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Learte-Aymamí S, Martínez-Castro L, González-González C, Condeminas M, Martin-Malpartida P, Tomás-Gamasa M, Baúlde S, Couceiro JR, Maréchal JD, Macias MJ, Mascareñas JL, Vázquez ME. De Novo Engineering of Pd-Metalloproteins and Their Use as Intracellular Catalysts. JACS AU 2024; 4:2630-2639. [PMID: 39055146 PMCID: PMC11267534 DOI: 10.1021/jacsau.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 07/27/2024]
Abstract
The development of transition metal-based catalytic platforms that promote bioorthogonal reactions inside living cells remains a major challenge in chemical biology. This is particularly true for palladium-based catalysts, which are very powerful in organic synthesis but perform poorly in the cellular environment, mainly due to their rapid deactivation. We now demonstrate that grafting Pd(II) complexes into engineered β-sheets of a model WW domain results in cell-compatible palladominiproteins that effectively catalyze depropargylation reactions inside HeLa cells. The concave shape of the WW domain β-sheet proved particularly suitable for accommodating the metal center and protecting it from rapid deactivation in the cellular environment. A thorough NMR and computational study confirmed the formation of the metal-stapled peptides and allowed us to propose a three-dimensional structure for this novel metalloprotein motif.
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Affiliation(s)
- Soraya Learte-Aymamí
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Laura Martínez-Castro
- Insilichem,
Departament de Química, Universitat
Autónoma de Barcelona, Cerdanyola 08193, Spain
| | - Carmen González-González
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Miriam Condeminas
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, Barcelona 08028, Spain
- Academic
institutional affiliation:Department of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS-UPF), Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Pau Martin-Malpartida
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, Barcelona 08028, Spain
| | - María Tomás-Gamasa
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Sandra Baúlde
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - José R. Couceiro
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Jean-Didier Maréchal
- Insilichem,
Departament de Química, Universitat
Autónoma de Barcelona, Cerdanyola 08193, Spain
| | - Maria J. Macias
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, Barcelona 08028, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - José L. Mascareñas
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - M. Eugenio Vázquez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15705, Spain
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2
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Marchese D, Guislain F, Pringels T, Bridoux L, Rezsohazy R. A poly-histidine motif of HOXA1 is involved in regulatory interactions with cysteine-rich proteins. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:194993. [PMID: 37952572 DOI: 10.1016/j.bbagrm.2023.194993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/05/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Homopolymeric amino acid repeats are found in about 24 % of human proteins and are over-represented in transcriptions factors and kinases. Although relatively rare, homopolymeric histidine repeats (polyH) are more significantly found in proteins involved in the regulation of embryonic development. To gain a better understanding of the role of polyH in these proteins, we used a bioinformatic approach to search for shared features in the interactomes of polyH-containing proteins in human. Our analysis revealed that polyH protein interactomes are enriched in cysteine-rich proteins and in proteins containing (a) cysteine repeat(s). Focusing on HOXA1, a HOX transcription factor displaying one long polyH motif, we identified that the polyH motif is required for the HOXA1 interaction with such cysteine-rich proteins. We observed a correlation between the length of the polyH repeat and the strength of the HOXA1 interaction with one Cys-rich protein, MDFI. We also found that metal ion chelators disrupt the HOXA1-MDFI interaction supporting that such metal ions are required for the interaction. Furthermore, we identified three polyH interactors which down-regulate the transcriptional activity of HOXA1. Taken together, our data point towards the involvement of polyH and cysteines in regulatory interactions between proteins, notably transcription factors like HOXA1.
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Affiliation(s)
- Damien Marchese
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - Florent Guislain
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Place Croix du Sud 5 (L7.07.10), B-1348 Louvain-la-Neuve, Belgium.
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3
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Ding Y, Huang J. DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. J Phys Chem Lett 2024; 15:616-627. [PMID: 38198685 DOI: 10.1021/acs.jpclett.3c03158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling.
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Affiliation(s)
- Ye Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
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4
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Aduriz-Arrizabalaga J, Lopez X, De Sancho D. Atomistic molecular simulations of Aβ-Zn conformational ensembles. Proteins 2024; 92:134-144. [PMID: 37746887 DOI: 10.1002/prot.26590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
The amyloid-forming Aβ peptide is able to interact with metal cations to form very stable complexes that influence fibril formation and contribute to the onset of Alzheimer's disease. Multiple structures of peptides derived from Aβ in complex with different metals have been resolved experimentally to provide an atomic-level description of the metal-protein interactions. However, Aβ is intrinsically disordered, and hence more amenable to an ensemble description. Molecular dynamics simulations can now reach the timescales needed to generate ensembles for these type of complexes. However, this requires accurate force fields both for the protein and the protein-metal interactions. Here we use state-of-the-art methods to generate force field parameters for the Zn(II) cations in a set of complexes formed by different Aβ variants and combine them with the Amber99SB*-ILDN optimized force field. Upon comparison of NMR experiments with the simulation results, further optimized with a Bayesian/Maximum entropy approach, we provide an accurate description of the molecular ensembles for most Aβ-metal complexes. We find that the resulting conformational ensembles are more heterogeneous than the NMR models deposited in the Protein Data Bank.
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Affiliation(s)
- Julen Aduriz-Arrizabalaga
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
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5
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Scrima S, Tiberti M, Ryde U, Lambrughi M, Papaleo E. Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140921. [PMID: 37230374 DOI: 10.1016/j.bbapap.2023.140921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
Molecular dynamics (MD) simulations are a powerful approach to studying the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging. NPL4 is a zinc-binding protein and works as a cofactor for p97 to regulate protein homeostasis. NPL4 is of biomedical importance and has been proposed as the target of disulfiram, a drug recently repurposed for cancer treatment. Experimental studies proposed that the disulfiram metabolites, bis-(diethyldithiocarbamate)‑copper and cupric ions, induce NPL4 misfolding and aggregation. However, the molecular details of their interactions with NPL4 and consequent structural effects are still elusive. Here, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. We examined different sets of non-bonded parameters because we want to study the misfolding mechanism and cannot rule out that the zinc may detach from the protein during the process and copper replaces it. We investigated the force-field ability to model the coordination geometry of the metal ions by comparing the results from MD simulations with optimized geometries from quantum mechanics (QM) calculations using model systems of NPL4. Furthermore, we investigated the performance of a force field including bonded parameters to treat copper ions in NPL4 that we obtained based on QM calculations.
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Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Ulf Ryde
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark.
