1
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Roy C, Islam RNU, Banerjee S, Bandyopadhyay AK. Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one. J Biomol Struct Dyn 2023:1-16. [PMID: 38147414 DOI: 10.1080/07391102.2023.2295972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chittran Roy
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
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2
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Gao S, Campbell JX, Oas TG, Franz KJ. Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics. Inorg Chem 2023; 62:7087-7096. [PMID: 37083393 DOI: 10.1021/acs.inorgchem.3c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide's biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M-1 and a buffer-independent association constant of ∼6 × 106 M-1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy-entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn-Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.
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Affiliation(s)
- Sean Gao
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Joanna X Campbell
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G Oas
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Katherine J Franz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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3
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Hajdu B, Hunyadi-Gulyás É, Kato K, Kawaguchi A, Nagata K, Gyurcsik B. Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA. J Biol Inorg Chem 2023; 28:301-315. [PMID: 36820987 PMCID: PMC10036435 DOI: 10.1007/s00775-023-01988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
Zinc finger proteins specifically recognize DNA sequences and, therefore, play a crucial role in living organisms. In this study the Zn(II)-, and DNA-binding of 1MEY#, an artificial zinc finger protein consisting of three finger units was characterized by multiple methods. Fluorimetric, circular dichroism and isothermal calorimetric titrations were applied to determine the accurate stability constant of a zinc finger protein. Assuming that all three zinc finger subunits behave identically, the obtained thermodynamic data for the Zn(II) binding were ΔHbinding site = - (23.5 - 28.0) kcal/mol (depending on the applied protonation state of the cysteines) and logβ'pH 7.4 = 12.2 ± 0.1, being similar to those of the CP1 consensus zinc finger peptide. The specific DNA binding of the protein can be characterized by logβ'pH 7.4 = 8.20 ± 0.08, which is comparable to the affinity of the natural zinc finger proteins (Sp1, WT1, TFIIIA) toward DNA. This value is ~ 1.9 logβ' unit higher than those determined for semi- or nonspecific DNA binding. Competitive circular dichroism and electrophoretic mobility shift measurements revealed that the conditional stability constant characteristic for Zn(II) binding of 1MEY# protein increased by 3.4 orders of magnitude in the presence of its target DNA sequence.
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Affiliation(s)
- Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary.
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4
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Grazioso R, García-Viñuales S, D'Abrosca G, Baglivo I, Pedone PV, Milardi D, Fattorusso R, Isernia C, Russo L, Malgieri G. The change of conditions does not affect Ros87 downhill folding mechanism. Sci Rep 2020; 10:21067. [PMID: 33273582 PMCID: PMC7713307 DOI: 10.1038/s41598-020-78008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/19/2020] [Indexed: 11/20/2022] Open
Abstract
Downhill folding has been defined as a unique thermodynamic process involving a conformations ensemble that progressively loses structure with the decrease of protein stability. Downhill folders are estimated to be rather rare in nature as they miss an energetically substantial folding barrier that can protect against aggregation and proteolysis. We have previously demonstrated that the prokaryotic zinc finger protein Ros87 shows a bipartite folding/unfolding process in which a metal binding intermediate converts to the native structure through a delicate barrier-less downhill transition. Significant variation in folding scenarios can be detected within protein families with high sequence identity and very similar folds and for the same sequence by varying conditions. For this reason, we here show, by means of DSC, CD and NMR, that also in different pH and ionic strength conditions Ros87 retains its partly downhill folding scenario demonstrating that, at least in metallo-proteins, the downhill mechanism can be found under a much wider range of conditions and coupled to other different transitions. We also show that mutations of Ros87 zinc coordination sphere produces a different folding scenario demonstrating that the organization of the metal ion core is determinant in the folding process of this family of proteins.
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Affiliation(s)
- Rinaldo Grazioso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | | | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Danilo Milardi
- Institute of Crystallography-CNR, Via Paolo Gaifami 18, 95126, Catania, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy.
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy.
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5
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Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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6
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Fox JM, Zhao M, Fink MJ, Kang K, Whitesides GM. The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition. Annu Rev Biophys 2018; 47:223-250. [DOI: 10.1146/annurev-biophys-070816-033743] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.
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Affiliation(s)
- Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA
| | - Mengxia Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Michael J. Fink
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104, Republic of Korea
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA
- The Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
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7
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Besold AN, Widger LR, Namuswe F, Michalek JL, Michel SLJ, Goldberg DP. Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1). MOLECULAR BIOSYSTEMS 2016; 12:1183-93. [PMID: 26936488 DOI: 10.1039/c5mb00796h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(II). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(II)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(II) and Co(II) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(II) and Zn(II) and a pentacoordinate geometry for Co(II)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(II)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(II)-CP-1(CAHH) and Co(II)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(II) complexes.
