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Villalba-Rodríguez AM, Martínez-González S, Sosa-Hernández JE, Parra-Saldívar R, Bilal M, Iqbal HMN. Nanoclay/Polymer-Based Hydrogels and Enzyme-Loaded Nanostructures for Wound Healing Applications. Gels 2021; 7:gels7020059. [PMID: 34068868 PMCID: PMC8162325 DOI: 10.3390/gels7020059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Multi-polymeric nanocomposite hydrogels with multi-functional characteristics have been engineered with high interest around the globe. The ease in fine tunability with maintained compliance makes an array of nanocomposite biomaterials outstanding candidates for the biomedical sector of the modern world. In this context, the present work intends to tackle the necessity of alternatives for the treatment of diabetic foot ulcers through the formulation of nanoclay and/or polymer-based nanocomposite hydrogels. Laponite RD, a synthetic 2-D nanoclay that becomes inert when in a physiological environment, while mixed with water, becomes a clear gel with interesting shear-thinning properties. Adding Laponite RD to chitosan or gelatin allows for the modification of the mechanical properties of such materials. The setup explored in this research allows for a promising polymeric matrix that can potentially be loaded with active compounds for antibacterial support in foot ulcers, as well as enzymes for wound debridement.
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Affiliation(s)
- Angel M. Villalba-Rodríguez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Sara Martínez-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Correspondence: (M.B.); (H.M.N.I.)
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; (A.M.V.-R.); (S.M.-G.); (J.E.S.-H.); (R.P.-S.)
- Correspondence: (M.B.); (H.M.N.I.)
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2
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Ruben EA, Gandhi PS, Chen Z, Koester SK, DeKoster GT, Frieden C, Di Cera E. 19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2. J Biol Chem 2020; 295:8227-8235. [PMID: 32358061 PMCID: PMC7294081 DOI: 10.1074/jbc.ra120.013419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/28/2020] [Indexed: 11/06/2022] Open
Abstract
The conformational properties of trypsin-like proteases and their zymogen forms remain controversial because of a lack of sufficient information on their free forms. Specifically, it is unclear whether the free protease is zymogen-like and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equilibrium from which the ligand selects the optimal fit via conformational selection. Here we report the results of 19F NMR measurements that reveal the conformational properties of a protease and its zymogen precursor in the free form. Using the trypsin-like, clotting protease thrombin as a relevant model system, we show that its conformation is quite different from that of its direct zymogen precursor prethrombin-2 and more similar to that of its fully active Na+-bound form. The results cast doubts on recent hypotheses that free thrombin is zymogen-like and transitions to protease-like forms upon ligand binding. Rather, they validate the scenario emerged from previous findings of X-ray crystallography and rapid kinetics supporting a pre-existing equilibrium between open (E) and closed (E*) forms of the active site. In this scenario, prethrombin-2 is more dynamic and exists predominantly in the E* form, whereas thrombin is more rigid and exists predominantly in the E form. Ligand binding to thrombin takes place exclusively in the E form without significant changes in the overall conformation. In summary, these results disclose the structural architecture of the free forms of thrombin and prethrombin-2, consistent with an E*-E equilibrium and providing no evidence that free thrombin is zymogen-like.
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Affiliation(s)
- Eliza A Ruben
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | | | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
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3
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Goettig P, Brandstetter H, Magdolen V. Surface loops of trypsin-like serine proteases as determinants of function. Biochimie 2019; 166:52-76. [PMID: 31505212 PMCID: PMC7615277 DOI: 10.1016/j.biochi.2019.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Trypsin and chymotrypsin-like serine proteases from family S1 (clan PA) constitute the largest protease group in humans and more generally in vertebrates. The prototypes chymotrypsin, trypsin and elastase represent simple digestive proteases in the gut, where they cleave nearly any protein. Multidomain trypsin-like proteases are key players in the tightly controlled blood coagulation and complement systems, as well as related proteases that are secreted from diverse immune cells. Some serine proteases are expressed in nearly all tissues and fluids of the human body, such as the human kallikreins and kallikrein-related peptidases with specialization for often unique substrates and accurate timing of activity. HtrA and membrane-anchored serine proteases fulfill important physiological tasks with emerging roles in cancer. The high diversity of all family members, which share the tandem β-barrel architecture of the chymotrypsin-fold in the catalytic domain, is conferred by the large differences of eight surface loops, surrounding the active site. The length of these loops alters with insertions and deletions, resulting in remarkably different three-dimensional arrangements. In addition, metal binding sites for Na+, Ca2+ and Zn2+ serve as regulatory elements, as do N-glycosylation sites. Depending on the individual tasks of the protease, the surface loops determine substrate specificity, control the turnover and allow regulation of activation, activity and degradation by other proteins, which are often serine proteases themselves. Most intriguingly, in some serine proteases, the surface loops interact as allosteric network, partially tuned by protein co-factors. Knowledge of these subtle and complicated molecular motions may allow nowadays for new and specific pharmaceutical or medical approaches.
