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Araujo-Abad S, Rizzuti B, Vidal M, Abian O, Fárez-Vidal ME, Velazquez-Campoy A, de Juan Romero C, Neira JL. Unveiling the Binding between the Armadillo-Repeat Domain of Plakophilin 1 and the Intrinsically Disordered Transcriptional Repressor RYBP. Biomolecules 2024; 14:561. [PMID: 38785968 PMCID: PMC11117474 DOI: 10.3390/biom14050561] [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: 04/11/2024] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Plakophilin 1 (PKP1), a member of the p120ctn subfamily of the armadillo (ARM)-repeat-containing proteins, is an important structural component of cell-cell adhesion scaffolds although it can also be ubiquitously found in the cytoplasm and the nucleus. RYBP (RING 1A and YY1 binding protein) is a multifunctional intrinsically disordered protein (IDP) best described as a transcriptional regulator. Both proteins are involved in the development and metastasis of several types of tumors. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with RYBP by using in cellulo methods, namely immunofluorescence (IF) and proximity ligation assay (PLA), and in vitro biophysical techniques, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), and isothermal titration calorimetry (ITC). We also characterized the binding of the two proteins by using in silico experiments. Our results showed that there was binding in tumor and non-tumoral cell lines. Binding in vitro between the two proteins was also monitored and found to occur with a dissociation constant in the low micromolar range (~10 μM). Finally, in silico experiments provided additional information on the possible structure of the binding complex, especially on the binding ARM-PKP1 hot-spot. Our findings suggest that RYBP might be a rescuer of the high expression of PKP1 in tumors, where it could decrease the epithelial-mesenchymal transition in some cancer cells.
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Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador;
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy;
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain;
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain;
- Instituto de Investigación Biomédica IBS, Granada, Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l’Almazara 11, 03203 Elche, Spain
| | - José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
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Sun K, Nguyen CV, Nguyen NN, Ma X, Nguyen AV. Crucial roles of ion-specific effects in the flotation of water-soluble KCl and NaCl crystals with fatty acid salts. J Colloid Interface Sci 2023; 636:413-424. [PMID: 36640552 DOI: 10.1016/j.jcis.2023.01.038] [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: 10/14/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
HYPOTHESIS Flotation of water-soluble KCl and NaCl minerals in brines is significant for K-fertilizer production, but its mechanism is controversial. Dissolved salt ions are expected to change the physicochemical properties of solvents, interfaces, and collector colloids, thereby affecting flotation significantly. EXPERIMENTS Flotation experiments of KCl and NaCl crystals in brines were conducted using potassium and sodium laurates as collectors. Contact angle (CA) and surface tension measurements, X-ray photoelectron spectroscopy (XPS) analysis, and molecular dynamics simulations (MD) were applied to gain a molecular understanding of changing interfacial properties and crystal-collector colloid interactions in the presence of dissolved ions in terms of salt flotation. FINDINGS While K+ ions activate the NaCl crystal flotation, Na+ ions depress the KCl crystal flotation, in agreement with the studies of CA, XPS, and MD results with these crystals. XPS results showed no collector adsorption at crystal surfaces which is a requirement of conventional flotation and presents a new theoretical challenge. We argue the crucial role of ion specificity: Na-laurate colloids adsorb at the bubble surface as a monolayer but solvent-separated from KCl crystals, inhibiting their flotation, or in interactive contact with NaCl crystals, enhancing their flotation. Increasing K+ concentration weakens NaCl crystal hydration, increasing Na-laurate colloid attraction with crystals for better flotation. The Contact Interactive Collector Colloid (CICC) and Solvent-separated Interactive Collector Colloid (SICC) hydration states are critical to salt crystal flotation via collector colloid-crystal attraction by dispersion forces.
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Affiliation(s)
- Kangkang Sun
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cuong V Nguyen
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ngoc N Nguyen
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Xiaozhen Ma
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anh V Nguyen
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia.