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Maksudov F, Kliuchnikov E, Pierson D, Ujwal M, Marx KA, Chanda A, Barsegov V. Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:631-647. [PMID: 36910708 PMCID: PMC9996446 DOI: 10.1016/j.omtn.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | | | - Daniel Pierson
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | | | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
| | - Arani Chanda
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
- Corresponding author: Arani Chanda, Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
- Corresponding author: Valeri Barsegov, Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.
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7
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Nagarajan H, Vetrivel U. Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach. J Biomol Struct Dyn 2022; 40:11758-11770. [PMID: 34402752 DOI: 10.1080/07391102.2021.1965030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Early growth response-1 (Egr1) is a zinc-finger transcription factor that plays a critical role in controlling cell growth, proliferation, differentiation, angiogenesis, and apoptosis. Egr1 is induced by many growth factors, cytokines, and stress signals and is also known to be involved in several pathological conditions like cancer, neurological and ocular disorders. The DNA binding domain of Egr1 is a highly conserved Cys2His2 (C2H2) zinc finger (ZNF) domain which specifically binds to GC-rich consensus sequence GcG (G/T) GGGCG and activates transcription. As the C2H2 domain specifically recognizes its DNA target, the mutations spanning this region shall perturb DNA recognition and may hinder transcription of target genes. Therefore, in this study, the missense mutations occurring specifically at the DNA binding domain (DBD) of Egr1 were probed by computational approaches involving in silico screening of pathogenic and functional mutants coupled with extensive molecular dynamics simulations, to determine the mutants that affect its structural stability and interactions with DNA. From the pathogenicity analysis of 38 missense mutations spanning Egr1-DBD, 17 were predicted as pathogenic, and 7 amongst these were found to have functional impact on Egr1. On combined analysis of molecular dynamics simulation, Residue interaction analysis and Egr1-DNA interaction analysis results, the mutants R371C and R375C showed least impact, whilst, H382R tend to increase the structural stability, whereas R360H, H390R, E393V, and H414Y conferred greater impact by altering the structural stability and DNA interactions. Hence, this study exposes the prospects of considering these 4 deleterious mutations for clinical significance, but needs further experimental validation.HighlightsEgr1's DNA binding domain is a highly conserved Cys2His2 (C2H2) zinc finger domain that specifically recognizes its DNA target.Mutations spanning in the DNA binding domain shall perturb DNA recognition and may hinder transcription.Among the missense mutations, mutants R360H, H390R, E393V, and H414Y were inferred to have a greater impact on Egr1 by altering the structural stability and DNA interactions.
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Affiliation(s)
- Hemavathy Nagarajan
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India.,National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research (Govt. of India), Belagavi, Karnataka, India
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Kluska K, Chorążewska A, Peris-Díaz MD, Adamczyk J, Krężel A. Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains. Int J Mol Sci 2022; 23:ijms232314602. [PMID: 36498928 PMCID: PMC9735795 DOI: 10.3390/ijms232314602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability.
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Guan X, Tan C, Li W, Wang W, Thirumalai D. Role of water-bridged interactions in metal ion coupled protein allostery. PLoS Comput Biol 2022; 18:e1010195. [PMID: 35653400 PMCID: PMC9197054 DOI: 10.1371/journal.pcbi.1010195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/14/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca2+ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca2+ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca2+ binding and protein allostery. The bridging water molecules between Ca2+ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca2+ coupled protein allostery. Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca2+ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery. Natural proteins often utilize allostery in executing a variety of functions. Metal ions are typical cofactors to trigger the allosteric cascade. In this work, using the Ca2+ sensor protein calmodulin as the model system, we revealed crucial roles of water-bridged interactions in the metal ion coupled protein allostery. The coordination of the Ca2+ to the binding site involves an intermediate in which the water molecule bridges the Ca2+ and the liganding residue. The bridging water reduces the free energy barrier height of ligand exchange, therefore facilitating the ligand exchange and allosteric coupling by acting as a lubricant. We also showed that the response of the two symmetrically arranged EF-hand motifs of CaM domains upon Ca2+ binding is asymmetric, which is directly attributed to the differing dehydration process of the Ca2+ ions and is needed for efficient allosteric communication.
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Affiliation(s)
- Xingyue Guan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Cheng Tan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- * E-mail: (WL); (WW); (DT)
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- * E-mail: (WL); (WW); (DT)
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Texas, United States of America
- * E-mail: (WL); (WW); (DT)
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10
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Zinc transporters ZIPT-2.4 and ZIPT-15 are required for normal C. elegans fecundity. J Assist Reprod Genet 2022; 39:1261-1276. [PMID: 35501415 DOI: 10.1007/s10815-022-02495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/11/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The requirement of zinc for the development and maturation of germ lines and reproductive systems is deeply conserved across evolution. The nematode Caenorhabditis elegans offers a tractable platform to study the complex system of distributing zinc to the germ line. We investigated several zinc importers to investigate how zinc transporters play a role in the reproductive system in nematodes, as well as establish a platform to study zinc transporter biology in germline and reproductive development. METHODS Previous high throughput transcriptional datasets as well as phylogenetic analysis identified several putative zinc transporters that have a function in reproduction in worms. Phenotypic analysis of CRISPR-generated knockouts and tags included characterization of offspring output, gonad development, and protein localization. Light and immunofluorescence microscopy allowed for visualization of physiological and molecular effects of zinc transporter mutations. RESULTS Disruption of two zinc transporters, ZIPT-2.4 and ZIPT-15, was shown to lead to defects in reproductive output. A mutation in zipt-2.4 has subtle effects on reproduction, while a mutation in zipt-15 has a clear impact on gonad and germline development that translates into a more pronounced defect in fecundity. Both transporters have germline expression, as well as additional expression in other cell types. CONCLUSIONS Two ZIP-family zinc transporter orthologs of human ZIP6/10 and ZIP1/2/3 proteins are important for full reproductive fecundity and participate in development of the gonad. Notably, these zinc transporters are present in gut and reproductive tissues in addition to the germ line, consistent with a complex zinc trafficking network important for reproductive success.
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Esposito S, D’Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G. Host and Viral Zinc-Finger Proteins in COVID-19. Int J Mol Sci 2022; 23:ijms23073711. [PMID: 35409070 PMCID: PMC8998646 DOI: 10.3390/ijms23073711] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
An unprecedented effort to tackle the ongoing COVID-19 pandemic has characterized the activity of the global scientific community over the last two years. Hundreds of published studies have focused on the comprehension of the immune response to the virus and on the definition of the functional role of SARS-CoV-2 proteins. Proteins containing zinc fingers, both belonging to SARS-CoV-2 or to the host, play critical roles in COVID-19 participating in antiviral defenses and regulation of viral life cycle. Differentially expressed zinc finger proteins and their distinct activities could thus be important in determining the severity of the disease and represent important targets for drug development. Therefore, we here review the mechanisms of action of host and viral zinc finger proteins in COVID-19 as a contribution to the comprehension of the disease and also highlight strategies for therapeutic developments.