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Affiliation(s)
- Angelique N Besold
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
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8
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Yang C, Zhang S, Bai Z, Hou S, Wu D, Huang J, Zhou P. A two-step binding mechanism for the self-binding peptide recognition of target domains. MOLECULAR BIOSYSTEMS 2016; 12:1201-13. [DOI: 10.1039/c5mb00800j] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By using state-of-the-art molecular dynamics to reconstruct the complete structural dynamics picture of self-binding peptides, a two-step binding mechanism was proposed, including a fast, nonspecific diffusive phase and a slow, specific organizational phase.
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Affiliation(s)
- Chao Yang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Shilei Zhang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Zhengya Bai
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Shasha Hou
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Di Wu
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Jian Huang
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
| | - Peng Zhou
- Center of Bioinformatics (COBI)
- School of Life Science and Technology
- University of Electronic Science and Technology of China (UESTC)
- Chengdu 610054
- China
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9
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Palmieri M, Russo L, Malgieri G, Esposito S, Baglivo I, Rivellino A, Farina B, de Paola I, Zaccaro L, Milardi D, Isernia C, Pedone PV, Fattorusso R. Deciphering the zinc coordination properties of the prokaryotic zinc finger domain: The solution structure characterization of Ros87 H42A functional mutant. J Inorg Biochem 2014; 131:30-6. [DOI: 10.1016/j.jinorgbio.2013.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/26/2022]
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10
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Palmieri M, Malgieri G, Russo L, Baglivo I, Esposito S, Netti F, Del Gatto A, de Paola I, Zaccaro L, Pedone PV, Isernia C, Milardi D, Fattorusso R. Structural Zn(II) Implies a Switch from Fully Cooperative to Partly Downhill Folding in Highly Homologous Proteins. J Am Chem Soc 2013; 135:5220-8. [DOI: 10.1021/ja4009562] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maddalena Palmieri
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Luigi Russo
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Sabrina Esposito
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Fortuna Netti
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Ivan de Paola
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Paolo V. Pedone
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Carla Isernia
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Danilo Milardi
- Institute of Biostructures and Bioimaging-CNR (Catania), Viale A. Doria 6, 95125
Catania, Italy
| | - Roberto Fattorusso
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
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11
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Movileanu L, Schiff EA. Entropy-enthalpy Compensation of Biomolecular Systems in Aqueous Phase: a Dry Perspective. MONATSHEFTE FUR CHEMIE 2012; 144:59-65. [PMID: 23976794 DOI: 10.1007/s00706-012-0839-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We survey thermodynamic measurements on processes involving biological macromolecules in aqueous solution, which illustrate well the ubiquitous phenomenon of entropy-enthalpy compensation. The processes include protein folding/unfolding and ligand binding/unbinding, with compensation temperatures varying by about 50 K around an average near 293 K. We show that incorporating both near-exact entropy-enthalpy compensation (due to solvent relaxation) and multi-excitation entropy (from vibrational quanta) leads to a compensation temperature in water of about 230 K. We illustrate a general procedure for subtracting solvent and environment-related terms to determine the bare Gibbs free energy changes of chemical processes.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, Syracuse, New York USA
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12
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King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MNL, Nalivaika EA, Özen A, Haliloǧlu T, Yılmaz NK, Schiffer CA. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. ACS Chem Biol 2012; 7:1536-46. [PMID: 22712830 DOI: 10.1021/cb300191k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug-resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5-15 kcal/mol, while losing only 1-3 kcal/mol in total binding free energy for any of six FDA-approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wild-type protease and another drug-resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug-resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design.
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Affiliation(s)
- Nancy M. King
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Moses Prabu-Jeyabalan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Rajintha M. Bandaranayake
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Ayşegül Özen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Türkan Haliloǧlu
- Polymer Research Center and Department
of Chemical Engineering, Bogazici University, TR-34342, Bebek, Istanbul, Turkey
| | - Neşe Kurt Yılmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
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13
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Michalek JL, Besold AN, Michel SLJ. Cysteine and histidine shuffling: mixing and matching cysteine and histidine residues in zinc finger proteins to afford different folds and function. Dalton Trans 2011; 40:12619-32. [PMID: 21952363 DOI: 10.1039/c1dt11071c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Zinc finger proteins utilize zinc for structural purposes: zinc binds to a combination of cysteine and histidine ligands in a tetrahedral coordination geometry facilitating protein folding and function. While much is known about the classical zinc finger proteins, which utilize a Cys(2)His(2) ligand set to coordinate zinc and fold into an anti-parallel beta sheet/alpha helical fold, there are thirteen other families of 'non-classical' zinc finger proteins for which relationships between metal coordination and protein structure/function are less defined. This 'Perspective' article focuses on two classes of these non-classical zinc finger proteins: Cys(3)His type zinc finger proteins and Cys(2)His(2)Cys type zinc finger proteins. These proteins bind zinc in a tetrahedral geometry, like the classical zinc finger proteins, yet they adopt completely different folds and target different oligonucleotides. Our current understanding of the relationships between ligand set, metal ion, fold and function for these non-classical zinc fingers is discussed.