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Affiliation(s)
- Peter Goettig
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
| | - Hans Brandstetter
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Viktor Magdolen
- Clinical Research Unit, Department of Obstetrics and Gynecology, School of Medicine, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany
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4
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Xiao J, Salsbury FR. Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. J Biomol Struct Dyn 2017; 35:3354-3369. [PMID: 27794633 PMCID: PMC6876308 DOI: 10.1080/07391102.2016.1254682] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/21/2016] [Indexed: 01/11/2023]
Abstract
Thrombin is an attractive target for antithrombotic therapy due to its central role in thrombosis and hemostasis as well as its role in inducing tumor growth, metastasis, and tumor invasion. The thrombin-binding DNA aptamer (TBA), is under investigation for anticoagulant drugs. Although aptamer binding experiments have been revealed various effects on thrombin's enzymatic activities, the detailed picture of the thrombin's allostery from TBA binding is still unclear. To investigate thrombin's response to the aptamer-binding at the molecular level, we compare the mechanical properties and free energy landscapes of the free and aptamer-bound thrombin using microsecond-scale all-atom GPU-based molecular dynamics simulations. Our calculations on residue fluctuations and coupling illustrate the allosteric effects of aptamer-binding at the atomic level, highlighting the exosite II, 60s, γ and the sodium loops, and the alpha helix region in the light chains involved in the allosteric changes. This level of details clarifies the mechanisms of previous experimentally demonstrated phenomena, and provides a prediction of the reduced autolysis rate after aptamer-binding. The shifts in thrombin's ensemble of conformations and free energy surfaces after aptamer-binding demonstrate that the presence of bound-aptamer restricts the conformational freedom of thrombin suggesting that conformational selection, i.e. generalized allostery, is the dominant mechanism of thrombin-aptamer binding. The profound perturbation on thrombin's mechanical and thermodynamic properties due to the aptamer-binding, which was revealed comprehensively as a generalized allostery in this work, may be exploited in further drug discovery and development.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
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5
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Su K, Jin Y, Miao Z, Cheng X, Yang L, Wang M. Phenotypic and genetic analysis of dysprothrombinemia due to a novel homozygous mutation. ACTA ACUST UNITED AC 2017; 22:380-385. [PMID: 28196451 DOI: 10.1080/10245332.2017.1287332] [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] [Indexed: 10/20/2022]
Abstract
OBJECTIVE We study the phenotype and genotype of a novel gene mutation of factor II (FII) that leads to dysprothrombinemia, and do the meta-analysis to illuminate its molecular pathogenesis. It will further contribute to our comprehension of the pathogenesis of this type of disease. METHODS The prothrombin time (PT), activated partial thromboplastin time (APTT) and the activities of other factors were determined by the one-stage clotting method. The prothrombin antigen was measured with enzyme-linked immunosorbent assay (ELISA). Function of the mutant protein was evaluated by thrombin generation tests. Potential mutations in exons, exon-intron boundaries and 5', 3' untranslated sequences of prothrombin gene were screened by polymerase chain reaction and direct sequencing. Suspected mutations were confirmed by reverse sequencing. The structure change of this protein was analyzed by model and bioinformatics analyses. RESULTS Phenotypic analysis revealed that the proband had an obviously prolonged PT, APTT, reduced prothrombin activity but normal antigen levels. The other tests were normal. Sequencing analysis detected a homozygous g.26329T>G in the catalytic domain resulting in p.Tyr510Asp. His parents and uncle were heterozygous for this mutation. The thrombin generation test showed that the mutant protein had obstacles in thrombin generation. Bioinformatics and model analyses illuminated that the mutation will be probably damaging and perturbing the structure of Na+-binding site, which will affect the activation of prothrombin. CONCLUSION This was the first report of such a mutation in the position which was associated with dysprothrombinemia.