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13
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Su Z, Li T, Wu D, Wu Y, Li G. Recent Progress on Single-Molecule Detection Technologies for Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:458-469. [PMID: 34985271 DOI: 10.1021/acs.jafc.1c06808] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rapid and sensitive detection technologies for food contaminants play vital roles in food safety. Due to the complexity of the food matrix and the trace amount distribution, traditional methods often suffer from unsatisfying accuracy, sensitivity, or specificity. In past decades, single-molecule detection (SMD) has emerged as a way to realize the rapid and ultrasensitive measurement with low sample consumption, showing a great potential in food contaminants detection. For instance, based on the nanopore technique, simple and effective methods for single-molecule analysis of food contaminants have been developed. To our knowledge, there has been a rare review that focuses on SMD techniques for food safety. The present review attempts to cover some typical SMD methods in food safety, including electrochemistry, optical spectrum, and atom force microscopy. Then, recent applications of these techniques for detecting food contaminants such as biotoxins, pesticides, heavy metals, and illegal additives are reviewed. Finally, existing research challenges and future trends of SMD in food safety are also tentatively proposed.
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Affiliation(s)
- Zhuoqun Su
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Tong Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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14
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Lella M, Mahalakshmi R. De novo
design of metal‐binding cleft in a
Trp‐Trp
stapled thermostable β‐hairpin peptide. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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15
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Unveiling the N-Terminal Homodimerization of BCL11B by Hybrid Solvent Replica-Exchange Simulations. Int J Mol Sci 2021; 22:ijms22073650. [PMID: 33807484 PMCID: PMC8036541 DOI: 10.3390/ijms22073650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/28/2023] Open
Abstract
Transcription factors play a crucial role in regulating biological processes such as cell growth, differentiation, organ development and cellular signaling. Within this group, proteins equipped with zinc finger motifs (ZFs) represent the largest family of sequence-specific DNA-binding transcription regulators. Numerous studies have proven the fundamental role of BCL11B for a variety of tissues and organs such as central nervous system, T cells, skin, teeth, and mammary glands. In a previous work we identified a novel atypical zinc finger domain (CCHC-ZF) which serves as a dimerization interface of BCL11B. This domain and formation of the dimer were shown to be critically important for efficient regulation of the BCL11B target genes and could therefore represent a promising target for novel drug therapies. Here, we report the structural basis for BCL11B-BCL11B interaction mediated by the N-terminal ZF domain. By combining structure prediction algorithms, enhanced sampling molecular dynamics and fluorescence resonance energy transfer (FRET) approaches, we identified amino acid residues indispensable for the formation of the single ZF domain and directly involved in forming the dimer interface. These findings not only provide deep insight into how BCL11B acquires its active structure but also represent an important step towards rational design or selection of potential inhibitors.
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16
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Zhang H, Zhang H, Chen C. Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9. Proteins 2021; 89:832-844. [PMID: 33576138 DOI: 10.1002/prot.26062] [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: 10/07/2020] [Revised: 01/04/2021] [Accepted: 01/31/2021] [Indexed: 11/10/2022]
Abstract
Protein folding is a popular topic in the life science. However, due to the limited sampling ability of experiments and simulations, the general folding mechanism is not yet clear to us. In this work, we study the folding of the N-terminal domain of ribosomal protein L9 (NTL9) in detail by a mixing replica exchange molecular dynamics method. The simulation results are close to previous experimental observations. According to the Markov state model, the folding of the protein follows a nucleation-condensation path. Moreover, after the comparison to its 39-residue β-α-β motif, we find that the helix at the C-terminal has a great influence on the folding process of the intact protein, including the nucleation of the key residues in the transition state ensemble and the packing of the hydrophobic residues in the native state.
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Affiliation(s)
- Haozhe Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Haomiao Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, China
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17
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Wang Z, Zhou X, Zuo G. EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space. Front Mol Biosci 2020; 7:589718. [PMID: 33195438 PMCID: PMC7653181 DOI: 10.3389/fmolb.2020.589718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/24/2020] [Indexed: 11/27/2022] Open
Abstract
The transition network provides a key to reveal the thermodynamic and kinetic properties of biomolecular systems. In this paper, we introduce a new method, named effective energy rescaling space trajectory mapping (EspcTM), to detect metastable states and construct transition networks based on the simulation trajectories of the complex biomolecular system. It mapped simulation trajectories into an orthogonal function space, whose bases were rescaled by effective energy, and clustered the interrelation between these trajectories to locate metastable states. By using the EspcTM method, we identified the metastable states and elucidated interstate transition kinetics of a Brownian particle and a dodecapeptide. It was found that the scaling parameters of effective energy also provided a clue to the dominating factors in dynamics. We believe that the EspcTM method is a useful tool for the studies of dynamics of the complex system and may provide new insight into the understanding of thermodynamics and kinetics of biomolecular systems.
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Affiliation(s)
- Zhenyu Wang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guanghong Zuo
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
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18
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Substitution of the Native Zn(II) with Cd(II), Co(II) and Ni(II) Changes the Downhill Unfolding Mechanism of Ros87 to a Completely Different Scenario. Int J Mol Sci 2020; 21:ijms21218285. [PMID: 33167398 PMCID: PMC7663847 DOI: 10.3390/ijms21218285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
The structural effects of zinc replacement by xenobiotic metal ions have been widely studied in several eukaryotic and prokaryotic zinc-finger-containing proteins. The prokaryotic zinc finger, that presents a bigger βββαα domain with a larger hydrophobic core with respect to its eukaryotic counterpart, represents a valuable model protein to study metal ion interaction with metallo-proteins. Several studies have been conducted on Ros87, the DNA binding domain of the prokaryotic zinc finger Ros, and have demonstrated that the domain appears to structurally tolerate Ni(II), albeit with important structural perturbations, but not Pb(II) and Hg(II), and it is in vitro functional when the zinc ion is replaced by Cd(II). We have previously shown that Ros87 unfolding is a two-step process in which a zinc binding intermediate converts to the native structure thorough a delicate downhill folding transition. Here, we explore the folding/unfolding behaviour of Ros87 coordinated to Co(II), Ni(II) or Cd(II), by UV-Vis, CD, DSC and NMR techniques. Interestingly, we show how the substitution of the native metal ion results in complete different folding scenarios. We found a two-state unfolding mechanism for Cd-Ros87 whose metal affinity Kd is comparable to the one obtained for the native Zn-Ros87, and a more complex mechanism for Co-Ros87 and Ni-Ros87, that show higher Kd values. Our data outline the complex cross-correlation between the protein-metal ion equilibrium and the folding mechanism proposing such an interplay as a key factor in the proper metal ion selection by a specific metallo-protein.
