Ca2+/Mg2+ selectivity in alpha-lactalbumin and Ca(2+)-binding lysozyme reveals a distinct Mg(2+)-specific site in lysozyme. Proteins 2010; 78:2609-24. [PMID: 20602456 DOI: 10.1002/prot.22776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The triggering of Ca(2+) signaling pathways relies on Ca(2+)/Mg(2+) specificity of proteins mediating these pathways. Two homologous milk Ca(2+)-binding proteins, bovine alpha-lactalbumin (bLA) and equine lysozyme (EQL), were analyzed using the simplest "four-state" scheme of metal- and temperature-induced structural changes in a protein. The association of Ca(2+)/Mg(2+) by native proteins is entropy-driven. Both proteins exhibit strong temperature dependences of apparent affinities to Ca(2+) and Mg(2+), due to low thermal stabilities of their apo-forms and relatively high unfavorable enthalpies of Mg(2+) association. The ratios of their apparent affinities to Ca(2+) and Mg(2+), being unusually high at low temperatures (5.3-6.5 orders of magnitude), reach the values inherent to classical EF-hand motifs at physiological temperatures. The comparison of phase diagrams predicted within the model of competitive Ca(2+) and Mg(2+) binding with experimental data strongly suggests that the association of Ca(2+) and Mg(2+) ions with bLA is a competitive process, whereas the primary Mg(2+) site of EQL is different from its Ca(2+)-binding site. The later conclusion is corroborated by qualitatively different molar ellipticity changes in near-UV region accompanying Mg(2+) and Ca(2+) association. The Ca(2+)/Mg(2+) selectivity of Mg(2+)-site of EQL is below an order of magnitude. EQL exhibits a distinct Mg(2+)-specific site, probably arising as an adaptation to the extracellular environment.
Collapse
Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | | | | | | |
Collapse
|
9
|
Ferreon ACM, Moran CR, Gambin Y, Deniz AA. Single-molecule fluorescence studies of intrinsically disordered proteins. Methods Enzymol 2010; 472:179-204. [PMID: 20580965 DOI: 10.1016/s0076-6879(10)72010-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) (also referred to as natively unfolded proteins) play critical roles in a variety of cellular processes such as transcription and translation and also are linked to several human diseases. Biophysical studies of IDPs present unusual experimental challenges due in part to their broad conformational heterogeneity and potentially complex binding-induced folding behavior. By minimizing the averaging over an ensemble (which is typical of most conventional experiments), single-molecule fluorescence (SMF) techniques have recently begun to add advanced capabilities for structural studies to the experimental arsenal of IDP investigators. Here, we briefly discuss a few common SMF methods that are particularly useful for IDP studies, including SMF resonance energy transfer and fluorescence correlation spectroscopy, along with site-specific protein-labeling methods that are essential for application of these methods to IDPs. We then present an overview of a few studies in this area, highlighting how SMF methods are being used to gain valuable information about two amyloidogenic IDPs, the Parkinson's disease-linked alpha-synuclein and the NM domain of the yeast prion protein Sup 35. SMF experiments provided new information about the proteins' rapidly fluctuating IDP forms, and the complex alpha-synuclein folding behavior upon its binding to lipid and membrane mimics. We anticipate that SMF and single-molecule methods, in general, will find broad application for structural and mechanistic studies of a wide variety of IDPs, both of their disordered conformations, and their ordered ensembles relevant for function and disease.