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Affiliation(s)
- Kankan Su
- a Department of Clinical Laboratory , The First Affiliated Hospital of Wenzhou Medical University , China
| | - Yanhui Jin
- a Department of Clinical Laboratory , The First Affiliated Hospital of Wenzhou Medical University , China
| | - Zhihai Miao
- a Department of Clinical Laboratory , The First Affiliated Hospital of Wenzhou Medical University , China
| | - Xiaoli Cheng
- a Department of Clinical Laboratory , The First Affiliated Hospital of Wenzhou Medical University , China
| | - Lihong Yang
- a Department of Clinical Laboratory , The First Affiliated Hospital of Wenzhou Medical University , China
| | - Mingshan Wang
- a Department of Clinical Laboratory , The First Affiliated Hospital of Wenzhou Medical University , China
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6
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Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Biochem J 2016; 473:2395-411. [DOI: 10.1042/bcj20160336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 01/27/2023]
Abstract
Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascades. Factor IXa (activated Factor IX) serves as the trigger for amplification of coagulation through formation of the so-called Xase complex, which is a ternary complex of Factor IXa, its substrate Factor X and the cofactor Factor VIIIa on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is enhanced 200000-fold; however, the mechanistic and structural basis for this dramatic enhancement remains only partly understood. A multifaceted approach using enzymatic, biophysical and crystallographic methods to evaluate a key set of activity-enhanced Factor IXa variants has demonstrated a delicately balanced bidirectional network. Essential molecular interactions across multiple regions of the Factor IXa molecule co-operate in the maturation of the active site. This maturation is specifically facilitated by long-range communication through the Ile212–Ile213 motif unique to Factor IXa and a flexibility of the 170-loop that is further dependent on the conformation in the Cys168–Cys182 disulfide bond. Ultimately, the network consists of compensatory brakes (Val16 and Ile213) and accelerators (Tyr99 and Phe174) that together allow for a subtle fine-tuning of enzymatic activity.
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7
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Pozzi N, Zerbetto M, Acquasaliente L, Tescari S, Frezzato D, Polimeno A, Gohara DW, Di Cera E, De Filippis V. Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin. Biochemistry 2016; 55:3984-94. [PMID: 27347732 DOI: 10.1021/acs.biochem.6b00385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold.
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Affiliation(s)
- Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
| | | | | | | | | | | | - David W Gohara
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
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8
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Dabigatran and Argatroban Diametrically Modulate Thrombin Exosite Function. PLoS One 2016; 11:e0157471. [PMID: 27305147 PMCID: PMC4909201 DOI: 10.1371/journal.pone.0157471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022] Open
Abstract
Thrombin is a highly plastic molecule whose activity and specificity are regulated by exosites 1 and 2, positively-charged domains that flank the active site. Exosite binding by substrates and cofactors regulates thrombin activity by localizing thrombin, guiding substrates, and by inducing allosteric changes at the active site. Although inter-exosite and exosite-to-active-site allostery have been demonstrated, the impact of active site ligation on exosite function has not been examined. To address this gap, we used surface plasmon resonance to determine the effects of dabigatran and argatroban, active site-directed inhibitors, on thrombin binding to immobilized γA/γA-fibrin or glycoprotein Ibα peptide via exosite 1 and 2, respectively, and thrombin binding to γA/γ′-fibrin or factor Va, which is mediated by both exosites. Whereas dabigatran attenuated binding, argatroban increased thrombin binding to γA/γA- and γA/γ′-fibrin and to factor Va. The results with immobilized fibrin were confirmed by examining the binding of radiolabeled thrombin to fibrin clots. Thus, dabigatran modestly accelerated the dissociation of thrombin from γA/γA-fibrin clots, whereas argatroban attenuated dissociation. Dabigatran had no effect on thrombin binding to glycoprotein Ibα peptide, whereas argatroban promoted binding. These findings not only highlight functional effects of thrombin allostery, but also suggest that individual active site-directed thrombin inhibitors uniquely modulate exosite function, thereby identifying potential novel mechanisms of action.