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19
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Roozbahani GM, Chen X, Zhang Y, Wang L, Guan X. Nanopore detection of metal ions: Current status and future directions. SMALL METHODS 2020; 4:2000266. [PMID: 33365387 PMCID: PMC7751931 DOI: 10.1002/smtd.202000266] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Indexed: 05/27/2023]
Abstract
In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.
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Affiliation(s)
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- The University of Chinese Academy of Science, Beijing, 100049, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
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20
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Yoon C, Lee D, Lee SJ. Regulation of the Central Dogma through Bioinorganic Events with Metal Coordination for Specific Interactions. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chungwoon Yoon
- Department of Chemistry Institute for Molecular Biology and Genetics, Jeonbuk National University Jeonju 54896 Republic of Korea
| | - Dong‐Heon Lee
- Department of Chemistry Institute for Molecular Biology and Genetics, Jeonbuk National University Jeonju 54896 Republic of Korea
| | - Seung Jae Lee
- Department of Chemistry Institute for Molecular Biology and Genetics, Jeonbuk National University Jeonju 54896 Republic of Korea
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21
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Zmuda F, Chamberlain LH. Regulatory effects of post-translational modifications on zDHHC S-acyltransferases. J Biol Chem 2020; 295:14640-14652. [PMID: 32817054 PMCID: PMC7586229 DOI: 10.1074/jbc.rev120.014717] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
The human zDHHC S-acyltransferase family comprises 23 enzymes that mediate the S-acylation of a multitude of cellular proteins, including channels, receptors, transporters, signaling molecules, scaffolds, and chaperones. This reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usually derived from palmitoyl-CoA, to specific cysteine residues on target proteins, which affects their stability, localization, and function. These outcomes are essential to control many processes, including synaptic transmission and plasticity, cell growth and differentiation, and infectivity of viruses and other pathogens. Given the physiological importance of S-acylation, it is unsurprising that perturbations in this process, including mutations in ZDHHC genes, have been linked to different neurological pathologies and cancers, and there is growing interest in zDHHC enzymes as novel drug targets. Although zDHHC enzymes control a diverse array of cellular processes and are associated with major disorders, our understanding of these enzymes is surprisingly incomplete, particularly with regard to the regulatory mechanisms controlling these enzymes. However, there is growing evidence highlighting the role of different PTMs in this process. In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiquitination, affect the stability, localization, and function of zDHHC enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies. Developing a better understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the intracellular dynamics of S-acylation and may also highlight novel approaches to modulate S-acylation for clinical gain.
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Affiliation(s)
- Filip Zmuda
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
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22
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Klein F, Cáceres D, Carrasco MA, Tapia JC, Caballero J, Alzate-Morales J, Pantano S. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. J Chem Inf Model 2020; 60:3935-3943. [DOI: 10.1021/acs.jcim.0c00160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florencia Klein
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Daniela Cáceres
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Mónica A. Carrasco
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Juan Carlos Tapia
- Escuela de Medicina, Universidad de Talca, 1 Poniente 1141, Talca 3460000, Chile
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingenierı́a, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Talca 3460000, Chile
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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23
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Rao SR, Horne WS. Proteomimetic Zinc Finger Domains with Modified Metal-binding β-Turns. Pept Sci (Hoboken) 2020; 112. [PMID: 33733039 DOI: 10.1002/pep2.24177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mimicry of protein tertiary folds by chains artificial in backbone chemical composition leads to proteomimetic analogues with potential utility as bioactive agents and as tools to shed light on biomacromolecule behavior. Notable successes toward such molecules have been achieved; however, as protein structural diversity is vast, design principles must be continually honed as they are applied to new prototype folding patterns. One specific structure where a gap remains in understanding how to effectively generate modified backbone analogues is the metal-binding β-turn found in zinc finger domains. Literature precedent suggests several factors that may act in concert, including the artificial moiety used to modify the turn, the sequence in which it is applied, and modifications present elsewhere in the domain. Here, we report efforts to gain insights into these issues and leverage these insights to construct a zinc finger mimetic with backbone modifications throughout its constituent secondary structures. We first conduct a systematic comparison of four turn mimetics in a common host sequence, quantifying relative efficacy for use in a metal-binding context. We go on to construct a proteomimetic zinc finger domain in which the helix, strands, and turn are simultaneously modified, resulting in a variant with 23% artificial residues, a tertiary fold indistinguishable from the prototype, and a folded stability comparable to the natural backbone on which the variant is based. Collectively, the results reported provide new insights into the effects of backbone modification on structure and stability of metal-binding domains and help inform the design of metalloprotein mimetics.
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Affiliation(s)
- Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
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24
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Padjasek M, Kocyła A, Kluska K, Kerber O, Tran JB, Krężel A. Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains. J Inorg Biochem 2020; 204:110955. [DOI: 10.1016/j.jinorgbio.2019.110955] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022]
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25
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Nguyen LH, Tran TT, Truong LTN, Mai HH, Nguyen TT. Overcharging of the Zinc Ion in the Structure of the Zinc-Finger Protein Is Needed for DNA Binding Stability. Biochemistry 2020; 59:1378-1390. [DOI: 10.1021/acs.biochem.9b01055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ly H. Nguyen
- Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 120000, Vietnam
| | - Tuyen T. Tran
- Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 120000, Vietnam
| | - Lien Thi Ngoc Truong
- Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hai Ba Trung District, Hanoi 112400, Vietnam
| | - Hanh Hong Mai
- Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 120000, Vietnam
| | - Toan T. Nguyen
- Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 120000, Vietnam
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26
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Kluska K, Peris-Díaz MD, Płonka D, Moysa A, Dadlez M, Deniaud A, Bal W, Krężel A. Formation of highly stable multinuclear Ag nS n clusters in zinc fingers disrupts their structure and function. Chem Commun (Camb) 2020; 56:1329-1332. [PMID: 31912071 DOI: 10.1039/c9cc09418k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Silver (Ag(i)) binding to consensus zinc fingers (ZFs) causes Zn(ii) release inducing a gradual disruption of the hydrophobic core, followed by an overall conformational change and formation of highly stable AgnSn clusters. A compact eight-membered Ag4S4 structure formed by a CCCC ZF is the first cluster example reported for a single biological molecule. Ag(i)-induced conformational changes of ZFs can, as a consequence, affect transcriptional regulation and other cellular processes.