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Neira JL, Rizzuti B, Araujo-Abad S, Abian O, Fárez-Vidal ME, Velazquez-Campoy A, de Juan Romero C. The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140868. [PMID: 36372391 DOI: 10.1016/j.bbapap.2022.140868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
Plakophilin 1 (PKP1), a member of the armadillo repeat family of proteins, is a key structural component of cell-cell adhesion scaffolds, although it can also be found in other cell locations, including the cytoplasm and the nucleus. PADI4 (peptidyl-arginine deiminase 4) is one of the human isoforms of a family of enzymes engaged in the conversion of arginine to citrulline, and is present in monocytes, macrophages, granulocytes, and in several types of cancer cells. It is the only family member observed both within the nucleus and the cytoplasm under ordinary conditions. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with PADI4, by using several biophysical methods, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), isothermal titration calorimetry (ITC), and molecular simulations; furthermore, binding was also tested by Western-blot (WB) analyses. Our results show that there was binding between the two proteins, with a dissociation constant in the low micromolar range (∼ 1 μM). Molecular modelling provided additional information on the possible structure of the binding complex, and especially on the binding hot-spot predicted for PADI4. This is the first time that the interaction between these two proteins has been described and studied. Our findings could be of importance to understand the development of tumors, where PKP1 and PADI4 are involved. Moreover, our findings pave the way to describe the formation of neutrophil extracellular traps (NETs), whose construction is modulated by PADI4, and which mediate the proteolysis of cell-cell junctions where PKP1 intervenes.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Salome Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, Loja, 110111 Loja, Ecuador
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; Instituto de Investigación Biomédica IBS, Granada, Spain; Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
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Fabijanczuk KC, Altalhi WAO, Aldajani AMO, Canty AJ, McLuckey SA, O'Hair RAJ. Ion-pairs as a gateway to transmetalation: aryl transfer from boron to nickel and magnesium. Dalton Trans 2022; 51:5699-5705. [PMID: 35323833 DOI: 10.1039/d2dt00746k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas-phase ion-ion reactions between tris-1,10-phenantholine metal dications, [(phen)3M]2+ (where M = Ni and Mg), and the tetraphenylborate anion yield the ion-pairs {[(phen)3M]2+[BPh4]-}+. The ion-pairs undergo transmetalation upon loss of a phen ligand to give the organometallic complexes [(phen)2M(Ph)]+. DFT calculations, used to determine the energy barriers for the transmetalation reactions and the hydrolysis reactions, are entirely consistent with the experimental results.
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Affiliation(s)
| | - Weam A O Altalhi
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Victoria 3010, Australia. .,Department of Chemistry, Prince Sattam Bin Abdulaziz University, Hotat Bani Tamim, 16511 Saudi Arabia
| | - Asma M O Aldajani
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Victoria 3010, Australia. .,Department of Chemistry, College of Science, University of Bisha, Bisha 61922, P.O. Box 551, Saudi Arabia
| | - Allan J Canty
- School of Physical Sciences - Chemistry, University of Tasmania, Private Bag 75, Hobart, Tasmania 7001, Australia
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Victoria 3010, Australia.
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5
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Bakhshandeh A, Frydel D, Levin Y. Reactive Monte Carlo simulations for charge regulation of colloidal particles. J Chem Phys 2022; 156:014108. [PMID: 34998334 DOI: 10.1063/5.0077956] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We use a reactive Monte Carlo simulation method and the primitive model of electrolyte to study acid-base equilibrium that controls charge regulation in colloidal systems. The simulations are performed in a semi-grand canonical ensemble in which colloidal suspension is in contact with a reservoir of salt and strong acid. The interior of colloidal particles is modeled as a low dielectric medium, different from the surrounding water. The effective colloidal charge is calculated for different numbers of surface acidic groups, pH, salt concentrations, and types of electrolyte. In the case of potassium chloride, the titration curves are compared with the experimental measurements obtained using potentiometric titration. A good agreement is found between simulations and experiments. In the case of lithium chloride, the specific ionic adsorption is taken into account through the partial dehydration of lithium ion.