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9
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Kurisaki I, Takayanagi M, Nagaoka M. Bound Na+ is a Negative Effecter for Thrombin-Substrate Stereospecific Complex Formation. J Phys Chem B 2016; 120:4540-7. [DOI: 10.1021/acs.jpcb.6b00976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ikuo Kurisaki
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Masayoshi Takayanagi
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
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10
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Vogt AD, Chakraborty P, Di Cera E. Kinetic dissection of the pre-existing conformational equilibrium in the trypsin fold. J Biol Chem 2015. [PMID: 26216877 DOI: 10.1074/jbc.m115.675538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold.
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Affiliation(s)
- Austin D Vogt
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Pradipta Chakraborty
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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11
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Boudker O, Oh S. Isothermal titration calorimetry of ion-coupled membrane transporters. Methods 2015; 76:171-182. [PMID: 25676707 PMCID: PMC4912014 DOI: 10.1016/j.ymeth.2015.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/17/2022] Open
Abstract
Binding of ligands, ranging from proteins to ions, to membrane proteins is associated with absorption or release of heat that can be detected by isothermal titration calorimetry (ITC). Such measurements not only provide binding affinities but also afford direct access to thermodynamic parameters of binding--enthalpy, entropy and heat capacity. These parameters can be interpreted in a structural context, allow discrimination between different binding mechanisms and guide drug design. In this review, we introduce advantages and limitations of ITC as a methodology to study molecular interactions of membrane proteins. We further describe case studies where ITC was used to analyze thermodynamic linkage between ions and substrates in ion-coupled transporters. Similar type of linkage analysis will likely be applicable to a wide range of transporters, channels, and receptors.
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Affiliation(s)
- Olga Boudker
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York 10021, USA.
| | - SeCheol Oh
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York 10021, USA.
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12
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Kurisaki I, Takayanagi M, Nagaoka M. Toward understanding allosteric activation of thrombin: a conjecture for important roles of unbound Na(+) molecules around thrombin. J Phys Chem B 2015; 119:3635-42. [PMID: 25654267 DOI: 10.1021/jp510657n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We shed light on important roles of unbound Na(+) molecules in enzymatic activation of thrombin. Molecular mechanism of Na(+)-activation of thrombin has been discussed in the context of allostery. However, the recent challenge to redesign K(+)-activated thrombin revealed that the allosteric interaction is insufficient to explain the mechanism. Under these circumstances, we have examined the roles of unbound Na(+) molecule in maximization of thrombin-substrate association reaction rate. We performed all-atomic molecular dynamics (MD) simulations of thrombin in the presence of three different cations; Li(+), Na(+), and Cs(+). Although these cations are commonly observed in the vicinity of the S1-pocket of thrombin, smaller cations are distributed more densely and extensively than larger ones. This suggests the two observation rules: (i) thrombin surrounded by Na(+) is at an advantage in the initial step of association reaction, namely, the formation of an encounter complex ensemble, and (ii) the presence of Na(+) molecules does not necessarily have an advantage in the final step of association reaction, namely, the formation of the stereospecific complex. In conclusion, we propose a conjecture that unbound Na(+) molecules also affect the maximization of rate constant of thrombin-substrate association reaction through optimally forming an encounter complex ensemble.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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13
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Boechi L, Pierce L, Komives EA, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci 2014; 23:1550-8. [PMID: 25131668 DOI: 10.1002/pro.2532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 06/17/2014] [Accepted: 08/03/2014] [Indexed: 11/07/2022]
Abstract
Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus's group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme.
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Affiliation(s)
- Leonardo Boechi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
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14
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Noppen B, Fonteyn L, Aerts F, De Vriese A, De Maeyer M, Le Floch F, Barbeaux P, Zwaal R, Vanhove M. Autolytic degradation of ocriplasmin: a complex mechanism unraveled by mutational analysis. Protein Eng Des Sel 2014; 27:215-23. [PMID: 24795342 DOI: 10.1093/protein/gzu015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ocriplasmin, a truncated form of plasmin, is commercialized in the USA and in Europe under the trade name Jetrea(®), and indicated for the treatment of symptomatic vitreomacular adhesion and vitreomacular traction including when associated with macular hole ≤400 µm, respectively. We have shown in a previous study that ocriplasmin undergoes autolytic degradation when injected in eye vitreous, which leads to its rapid inactivation. In order to investigate this process further, we have introduced in ocriplasmin a variety of amino acid substitutions within or in the immediate vicinity of the three major autolytic cleavage sites. We demonstrate here that autolytic inactivation of ocriplasmin is a sequential process where initial cleavage occurs primarily between residues 156 and 157. Reduction or even blocking of autolysis can be achieved by mutating a limited number of key residues. In this study, we also report the identification of a series of ocriplasmin variants with improved resistance to autolysis and unimpaired catalytic activity. Such variants represent useful tools for the exploration of therapeutic approaches aiming at non-surgical resolution of vitreomacular adhesion.