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Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Manuel D Peris-Díaz
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Dawid Płonka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Alexander Moysa
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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27
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Zhang H, Gong Q, Zhang H, Chen C. Combining the biased and unbiased sampling strategy into one convenient free energy calculation method. J Comput Chem 2019; 40:1806-1815. [PMID: 30942500 DOI: 10.1002/jcc.25834] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/15/2019] [Accepted: 03/17/2019] [Indexed: 12/14/2022]
Abstract
Constructing a free energy landscape for a large molecule is difficult. One has to use either a high temperature or a strong driving force to enhance the sampling on the free energy barriers. In this work, we propose a mixed method that combines these two kinds of acceleration strategies into one simulation. First, it applies an adaptive biasing potential to some replicas of the molecule. These replicas are particularly accelerated in a collective variable space. Second, it places some unbiased and exchangeable replicas at various temperature levels. These replicas generate unbiased sampling data in the canonical ensemble. To improve the sampling efficiency, biased replicas transfer their state variables to the unbiased replicas after equilibrium by Monte Carlo trial moves. In comparison to previous integrated methods, it is more convenient for users. It does not need an initial reference biasing potential to guide the sampling of the molecule. And it is also unnecessary to insert many replicas for the requirement of passing the free energy barriers. The free energy calculation is accomplished in a single stage. It samples the data as fast as a biased simulation and it processes the data as simple as an unbiased simulation. The method provides a minimalist approach to the construction of the free energy landscape. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Haomiao Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qiankun Gong
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Haozhe Zhang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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28
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Chen K, Li W, Wang J, Wang W. Binding of Copper Ions with Octapeptide Region in Prion Protein: Simulations with Charge Transfer Model. J Phys Chem B 2019; 123:5216-5228. [PMID: 31242743 DOI: 10.1021/acs.jpcb.9b02457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper ions are important cofactors of many metalloproteins. The binding dynamics of proteins to the copper ion is important for biological functions but is less understood at the microscopic level. What are the key factors determining the recognition and the stabilization of the copper ion during the binding? Our work investigates the binding dynamics of the copper ion with a simple system (the N-terminus of PrP) using simulation methods. To precisely characterize the protein?ion interaction, we build up an effective copper?peptide force field based on quantum chemistry calculations. In our model, the effects of charge transfer, protonation/deprotonation, and induced polarization are considered. With this force field, we successfully characterize the local structures and the complex interactions of the octapeptide around the copper ion. Furthermore, using an enhanced sampling method, the binding/unbinding processes of the copper ion with the octapeptide are simulated. Free-energy landscapes are generated in consequence, and multiple binding pathways are characterized. It is observed that various native ligands contribute differently to the binding processes. Some residues are related to the capture of the ion (behaving like ?arm?s), and some others contribute to the stabilization of the coordination structure (acting like ?core?s). These different interactions induce various pathways. Besides, a nonnative binding ligand is determined, and it has essential contributions and modulations to the binding pathways. With all these results, the picture of copper?octapeptide binding is outlined. These features are believed to happen in many ion?peptide interactions, such as the cooperative stabilization between the coordinations with neighboring backbone nitrogens and an auxiliary intermediate coordination with the neighboring oxygen from the N-terminal direction. We believe that our studies are valuable to understand the complicated ion?peptide binding processes.
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Affiliation(s)
- Ke Chen
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Jun Wang
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, and School of Physics , Nanjing University , Nanjing 210093 , P.R. China
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29
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Strodel B, Coskuner-Weber O. Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies. J Chem Inf Model 2019; 59:1782-1805. [PMID: 30933519 DOI: 10.1021/acs.jcim.8b00983] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monomers and oligomers of the amyloid-β peptide aggregate to form the fibrils found in the brains of Alzheimer's disease patients. These monomers and oligomers are largely disordered and can interact with transition metal ions, affecting the mechanism and kinetics of amyloid-β aggregation. Due to the disordered nature of amyloid-β, its rapid aggregation, as well as solvent and paramagnetic effects, experimental studies face challenges in the characterization of transition metal ions bound to amyloid-β monomers and oligomers. The details of the coordination chemistry between transition metals and amyloid-β obtained from experiments remain debated. Furthermore, the impact of transition metal ion binding on the monomeric or oligomeric amyloid-β structures and dynamics are still poorly understood. Computational chemistry studies can serve as an important complement to experimental studies and can provide additional knowledge on the binding between amyloid-β and transition metal ions. Many research groups conducted first-principles calculations, ab initio molecular dynamics simulations, quantum mechanics/classical mechanics simulations, and classical molecular dynamics simulations for studying the interplay between transition metal ions and amyloid-β monomers and oligomers. This review summarizes the current understanding of transition metal interactions with amyloid-β obtained from computational chemistry studies. We also emphasize the current view of the coordination chemistry between transition metal ions and amyloid-β. This information represents an important foundation for future metal ion chelator and drug design studies aiming to combat Alzheimer's disease.
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Affiliation(s)
- Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , Jülich 52425 , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , Düsseldorf 40225 , Germany
| | - Orkid Coskuner-Weber
- Molecular Biotechnology , Turkish-German University , Sahinkaya Caddesi, No. 86, Beykoz , Istanbul 34820 , Turkey
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Kluska K, Adamczyk J, Krężel A. Metal binding properties of zinc fingers with a naturally altered metal binding site. Metallomics 2019; 10:248-263. [PMID: 29230465 DOI: 10.1039/c7mt00256d] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc fingers (ZFs) are among the most abundant motifs found in proteins, and are commonly known for their structural role. Classical ZFs (CCHH) are part of the transcription factors that participate in DNA binding. Although biochemical studies of classical ZFs have a long history, there is limited knowledge about the sequential and structural diversity of ZFs. We have found that classical ZFs, with metal binding sites consisting of amino acids other than conserved Cys or His residues, are frequently encoded in the human genome, and we refer to these peptides as ZFs with a naturally altered metal binding site. The biological role of the altered ZFs remains undiscovered. In this study, we characterized nine natural XCHH, CXHH, CCXH and CCHX ZFs in terms of their Zn(ii) and Co(ii) binding properties, such as complex stoichiometry, spectroscopic properties and metal-to-peptide affinity. We revealed that XCHH and CXHH ZFs form ML complexes that are 4-5 orders of magnitude weaker in comparison to CCHH ZFs. Nevertheless, spectroscopic studies demonstrate that, depending on the altered position, they may adopt an open coordination geometry with one or two water molecules bound to a central metal ion, which has not been demonstrated in natural ZFs before. Stability data show that both CCXH and CCHX peptides have high Zn(ii) affinity (with a Kd of 10-9 to 10-11 M), suggesting their potential biological function. This study is a comprehensive overview of the relationship between the sequence, structure, and stability of ZFs.