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Affiliation(s)
- Amin Bakhshandeh
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Derek Frydel
- Department of Chemistry, Universidad Técnica Federico Santa María, Campus San Joaquin, 7820275 Santiago, Chile
| | - Yan Levin
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970 Porto Alegre, RS, Brazil
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6
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Rajamanikandan S, Soundarya S, Paramasivam A, Prabhu D, Jeyakanthan J, Ramasamy V. Computational identification of potential lead molecules targeting rho receptor of Neisseria gonorrhoeae. J Biomol Struct Dyn 2021; 40:6415-6425. [PMID: 33590810 DOI: 10.1080/07391102.2021.1885491] [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: 10/22/2022]
Abstract
Gonorrhea, one of the sexually transmitted disease caused by a gram negative diplococcus bacteria Neisseria gonorrhoeae. Rho protein is indispensable for bacterial viability due to its versatile functions in physiology apart from RNA dependent transcription termination. Based on conserved function and wider role in several cellular processes, inhibitors specifically targeting Rho proteins are largely in use these days to treat various bacterial infections. In this study, three dimensional structure of Rho protein was modeled using the template protein from E. coli and further the optimized model was simulated for 100 ns to understand the structural stability and compactness. Owing to the therapeutic potential of Rho, traditional structure-based virtual screening was applied to identify potential inhibitors for the selected target. Based on empirical glide scoring functions two potent lead molecules (ChemBridge_6121956 and ChemBridge_5232688) were selected from ChemBridge database. The pharmacokinetic properties of these lead molecules are within the permissible range. DFT descriptor revealed that the lead molecules are more reactive, which also supports the molecular docking studies. The stability of Rho and Rho-inhibitor complexes was studied using molecular dynamics simulation. Parameters include binding free energy calculation, RMSD, RMSF and hydrogen bond analysis depicts the stability of Rho and Rho-inhibitors throughout the simulation. Altogether, the identified lead molecules require further optimization towards the design and development of new antibiotics against N. gonorrhoeae.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Anandhi Paramasivam
- Department of Biotechnology and Bioinformatics, Bishop Herber College, Trichy, Tamil Nadu, India
| | - Dhamodharan Prabhu
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
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7
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Santofimia-Castaño P, Rizzuti B, Pey AL, Fárez-Vidal ME, Iovanna JL, Neira JL. Intrinsically disordered protein NUPR1 binds to the armadillo-repeat domain of Plakophilin 1. Int J Biol Macromol 2021; 170:549-560. [PMID: 33385445 DOI: 10.1016/j.ijbiomac.2020.12.193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/08/2020] [Accepted: 12/25/2020] [Indexed: 11/16/2022]
Abstract
Plakophilin 1 (PKP1), a member of the armadillo repeat family of proteins, is a scaffold component of desmosomes, which are key structural components for cell-cell adhesion. However, PKP1 can be also found in the nucleus of several cells. NUPR1 is an intrinsically disordered protein (IDP) that localizes throughout the whole cell, and intervenes in the development and progression of several cancers. In this work, we studied the binding between PKP1 and NUPR1 by using several in vitro biophysical techniques and in cellulo approaches. The interaction occurred with an affinity in the low micromolar range (~10 μM), and involved the participation of at least one of the tryptophan residues of PKP1 (as shown by fluorescence and molecular docking). The binding region of NUPR1, mapped by NMR and molecular modelling, was a polypeptide patch at the 30s region of its sequence. The association between PKP1 and NUPR1 also occurred in cellulo and was localized in the nucleus, as tested by protein ligation assays (PLAs). We hypothesize that NUPR1 plays an active role in carcinogenesis modulating the function of PKP1.
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Affiliation(s)
- Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química aplicada a Biomedicina y Medio-Ambiente, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; Instituto de Investigación Biomédica IBS. Granada. Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France.
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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8
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Davies JA, Mugglestone M, Yang S, Ellis AM. IR Spectroscopy of the Cesium Iodide-Water Complex. J Phys Chem A 2020; 124:6528-6535. [PMID: 32687359 DOI: 10.1021/acs.jpca.0c05224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There has been much interest in I-(H2O) as a simple model for a hydrated iodide ion. Here we explore how this fundamental ion-solvent interaction is modified by the presence of a counterion, specifically Cs+. This has been achieved by forming the CsI(H2O) complex in superfluid helium nanodroplets and then probing this system using infrared spectroscopy. The complex retains the ionic hydrogen bond between the I- and a water OH group seen in I-(H2O), but the Cs+ ion substantially alters the anion-water interaction through formation of a cyclic Cs+-O-H-I- bonding motif. As with I-(H2O), the OH stretching band derived from the hydrogen-bonded OH group shows substructure, splitting into a clear doublet. However, in contrast to I-(H2O), where a tunneling splitting arising from hydrogen atom exchange plays a role, the doublet we observe is attributed solely to an anharmonic vibrational coupling effect.