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Affiliation(s)
- B Noppen
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - L Fonteyn
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - F Aerts
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - A De Vriese
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - M De Maeyer
- Laboratory for Biomolecular Modeling, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven, Belgium
| | - F Le Floch
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - P Barbeaux
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - R Zwaal
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - M Vanhove
- Thrombogenics N.V., Gaston Geenslaan 1, 3001 Leuven, Belgium
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15
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Singh N, D'Souza A, Cholleti A, Sastry GM, Bose K. Dual regulatory switch confers tighter control on HtrA2 proteolytic activity. FEBS J 2014; 281:2456-70. [DOI: 10.1111/febs.12799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Nitu Singh
- Advanced Centre for Treatment; Research and Education in Cancer (ACTREC); Tata Memorial Centre; Kharghar Navi Mumbai India
| | - Areetha D'Souza
- Advanced Centre for Treatment; Research and Education in Cancer (ACTREC); Tata Memorial Centre; Kharghar Navi Mumbai India
| | | | | | - Kakoli Bose
- Advanced Centre for Treatment; Research and Education in Cancer (ACTREC); Tata Memorial Centre; Kharghar Navi Mumbai India
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16
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Binding thermodynamics of a glutamate transporter homolog. Nat Struct Mol Biol 2013; 20:634-40. [PMID: 23563139 PMCID: PMC3711778 DOI: 10.1038/nsmb.2548] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 02/25/2013] [Indexed: 12/02/2022]
Abstract
Glutamate transporters catalyze concentrative uptake of the neurotransmitter into glial cells and neurons. Their transport cycle involves binding and release of the substrate on the extra- and intracellular sides of the plasma membranes, and translocation of the substrate-binding site across the lipid bilayers. The energy of the ionic gradients, mainly sodium, fuels the cycle. Here, we used a cross-linking approach to trap a glutamate transporter homologue from Pyrococcus horikoshii in key conformational states with substrate-binding site facing either the extracellular or intracellular sides of the membrane to study their binding thermodynamics. We show that the chemical potential of sodium ions in solution is exclusively coupled to substrate binding and release, and not to substrate translocation. Despite the structural symmetry, the binding mechanisms are distinct on the opposite sides of the membrane and more complex than the current models suggest.
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17
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Vogt AD, Di Cera E. Conformational selection or induced fit? A critical appraisal of the kinetic mechanism. Biochemistry 2012; 51:5894-902. [PMID: 22775458 DOI: 10.1021/bi3006913] [Citation(s) in RCA: 229] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For almost five decades, two competing mechanisms of ligand recognition, conformational selection and induced fit, have dominated our interpretation of ligand binding in biological macromolecules. When binding-dissociation events are fast compared to conformational transitions, the rate of approach to equilibrium, k(obs), becomes diagnostic of conformational selection or induced fit based on whether it decreases or increases, respectively, with the ligand concentration, [L]. However, this simple conclusion based on the rapid equilibrium approximation is not valid in general. Here we show that conformational selection is associated with a rich repertoire of kinetic properties, with k(obs) decreasing or increasing with [L] depending on the relative magnitude of the rate of ligand dissociation, k(off), and the rate of conformational isomerization, k(r). We prove that, even for the simplest two-step mechanism of ligand binding, a decrease in k(obs) with [L] is unequivocal evidence of conformational selection, but an increase in k(obs) with [L] is not unequivocal evidence of induced fit. Ligand binding to glucokinase, thrombin, and its precursor prethrombin-2 are used as relevant examples. We conclude that conformational selection as a mechanism for a ligand binding to its target may be far more common than currently believed.