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Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Abstract
Zinc ion binding is a principal event in the achievement of the correct fold in classical zinc finger domains since the motif is largely unfolded in the absence of metal. In the case of a prokaryotic zinc finger, the larger βββαα domain contributes to the folding mechanism with a larger hydrophobic core. For these reasons, following the great amount of attention devoted to unveiling the effect of xenobiotic metal ion replacement in zinc fingers and in zinc-containing proteins in general, the prokaryotic zinc finger domain appears to be an interesting model for studying metal ion interaction with metalloproteins. Here, we explore the binding of Ni(II), Hg(II), and Pb(II) to Ros87, the DNA binding domain of the prokaryotic zinc finger protein Ros. We measured Ros87-metal ion dissociation constants and monitored the effects on the structure and function of the domain. Interestingly, we found that the protein folds in the presence of Ni(II) with important structural perturbations, while in the presence of Pb(II) and Hg(II) it does not appear to be significantly folded. Accordingly, an overall strong reduction in the DNA binding capability is observed for all of the examined proteins. Our data integrate and complement the information collected in the past few years concerning the functional and structural effects of metal ion substitution in classical zinc fingers in order to contribute to a better comprehension of the toxicity of these metals in biological systems.
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32
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Zhao D, Huang Z, Liu J, Ma L, He J. Expression, purification, and characterization of N-terminal His-tagged proteins with mutations in zinc finger 3 of zinc finger protein ZNF191(243-368). Prep Biochem Biotechnol 2018; 48:914-919. [PMID: 30296200 DOI: 10.1080/10826068.2018.1514518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc finger protein ZNF191(243-368), the zinc finger region of ZNF191, is potentially associated with cell proliferation in hepatocellular carninoma. A His-tag expression system was used to express and purify proteins with mutations in the zinc finger 3 of ZNF191(243-368) for analysis of protein properties, structure, and functions. The purification of the His-tag fusion proteins was simpler and faster than that of the ZNF191(243-368) inclusion bodies. The properties and structures of the His-tag fusion mutant proteins were investigated using spectrographic techniques and DNA hydrolysis experiment. The His6-tag system could be used to express ZNF191(243-368). The presence of the His6-tag at the N-terminus of ZNF191(243-368) did not evidently affect its properties and structure. However, the site-directed mutations in zinc finger 3 affected the structure of the protein. The DNA hydrolase activity of His6-ZF-F3/H4 suggested that four histidines in zinc finger 3 might form a structure similar to that of the active center in a hydrolase. This work reports that continuous histidines need to form a certain structure for specific functions, and provides new insights into the design of an artificial nuclease.
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Affiliation(s)
- Dongxin Zhao
- a College of Chemistry, Chemical and Environmental Engineering , Henan University of Technology , Zhengzhou , Henan , China
| | - Zhongxian Huang
- b Department of Chemistry , Fudan University , Shanghai , China
| | - Jie Liu
- a College of Chemistry, Chemical and Environmental Engineering , Henan University of Technology , Zhengzhou , Henan , China
| | - Li Ma
- a College of Chemistry, Chemical and Environmental Engineering , Henan University of Technology , Zhengzhou , Henan , China
| | - Juan He
- a College of Chemistry, Chemical and Environmental Engineering , Henan University of Technology , Zhengzhou , Henan , China
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33
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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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34
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Liu C, Zhang Y, Zhang J, Wang J, Li W, Wang W. Interplay between translational diffusion and large-amplitude angular jumps of water molecules. J Chem Phys 2018; 148:184502. [DOI: 10.1063/1.5017935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chao Liu
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yangyang Zhang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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35
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Ren W, Ji D, Xu X. Metal cofactor modulated folding and target recognition of HIV-1 NCp7. PLoS One 2018; 13:e0196662. [PMID: 29715277 PMCID: PMC5929515 DOI: 10.1371/journal.pone.0196662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 nucleocapsid 7 (NCp7) plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3) recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.
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Affiliation(s)
- Weitong Ren
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Dongqing Ji
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Xiulian Xu
- School of Physical Science and Technology, Yangzhou University, Yangzhou 225002, China
- * E-mail:
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36
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Nedjoua D, Krallafa AM. Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus. Comput Biol Chem 2018; 74:86-93. [PMID: 29567490 DOI: 10.1016/j.compbiolchem.2018.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/28/2017] [Accepted: 03/07/2018] [Indexed: 11/18/2022]
Abstract
Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC.
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Affiliation(s)
- Drici Nedjoua
- LCPM, Department of Chemistry, University of Oran 1 Ahmed Benbella, PO Box 1524, El m'naouer, Oran, 31000, Algeria.
| | - Abdelghani Mohamed Krallafa
- LCPM, Department of Chemistry, University of Oran 1 Ahmed Benbella, PO Box 1524, El m'naouer, Oran, 31000, Algeria.