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Affiliation(s)
- Jamie L Michalek
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, USA
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14
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Quintal SM, dePaula QA, Farrell NP. Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences. Metallomics 2011; 3:121-39. [PMID: 21253649 DOI: 10.1039/c0mt00070a] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.
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Affiliation(s)
- Susana M Quintal
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main St., Richmond, VA 23284-2006, USA
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15
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Sénèque O, Latour JM. Coordination Properties of Zinc Finger Peptides Revisited: Ligand Competition Studies Reveal Higher Affinities for Zinc and Cobalt. J Am Chem Soc 2010; 132:17760-74. [DOI: 10.1021/ja104992h] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Olivier Sénèque
- Laboratoire de Chimie et Biologie des Métaux, CEA/iRTSV/LCBM, UMR 5249 CNRS/Université Joseph Fourier/CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble, France
| | - Jean-Marc Latour
- Laboratoire de Chimie et Biologie des Métaux, CEA/iRTSV/LCBM, UMR 5249 CNRS/Université Joseph Fourier/CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble, France
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16
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Abian O, Neira JL, Velazquez-Campoy A. Thermodynamics of zinc binding to hepatitis C virus NS3 protease: a folding by binding event. Proteins 2010; 77:624-36. [PMID: 19536779 DOI: 10.1002/prot.22475] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease is responsible for the processing of the non-structural region of the viral precursor polyprotein in infected hepatic cells. HCV NS3 is a zinc-dependent serine protease. The zinc ion, which is bound far away from the active site and considered to have a structural role, is essential for the structural integrity of the protein; furthermore, the ion is required for the hydrolytic activity. Consequently, the NS3 zinc binding site has been considered for a long time as a possible target for drug discovery. As a first step towards this goal, the energetics of the NS3-zinc interaction and its effect on the NS3 conformation must be established and discussed. The thermodynamic characterization of zinc binding to NS3 protease by isothermal titration calorimetry and spectroscopy is presented here. Spectroscopic and calorimetric results suggest that a considerable conformational change in the protein is coupled to zinc binding. The energetics of the conformational change is comparable to that of the folding of a protein of similar size. Therefore, zinc binding to NS3 protease can be considered as a "folding by binding" event.
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Affiliation(s)
- Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza 50009, Spain
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Ngu-Schwemlein M, Butko P, Cook B, Whigham T. Interactions of an acidic cyclooctapeptide with metal ions: microcalorimetric and fluorescence analyses. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1747-0285.2006.00335.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Klegerman ME, Zou Y, McPherson DD. Fibrin targeting of echogenic liposomes with inactivated tissue plasminogen activator. J Liposome Res 2008; 18:95-112. [PMID: 18569446 DOI: 10.1080/08982100802118482] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Fibrin-specific molecular targeting strategies are desirable for site-specific imaging and treatment of late stage atheroma, but fibrin-specific antibodies are difficult to produce and present immunogenicity problems. Tissue plasminogen activator (tPA) is an endogenous protein that has been shown to bind fibrin with high affinity and may circumvent antibody difficulties. Use of tPA-derived proteins or peptides, however, requires that the plasminogen-activating proteolytic activity be neutralized or removed. As an initial step in determining the feasibility of this targeting strategy, human recombinant tPA (Activase) was irreversibly inhibited with D-phe-L-pro-L-arg-chloromethyl ketone (PPACK) and conjugated to intrinsically echogenic liposomes (ELIP) by a thioether coupling protocol. Fibrin-binding affinities were assessed with a novel two-stage fibrin pad ELISA. We achieved 95-99% inactivation, while retaining both tPA fibrin-binding activities of K(D) approximately 2 nM and 33 nM. Thermodynamic analysis of the PPACK-inactivated tPA (tPA(P)) revealed highly exothermic interactions, indicative of ionic associations, especially for the higher affinity. The conjugation efficiency of tPA(P) to ELIP was within the range of that previously achieved for IgG and exhibited satisfactory fibrin targeting, characterized by striking increases of enthalpy and entropy increments. Evidence for coupling of noncovalent association energetics with the phosphatidylethanolamine major phase transition, observed in previous IgG antibody conjugations, was also evident in this case, but the nature of the transduction mechanism was different. These results demonstrate that tPA-derived components lacking proteolytic activity can be employed as fibrin-targeting agents for delivery of therapeutic and diagnostic formulations.