Collapse
Affiliation(s)
- Allan Chris M Ferreon
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | | | | | | |
Collapse
|
10
|
Arias-Moreno X, Cuesta-Lopez S, Millet O, Sancho J, Velazquez-Campoy A. Thermodynamics of protein-cation interaction: Ca+2and Mg+2binding to the fifth binding module of the LDL receptor. Proteins 2009; 78:950-61. [DOI: 10.1002/prot.22619] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
Zubrienė A, Matulienė J, Baranauskienė L, Jachno J, Torresan J, Michailovienė V, Cimmperman P, Matulis D. Measurement of nanomolar dissociation constants by titration calorimetry and thermal shift assay - radicicol binding to Hsp90 and ethoxzolamide binding to CAII. Int J Mol Sci 2009; 10:2662-2680. [PMID: 19582223 PMCID: PMC2705510 DOI: 10.3390/ijms10062662] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 05/30/2009] [Accepted: 06/03/2009] [Indexed: 01/28/2023] Open
Abstract
The analysis of tight protein-ligand binding reactions by isothermal titration calorimetry (ITC) and thermal shift assay (TSA) is presented. The binding of radicicol to the N-terminal domain of human heat shock protein 90 (Hsp90alphaN) and the binding of ethoxzolamide to human carbonic anhydrase (hCAII) were too strong to be measured accurately by direct ITC titration and therefore were measured by displacement ITC and by observing the temperature-denaturation transitions of ligand-free and ligand-bound protein. Stabilization of both proteins by their ligands was profound, increasing the melting temperature by more than 10 masculineC, depending on ligand concentration. Analysis of the melting temperature dependence on the protein and ligand concentrations yielded dissociation constants equal to 1 nM and 2 nM for Hsp90alphaN-radicicol and hCAII-ethoxzolamide, respectively. The ligand-free and ligand-bound protein fractions melt separately, and two melting transitions are observed. This phenomenon is especially pronounced when the ligand concentration is equal to about half the protein concentration. The analysis compares ITC and TSA data, accounts for two transitions and yields the ligand binding constant and the parameters of protein stability, including the Gibbs free energy and the enthalpy of unfolding.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Daumantas Matulis
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +370-5-269-1884; Fax: +370-5-260-2116
| |
Collapse
|
12
|
|
13
|
Cremades N, Velazquez-Campoy A, Freire E, Sancho J. The flavodoxin from Helicobacter pylori: structural determinants of thermostability and FMN cofactor binding. Biochemistry 2007; 47:627-39. [PMID: 18095659 DOI: 10.1021/bi701365e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Flavodoxin has been recently recognized as an essential protein for a number of pathogenic bacteria including Helicobacter pylori, where it has been proposed to constitute a target for antibacterial drug development. One way we are exploring to screen for novel inhibitory compounds is to perform thermal upshift assays, for which a detailed knowledge of protein thermostability and cofactor binding properties is of great help. However, very little is known on the stability and ligand binding properties of H. pylori flavodoxin, and its peculiar FMN binding site together with the variety of behaviors observed within the flavodoxin family preclude extrapolations. We have thus performed a detailed experimental and computational analysis of the thermostability and cofactor binding energetics of H. pylori flavodoxin, and we have found that the thermal unfolding equilibrium is more complex that any other previously described for flavodoxins as it involves the accumulation of two distinct equilibrium intermediates. Fortunately the entire stability and binding data can be satisfactorily fitted to a model, summarized in a simple phase diagram, where the cofactor only binds to the native state. On the other hand, we show how variability of thermal unfolding behavior within the flavodoxin family can be predicted using structure-energetics relationships implemented in the COREX algorithm. The different distribution and ranges of local stabilities of the Anabaena and H. pylori apoflavodoxins explain the essential experimental differences observed: much lower Tm1, greater resistance to global unfolding, and more pronounced cold denaturation in H. pylori. Finally, a new strategy is proposed to identify using COREX structural characteristics of equilibrium intermediate states populated during protein unfolding.
Collapse
Affiliation(s)
- Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute, Universidad de Zaragoza, 50009-Zaragoza, Spain
| | | | | | | |
Collapse
|
14
|
Permyakov SE, Permyakov EA. The use of the free metal-temperature 'phase diagrams' for studies of single site metal binding proteins. Protein J 2007; 26:1-12. [PMID: 17136617 DOI: 10.1007/s10930-006-9013-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Typical physico-chemical studies of metal binding proteins are usually aimed at determination of the metal binding constant K for a native protein (Kn), while the significance of the K value for the thermally denatured protein (Ku) is usually underestimated. Meanwhile, metal binding induced shift of thermal denaturation transition of a single site metal binding protein is defined by Kn to Ku ratio, implying that knowledge of both K values is required for full characterization of the system. In the present work, the most universal approach to the studies of single site metal binding proteins, namely construction of a protein "phase diagram" in coordinates of free metal ion concentration - temperature, is considered in detail. The detailed algorithm of construction of the phase diagrams along with underlying mathematic procedures developed here may be of use for studies of other simple protein-target type systems, where target represents low molecular weight ligand. Analysis of the simplest protein-ligand system reveals that thermodynamic properties of apo-protein dictate the maximal possible increase of its affinity to any simple ligand upon thermal denaturation of the protein. Experimental and general problems coupled with the use of the phase diagrams are discussed.