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37
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Chen C. Constructing a multidimensional free energy surface like a spider weaving a web. J Comput Chem 2017; 38:2298-2306. [PMID: 28718973 DOI: 10.1002/jcc.24881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 01/13/2023]
Abstract
Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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38
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Srinivasan E, Rajasekaran R. Exploring the cause of aggregation and reduced Zn binding affinity by G85R mutation in SOD1 rendering amyotrophic lateral sclerosis. Proteins 2017; 85:1276-1286. [PMID: 28321933 DOI: 10.1002/prot.25288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 11/08/2022]
Abstract
Amyotrophic lateral sclerosis (ALS), a lethal neurodegenerative disorder is characterized by the degeneration of upper and lower motor neuron. ALS occurs due to various notably prominent missense mutations, in gene encoding Cu-Zn superoxide dismutase (SOD1) thereby leading to aggregation, dysfunction and reduced Zn binding affinity. In this study, one such mutation, G85R was explored in comparison with wild type SOD1, using discrete molecular dynamics (DMD). Accordingly, the conformational changes were significantly observed in mutant SOD1, through various geometrical parameters, which substantiated the difference in conformational deviation, flexibility and compactness, thus stipulating a root cause for aggregation. Followed by, analysis of essential dynamics further authenticated the cause behind the protein dysfunction. In particular, the high content of beta sheet with structural deviations, down to dysfunction was established in mutant as compared to wild type, while passing through secondary structure analysis. Subsequently, the deviation of distance in Zn binding residues was distinctly portrayed in mutant as compared to wild type, thus confirming the cause of reduced Zn binding affinity. In addition, the steered molecular dynamics analysis also authenticated the above results indicating the reduced Zn binding affinity in the mutant as compared to that of the wild type. Hence, this work revealed the theoretical mechanism to unravel the mutational effects of cofactor dependent protein. Proteins 2017; 85:1276-1286. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
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39
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Keightley MC, Carradice DP, Layton JE, Pase L, Bertrand JY, Wittig JG, Dakic A, Badrock AP, Cole NJ, Traver D, Nutt SL, McCoey J, Buckle AM, Heath JK, Lieschke GJ. The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase-like HHCC zinc finger. Nat Commun 2017; 8:14911. [PMID: 28382966 PMCID: PMC5384227 DOI: 10.1038/ncomms14911] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
In response to infection and injury, the neutrophil population rapidly expands and then quickly re-establishes the basal state when inflammation resolves. The exact pathways governing neutrophil/macrophage lineage outputs from a common granulocyte-macrophage progenitor are still not completely understood. From a forward genetic screen in zebrafish, we identify the transcriptional repressor, ZBTB11, as critical for basal and emergency granulopoiesis. ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1, and TP53 is one direct ZBTB11 transcriptional target. TP53 repression is dependent on ZBTB11 cys116, which is a functionally critical, metal ion-coordinating residue within a novel viral integrase-like zinc finger domain. To our knowledge, this is the first description of a function for this domain in a cellular protein. We demonstrate that the PU.1–ZBTB11–TP53 pathway is conserved from fish to mammals. Finally, Zbtb11 mutant rescue experiments point to a ZBTB11-regulated TP53 requirement in development of other organs. Neutrophils are increased in response to injury and infection but how they form from a common granulocyte-macrophage progenitor is unclear. Here, the authors identify a role for the transcriptional repressor ZBTB11 in zebrafish, which is regulated by master myeloid regulators and represses TP53.
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Affiliation(s)
- Maria-Cristina Keightley
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia.,The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Duncan P Carradice
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Judith E Layton
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.,Ludwig Institute for Cancer Research, Melbourne-Parkville Branch, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Luke Pase
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia.,The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Julien Y Bertrand
- Department of Pathology and Immunology, University of Geneva-CMU, 1211 Geneva 4, Switzerland
| | - Johannes G Wittig
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Aleksandar Dakic
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia
| | - Andrew P Badrock
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Nicholas J Cole
- Motor Neuron Disease Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - David Traver
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Julia McCoey
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Joan K Heath
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia.,Ludwig Institute for Cancer Research, Melbourne-Parkville Branch, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia.,The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.,Ludwig Institute for Cancer Research, Melbourne-Parkville Branch, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
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40
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Kochańczyk T, Nowakowski M, Wojewska D, Kocyła A, Ejchart A, Koźmiński W, Krężel A. Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly. Sci Rep 2016; 6:36346. [PMID: 27808280 PMCID: PMC5093744 DOI: 10.1038/srep36346] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/14/2016] [Indexed: 01/26/2023] Open
Abstract
The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.
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Affiliation(s)
- Tomasz Kochańczyk
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Michał Nowakowski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dominika Wojewska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Anna Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
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41
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Effect of His-Tag on Expression, Purification, and Structure of Zinc Finger Protein, ZNF191(243-368). Bioinorg Chem Appl 2016; 2016:8206854. [PMID: 27524954 PMCID: PMC4971304 DOI: 10.1155/2016/8206854] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/13/2016] [Accepted: 06/23/2016] [Indexed: 11/17/2022] Open
Abstract
Zinc finger proteins are associated with hereditary diseases and cancers. To obtain an adequate amount of zinc finger proteins for studying their properties, structure, and functions, many protein expression systems are used. ZNF191(243-368) is a zinc finger protein and can be fused with His-tag to generate fusion proteins such as His6-ZNF191(243-368) and ZNF191(243-368)-His8. The purification of His-tag protein using Ni-NTA resin can overcome the difficulty of ZNF191(243-368) separation caused by inclusion body formation. The influences of His-tag on ZNF191(243-368) properties and structure were investigated using spectrographic techniques and hydrolase experiment. Our findings suggest that insertion of a His-tag at the N-terminal or C-terminal end of ZNF191(243-368) has different effects on the protein. Therefore, an expression system should be considered based on the properties and structure of the protein. Furthermore, the hydrolase activity of ZNF191(243-368)-His8 has provided new insights into the design of biological functional molecules.
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42
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Berezovskaya Y, Porrini M, Nortcliffe C, Barran PE. The use of ion mobility mass spectrometry to assist protein design: a case study on zinc finger fold versus coiled coil interactions. Analyst 2016; 140:2847-56. [PMID: 25734188 DOI: 10.1039/c4an00427b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dramatic conformational change in zinc fingers on binding metal ions for DNA recognition makes their structure-function behaviour an attractive target to mimic in de novo designed peptides. Mass spectrometry, with its high throughput and low sample consumption provides insight into how primary amino acid sequence can encode stable tertiary fold. We present here the use of ion mobility mass spectrometry (IM-MS) coupled with molecular dynamics (MD) simulations as a rapid analytical platform to inform de novo design efforts for peptide-metal and peptide-peptide interactions. A dual peptide-based synthetic system, ZiCop based on a zinc finger peptide motif, and a coiled coil partner peptide Pp, have been investigated. Titration mass spectrometry determines the relative binding affinities of different divalent metal ions as Zn(2+) > Co(2+) ≫ Ca(2+). With collision induced dissociation (CID), we probe complex stability, and establish that peptide-metal interactions are stronger and more 'specific' than those of peptide-peptide complexes, and the anticipated hetero-dimeric complex is more stable than the two homo-dimers. Collision cross-sections (CCS) measurements by IM-MS reveal increased stability with respect to unfolding of the metal-bound peptide over its apo-form, and further, larger collision cross sections for the hetero-dimeric forms suggest that dimeric species formed in the absence of metal are coiled coil like. MD supports these structural assignments, backed up by data from visible light absorbance measurements.