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Affiliation(s)
- Melvin E Klegerman
- Division of Cardiology, Department of Internal Medicine, University of Texas Health Science Center-Houston, Houston, TX 77030, USA.
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Ivanova E, Ball M, Lu H. Zinc binding of Tim10: Evidence for existence of an unstructured binding intermediate for a zinc finger protein. Proteins 2008; 71:467-75. [DOI: 10.1002/prot.21713] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Foulkes JE, Prabu-Jeyabalan M, Cooper D, Henderson GJ, Harris J, Swanstrom R, Schiffer CA. Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity. J Virol 2006; 80:6906-16. [PMID: 16809296 PMCID: PMC1489026 DOI: 10.1128/jvi.01900-05] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sequence variability associated with human immunodeficiency virus type 1 (HIV-1) is useful for inferring structural and/or functional constraints at specific residues within the viral protease. Positions that are invariant even in the presence of drug selection define critically important residues for protease function. While the importance of conserved active-site residues is easily understood, the role of other invariant residues is not. This work focuses on invariant Thr80 at the apex of the P1 loop of HIV-1, HIV-2, and simian immunodeficiency virus protease. In a previous study, we postulated, on the basis of a molecular dynamics simulation of the unliganded protease, that Thr80 may play a role in the mobility of the flaps of protease. In the present study, both experimental and computational methods were used to study the role of Thr80 in HIV protease. Three protease variants (T80V, T80N, and T80S) were examined for changes in structure, dynamics, enzymatic activity, affinity for protease inhibitors, and viral infectivity. While all three variants were structurally similar to the wild type, only T80S was functionally similar. Both T80V and T80N had decreased the affinity for saquinavir. T80V significantly decreased the ability of the enzyme to cleave a peptide substrate but maintained infectivity, while T80N abolished both activity and viral infectivity. Additionally, T80N decreased the conformational flexibility of the flap region, as observed by simulations of molecular dynamics. Taken together, these data indicate that HIV-1 protease functions best when residue 80 is a small polar residue and that mutations to other amino acids significantly impair enzyme function, possibly by affecting the flexibility of the flap domain.
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Affiliation(s)
- Jennifer E Foulkes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, 01605, USA
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Ababou A, Ladbury JE. Survey of the year 2004: literature on applications of isothermal titration calorimetry. J Mol Recognit 2005; 19:79-89. [PMID: 16220545 DOI: 10.1002/jmr.750] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The market for commercially available isothermal titration calorimeters continues to grow as new applications and methodologies are developed. Concomitantly the number of users (and abusers) increases dramatically, resulting in a steady increase in the number of publications in which isothermal titration calorimetry (ITC) plays a role. In the present review, we will focus on areas where ITC is making a significant contribution and will highlight some interesting applications of the technique. This overview of papers published in 2004 also discusses current issues of interest in the development of ITC as a tool of choice in the determination of the thermodynamics of molecular recognition and interaction.
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Affiliation(s)
- Abdessamad Ababou
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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Abstract
The metal binding properties of peptides corresponding to metal-binding sites spanning regions that normally function as linkers in tandem arrays of metal-binding domain-containing proteins were examined. For a peptide with two His residues from one TFIIIA-like zinc finger domain, a canonical TFIIIA-like linker, and two Cys residues from an adjacent zinc domain, the dissociation constant for the 1:1 peptide to cobalt(II) was found to be 15 +/- 10 microM, compared with 60 nM for the corresponding zinc finger domains themselves. Peptides overlapping two sets of metal-binding domains from human TRAF (tumor necrosis factor receptor-associated factor) proteins were examined. In one case, the affinity of the presumed metal-binding domain and that for the linker region were comparable, while in the second case, the affinity of the linker peptide was higher than that for the corresponding presumed metal-binding domain peptide. These studies revealed that cobalt(II) affinities in the micromolar range can occur even for peptides that do not correspond to natural zinc-binding domains and that the degree of distinction between authentic metal-binding domains and the corresponding linker-spanning peptides may be modest, at least for single domain peptide models.
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Affiliation(s)
- Karen R Thickman
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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