Collapse
Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia.
| | | |
Collapse
|
15
|
Ferreon ACM, Deniz AA. α-Synuclein Multistate Folding Thermodynamics: Implications for Protein Misfolding and Aggregation. Biochemistry 2007; 46:4499-509. [PMID: 17378587 DOI: 10.1021/bi602461y] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpha-synuclein aggregation has been tightly linked with the pathogenesis of Parkinson's disease and other neurodegenerative disorders. Despite the protein's putative function in presynaptic vesicle regulation, the roles of lipid binding in modulating alpha-synuclein conformations and the aggregation process remain to be fully understood. This study focuses on a detailed thermodynamic characterization of monomeric alpha-synuclein folding in the presence of SDS, a well-studied lipid mimetic. Far-UV CD spectroscopy was employed for detection of conformational transitions induced by SDS, temperature, and pH. The data we present here clearly demonstrate the multistate nature of alpha-synuclein folding, which involves two predominantly alpha-helical partially folded thermodynamic intermediates that we designate as F (most folded) and I (intermediately folded) states. Likely structures of these alpha-synuclein conformational states are also discussed. These partially folded forms can exist in the presence of either monomeric or micellar forms of SDS, which suggests that alpha-synuclein has an intrinsic propensity for adopting multiple alpha-helical structures even in the absence of micelle or membrane binding, a feature that may have implications for its biological activity and toxicity. Additionally, we discuss the relation between alpha-synuclein three-state folding and its aggregation, within the context of isothermal titration calorimetry and transmission electron microscopy measurements of SDS-initiated oligomer formation.
Collapse
Affiliation(s)
- Allan Chris M Ferreon
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines MB-19, La Jolla, California 92037, USA
| | | |
Collapse
|
16
|
Ferreon ACM, Ferreon JC, Bolen DW, Rösgen J. Protein phase diagrams II: nonideal behavior of biochemical reactions in the presence of osmolytes. Biophys J 2007; 92:245-56. [PMID: 17028144 PMCID: PMC1697851 DOI: 10.1529/biophysj.106.092262] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 09/20/2006] [Indexed: 11/18/2022] Open
Abstract
In the age of biochemical systems biology, proteomics, and high throughput methods, the thermodynamic quantification of cytoplasmatic reaction networks comes into reach of the current generation of scientists. What is needed to efficiently extract the relevant information from the raw data is a robust tool for evaluating the number and stoichiometry of all observed reactions while providing a good estimate of the thermodynamic parameters that determine the molecular behavior. The recently developed phase-diagram method, strictly speaking a graphical representation of linkage or Maxwell Relations, offers such capabilities. Here, we extend the phase diagram method to nonideal conditions. For the sake of simplicity, we choose as an example a reaction system involving the protein RNase A, its inhibitor CMP, the osmolyte urea, and water. We investigate this system as a function of the concentrations of inhibitor and osmolyte at different temperatures ranging from 280 K to 340 K. The most interesting finding is that the protein-inhibitor binding equilibrium depends strongly on the urea concentration--by orders-of-magnitude more than expected from urea-protein interaction alone. Moreover, the m-value of ligand binding is strongly concentration-dependent, which is highly unusual. It is concluded that the interaction between small molecules like urea and CMP can significantly contribute to cytoplasmic nonideality. Such a finding is highly significant because of its impact on renal tissue where high concentrations of cosolutes occur regularly.