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43
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Chen C, Huang Y. Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method. J Comput Chem 2016; 37:1565-75. [DOI: 10.1002/jcc.24371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modelling Group, School of Physics; Huazhong University of Science and Technology; Wuhan Hubei 430074 China
| | - Yanzhao Huang
- Biomolecular Physics and Modelling Group, School of Physics; Huazhong University of Science and Technology; Wuhan Hubei 430074 China
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Zheng S, Tang Q, He J, Du S, Xu S, Wang C, Xu Y, Lin F. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems. J Chem Inf Model 2016; 56:811-8. [PMID: 26998926 DOI: 10.1021/acs.jcim.5b00687] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Qing Tang
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Jian He
- Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Shahekou, Dalian, Liaoning 116023, P. R. China
| | - Shiyu Du
- Engineering Laboratory of Specialty Fibers and Nuclear Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , 519 Zhuangshi Avenue, Zhenhai, Ningbo, Zhejiang 315201, P. R. China
| | - Shaofang Xu
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Chaojie Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, P. R. China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
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45
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He E, Yan G, Zhang J, Wang J, Li W. Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine. J Biol Phys 2016; 42:247-58. [PMID: 26759163 DOI: 10.1007/s10867-015-9405-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/18/2015] [Indexed: 11/28/2022] Open
Abstract
Each amino acid has its intrinsic propensity for certain local backbone conformations, which can be further modulated by the physicochemical environment and post-translational modifications. In this work, we study the effects of phosphorylation on the intrinsic propensity for different local backbone conformations of serine/threonine by molecular dynamics simulations. We showed that phosphorylation has very different effects on the intrinsic propensity for certain local backbone conformations for the serine and threonine. The phosphorylation of serine increases the propensity of forming polyproline II, whereas that of threonine has the opposite effect. Detailed analysis showed that such different responses to phosphorylation mainly arise from their different perturbations to the backbone hydration and the geometrical constraints by forming side-chain-backbone hydrogen bonds due to phosphorylation. Such an effect of phosphorylation on backbone conformations can be crucial for understanding the molecular mechanism of phosphorylation-regulated protein structures/dynamics and functions.
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Affiliation(s)
- Erbin He
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China.,Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China
| | - Guanghui Yan
- Department of Mathematics and Physics, Nanjing Institute of Technology, Nanjing, 211167, People's Republic of China
| | - Jian Zhang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China.,Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China
| | - Jun Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China. .,Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China.
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, People's Republic of China. .,Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, People's Republic of China.
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46
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Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
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47
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Yan Z, Wang J. Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect. Proteins 2015; 83:1632-42. [PMID: 26111900 DOI: 10.1002/prot.24848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/03/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Solvation effect is an important factor for protein-ligand binding in aqueous water. Previous scoring function of protein-ligand interactions rarely incorporates the solvation model into the quantification of protein-ligand interactions, mainly due to the immense computational cost, especially in the structure-based virtual screening, and nontransferable application of independently optimized atomic solvation parameters. In order to overcome these barriers, we effectively combine knowledge-based atom-pair potentials and the atomic solvation energy of charge-independent implicit solvent model in the optimization of binding affinity and specificity. The resulting scoring functions with optimized atomic solvation parameters is named as specificity and affinity with solvation effect (SPA-SE). The performance of SPA-SE is evaluated and compared to 20 other scoring functions, as well as SPA. The comparative results show that SPA-SE outperforms all other scoring functions in binding affinity prediction and "native" pose identification. Our optimization validates that solvation effect is an important regulator to the stability and specificity of protein-ligand binding. The development strategy of SPA-SE sets an example for other scoring function to account for the solvation effect in biomolecular recognitions.
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Affiliation(s)
- Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun, Jilin, 130022, China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun, Jilin, 130022, China.,Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, New York, 11794-3400, USA
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48
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Liu L, Wade RC, Heermann DW. A multiscale approach to simulating the conformational properties of unbound multi-C₂H₂ zinc finger proteins. Proteins 2015; 83:1604-15. [PMID: 26062035 DOI: 10.1002/prot.24845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/18/2015] [Accepted: 06/03/2015] [Indexed: 12/25/2022]
Abstract
The conformational properties of unbound multi-Cys2 His2 (mC2H2) zinc finger proteins, in which zinc finger domains are connected by flexible linkers, are studied by a multiscale approach. Three methods on different length scales are utilized. First, atomic detail molecular dynamics simulations of one zinc finger and its adjacent flexible linker confirmed that the zinc finger is more rigid than the flexible linker. Second, the end-to-end distance distributions of mC2H2 zinc finger proteins are computed using an efficient atomistic pivoting algorithm, which only takes excluded volume interactions into consideration. The end-to-end distance distribution gradually changes its profile, from left-tailed to right-tailed, as the number of zinc fingers increases. This is explained by using a worm-like chain model. For proteins of a few zinc fingers, an effective bending constraint favors an extended conformation. Only for proteins containing more than nine zinc fingers, is a somewhat compacted conformation preferred. Third, a mesoscale model is modified to study both the local and the global conformational properties of multi-C2H2 zinc finger proteins. Simulations of the CCCTC-binding factor (CTCF), an important mC2H2 zinc finger protein for genome spatial organization, are presented.
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Affiliation(s)
- Lei Liu
- Institute for Theoretical Physics Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing Heidelberg University, Heidelberg, Germany
| | - Rebecca C Wade
- Interdisciplinary Center for Scientific Computing Heidelberg University, Heidelberg, Germany.,Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Dieter W Heermann
- Institute for Theoretical Physics Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing Heidelberg University, Heidelberg, Germany.,Shanghai Institute of Biological Sciences Chinese Academy of Science, Shanghai, People's Republic of China
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49
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Chen C, Xiao Y, Huang Y. Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052708. [PMID: 26066200 DOI: 10.1103/physreve.91.052708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Indexed: 06/04/2023]
Abstract
Replica-exchange molecular dynamics (REMD) is a popular sampling method in the molecular simulation. By frequently exchanging the replicas at different temperatures, the molecule can jump out of the minima and sample efficiently in the conformational space. Although REMD has been shown to be practical in a lot of applications, it does have a critical limitation. All the replicas at all the temperatures must be simulated for a period between the replica-exchange steps. This may be problematic for the reaction with high free energy barriers. In that case, too many replicas are required in the simulation. To reduce the calculation quantity and improve its performance, in this paper we propose a modified REMD method. During the simulation, each replica at each temperature can stay in either the active or inactive state and only switch between the states at the exchange step. In the active state, the replica moves freely in the canonical ensemble by the normal molecular dynamics, and in the inactive state, the replica is frozen temporarily until the next exchange step. The number of the replicas in the active states (active replicas) depends on the number of CPUs in the computer. Using the additional inactive replicas, one can perform an REMD simulation in a wider temperature space. The practical applications show that the modified REMD method is reliable. With the same number of active replicas, this REMD method can produce a more reasonable free energy surface around the free energy minima than the standard REMD method.
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Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yanzhao Huang
- Biomolecular Physics and Modelling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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50
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Li W, Wang J, Zhang J, Wang W. Molecular simulations of metal-coupled protein folding. Curr Opin Struct Biol 2015; 30:25-31. [DOI: 10.1016/j.sbi.2014.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/24/2014] [Accepted: 11/24/2014] [Indexed: 01/22/2023]
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