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Affiliation(s)
- Austin D Vogt
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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18
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Pozzi N, Vogt AD, Gohara DW, Di Cera E. Conformational selection in trypsin-like proteases. Curr Opin Struct Biol 2012; 22:421-31. [PMID: 22664096 DOI: 10.1016/j.sbi.2012.05.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 01/30/2023]
Abstract
For over four decades, two competing mechanisms of ligand recognition--conformational selection and induced-fit--have dominated our interpretation of protein allostery. Defining the mechanism broadens our understanding of the system and impacts our ability to design effective drugs and new therapeutics. Recent kinetics studies demonstrate that trypsin-like proteases exist in equilibrium between two forms: one fully accessible to substrate (E) and the other with the active site occluded (E*). Analysis of the structural database confirms existence of the E* and E forms and vouches for the allosteric nature of the trypsin fold. Allostery in terms of conformational selection establishes an important paradigm in the protease field and enables protein engineers to expand the repertoire of proteases as therapeutics.
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Affiliation(s)
- Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
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19
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Pozzi N, Chen Z, Zapata F, Pelc LA, Barranco-Medina S, Di Cera E. Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation. Biochemistry 2011; 50:10195-202. [PMID: 22049947 DOI: 10.1021/bi2015019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prethrombin-2 is the immediate zymogen precursor of the clotting enzyme thrombin, which is generated upon cleavage at R15 and separation of the A chain and catalytic B chain. The X-ray structure of prethrombin-2 determined in the free form at 1.9 Å resolution shows the 215-217 segment collapsed into the active site and occluding 49% of the volume available for substrate binding. Remarkably, some of the crystals harvested from the same crystallization well, under identical solution conditions, diffract to 2.2 Å resolution in the same space group but produce a structure in which the 215-217 segment moves >5 Å and occludes 24% of the volume available for substrate binding. The two alternative conformations of prethrombin-2 have the side chain of W215 relocating >9 Å within the active site and are relevant to the allosteric E*-E equilibrium of the mature enzyme. Another unanticipated feature of prethrombin-2 bears on the mechanism of prothrombin activation. R15 is found buried within the protein in ionic interactions with E14e, D14l, and E18, thereby making its exposure to solvent necessary for proteolytic attack and conversion to thrombin. On the basis of this structural observation, we constructed the E14eA/D14lA/E18A triple mutant to reduce the level of electrostatic coupling with R15 and promote zymogen activation. The mutation causes prethrombin-2 to spontaneously convert to thrombin, without the need for the snake venom ecarin or the physiological prothrombinase complex.
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Affiliation(s)
- Nicola Pozzi
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
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Shea MA, Correia JJ, Brenowitz MD. Introduction: twenty five years of the Gibbs Conference on Biothermodynamics. Biophys Chem 2011; 159:1-5. [PMID: 21840113 DOI: 10.1016/j.bpc.2011.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 07/05/2011] [Indexed: 11/16/2022]
Abstract
In 2011, the Gibbs Conference on Biothermodynamics will celebrate its 25th anniversary. Since the inaugural meeting in 1987, it has brought together laboratories that lived, breathed and argued about the molecular logic of macromolecular machines. The participants have a deep commitment to understanding the nature of physico-chemical forces that govern regulation of biological systems, and share a passion for applying linkage theory. The collective goal is to understand how ligand binding, subunit assembly and conformational change drive what we observe as physiological processes such as regulated transport, enzyme cascades, gene regulation, membrane permeability, viral infection, intracellular trafficking and folding of macromolecules. In this special issue, articles by former organizers of the Gibbs Conference showcase the current breadth and depth of the field of biothermodynamics, and how thoroughly it is integrated with the study of macromolecular structures, computational modeling and physiological studies of human health and disease.
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Allostery in trypsin-like proteases suggests new therapeutic strategies. Trends Biotechnol 2011; 29:577-85. [PMID: 21726912 DOI: 10.1016/j.tibtech.2011.06.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/19/2011] [Accepted: 06/02/2011] [Indexed: 11/21/2022]
Abstract
Trypsin-like proteases (TLPs) are a large family of enzymes responsible for digestion, blood coagulation, fibrinolysis, development, fertilization, apoptosis and immunity. A current paradigm posits that the irreversible transition from an inactive zymogen to the active protease form enables productive interaction with substrate and catalysis. Analysis of the entire structural database reveals two distinct conformations of the active site: one fully accessible to substrate (E) and the other occluded by the collapse of a specific segment (E*). The allosteric E*-E equilibrium provides a reversible mechanism for activity and regulation in addition to the irreversible zymogen to protease conversion and points to new therapeutic strategies aimed at inhibiting or activating the enzyme. In this review, we discuss relevant examples, with emphasis on the rational engineering of anticoagulant thrombin mutants.
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