Collapse
Affiliation(s)
- Allan Chris M Ferreon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | | | | | | |
Collapse
|
17
|
Nazmi AR, Reinisch T, Hinz HJ. Ca-binding to Bacillus licheniformis α-amylase (BLA). Arch Biochem Biophys 2006; 453:18-25. [PMID: 16712774 DOI: 10.1016/j.abb.2006.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 04/04/2006] [Accepted: 04/05/2006] [Indexed: 11/17/2022]
Abstract
Ca-induced renaturation of Bacillus licheniformis alpha-amylase in the presence of urea has been employed to determine the binding constants of the ion. The native enzyme is folded at 3M urea while the Ca-depleted protein is largely unfolded at this denaturant concentration. Refolding of the protein has been monitored by circular dichroism and the titration curves have been analyzed assuming a model of three independent binding sites. The stoichiometry has been taken from X-ray studies. The refolded protein exhibits a secondary structure that is similar but not identical to that of the native protein. The binding constants have been used to construct a phase diagram that illustrates the contribution of Ca-binding to the resistance against urea unfolding.
Collapse
Affiliation(s)
- Ali Reza Nazmi
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 30, 48149 Münster, Germany
| | | | | |
Collapse
|
18
|
Rajagopalan L, Rösgen J, Bolen DW, Rajarathnam K. Novel use of an osmolyte to dissect multiple thermodynamic linkages in a chemokine ligand-receptor system. Biochemistry 2005; 44:12932-9. [PMID: 16185062 DOI: 10.1021/bi051219z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used trimethylamine N-oxide (TMAO), a protecting osmolyte, to dissect the complex thermodynamic linkages involved in the interaction between the chemokine interleukin-8 (IL-8) and the N-domain of its receptor CXCR1. Our results show that TMAO induces folding in the CXCR1 receptor N-domain and that the N-domain upon folding binds ligand with higher affinity. This represents, to our knowledge, the smallest domain that has been shown to be folded in osmolyte. Using the phase diagram method to analyze this thermodynamic relationship graphically, we also observe that TMAO favors ligand dimerization and that the dimeric ligand binds the receptor domain with lower affinity. We have thus been able to dissect coupling among three distinct processes, receptor domain folding, ligand dimerization, and ligand-receptor domain binding in this chemokine-receptor system. We also observe that the affinity of the related chemokine, melanoma growth stimulatory activity (MGSA), increases concurrent with N-domain folding similar to IL-8 but shows more profound differences on ligand dimerization. These studies establish a novel and innovative use of osmolytes to dissect linkages among different processes and exploit the phase diagram as a tool to graphically represent and dissect complex thermodynamic relationships in biological systems. On the basis of our observations and earlier work, we discuss the relevance of ligand dimerization in chemokine regulation.
Collapse
Affiliation(s)
- Lavanya Rajagopalan
- Department of Human Biological Chemistry and Genetics and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555-1055, USA
| | | | | | | |
Collapse
|
19
|
Masson P, Balny C. Linear and non-linear pressure dependence of enzyme catalytic parameters. Biochim Biophys Acta Gen Subj 2005; 1724:440-50. [PMID: 15951113 DOI: 10.1016/j.bbagen.2005.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 05/03/2005] [Accepted: 05/04/2005] [Indexed: 11/21/2022]
Abstract
The pressure dependence of enzyme catalytic parameters allows volume changes associated with substrate binding and activation volumes for the chemical steps to be determined. Because catalytic constants are composite parameters, elementary volume change contributions can be calculated from the pressure differentiation of kinetic constants. Linear and non-linear pressure-dependence of single-step enzyme reactions and steady-state catalytic parameters can be observed. Non-linearity can be interpreted either in terms of interdependence between the pressure and other environmental parameters (i.e., temperature, solvent composition, pH), pressure-induced enzyme unfolding, compressibility changes and pressure-induced rate limiting changes. These different situations are illustrated with several examples.
Collapse
Affiliation(s)
- Patrick Masson
- Centre de Recherches du Service de Santé des Armées, Département de Toxicologie, Unité d'Enzymologie, BP. 87, 38702 La Tronche cédex, France.
| | | |
Collapse
|