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Affiliation(s)
- Julia A Davies
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Martin Mugglestone
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Shengfu Yang
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Andrew M Ellis
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
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9
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Yu B, Montgomery Pettitt B, Iwahara J. Experimental Evidence of Solvent-Separated Ion Pairs as Metastable States in Electrostatic Interactions of Biological Macromolecules. J Phys Chem Lett 2019; 10:7937-7941. [PMID: 31809050 PMCID: PMC6936746 DOI: 10.1021/acs.jpclett.9b03084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electrostatic interactions via ion pairs are vital for biological macromolecules. Regarding the free energy of each ion pair as a function of the interionic distance, continuum electrostatic models predict a single energy minimum corresponding to the contact ion-pair (CIP) state, whereas atomically detailed theoretical hydration studies predict multiple energy minima corresponding to the CIP and solvent-separated ion-pair (SIP) states. Through a statistical analysis of high-resolution crystal structures, we present experimental evidence of the SIP as a metastable state. The histogram of interionic distances between protein side-chain NH3+ and DNA phosphate groups clearly shows two major peaks corresponding to the CIP and SIP states. The statistical data are consistent with the probability distribution of the CIP-SIP equilibria previously obtained with molecular dynamics simulations. Spatial distributions of NH3+ ions and water molecules around phosphates reveal preferential sites for CIP and SIP formations and show how the ions compete with water molecules.
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10
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Disordered domains in chromatin-binding proteins. Essays Biochem 2019; 63:147-156. [PMID: 30940742 DOI: 10.1042/ebc20180068] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 02/08/2023]
Abstract
Chromatin comprises proteins, DNA and RNA, and its function is to condense and package the genome in a way that allows the necessary transactions such as transcription, replication and repair to occur in a highly organised and regulated manner. The packaging of chromatin is often thought of in a hierarchical fashion starting from the most basic unit of DNA packaging, the nucleosome, to the condensation of nucleosomal 'beads on a string' by linker histones to form the 30-nm fibre and eventually large chromatin domains. However, a picture of a more heterogeneous, dynamic and liquid-like assembly is emerging, in which intrinsically disordered proteins (IDPs) and proteins containing intrinsically disordered regions (IDRs) play a central role. Disorder features at all levels of chromatin organisation, from the histone tails, which are sites of extensive post-translational modification (PTM) that change the fate of the underlying genomic information, right through to transcription hubs, and the recently elucidated roles of IDPs and IDRs in the condensation of large regions of the genome through liquid-liquid phase separation.
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11
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Yang X, Wang M, Yang Y, Cui B, Xu Z, Yang X. Physical origin underlying the prenucleation-cluster-mediated nonclassical nucleation pathways for calcium phosphate. Phys Chem Chem Phys 2019; 21:14530-14540. [PMID: 30984939 DOI: 10.1039/c9cp00919a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The involvement of prenucleation clusters (PNCs) in crystallization from a supersaturated solution has been recently admitted within the framework of nonclassical nucleation theory; however, little is known about PNCs, at the quantitative level, for their formation mechanism and stability, the new phase formed by them, as well as their impact on nucleation barriers. Herein, using the sophisticated free energy calculations with a cumulative simulation time of over 5 μs, we identify a thermodynamically favored pathway of the PNC-mediated nucleation for calcium phosphate, starting with the ion pair association in solution. We demonstrate that such an ion association occurs not only between cations and anions, but also for the polyatomic species with charges of the same sign, which, in fact, leads to PNC formation via the consecutive coordination of the phosphate ions to calcium. The free energy decomposition calculations illustrate that the water phase is capable to either hinder or promote ion association for the abovementioned processes, and its specific role is intricately related to the characteristics of the hydration shell around calcium ions. The favorable interactions between the highly charged species play a crucial role in stabilizing the PNC complexes and the aggregates formed by PNCs. Furthermore, our present work reveals that the uptake of an extra calcium ion is the first and mandatory step to trigger PNC aggregation into amorphous calcium phosphate (ACP) by eliminating the related free energy barriers. Our theoretical study successfully provides quantitative explanations to a large set of experimental data in the field, which is currently under intense discussions associated with the nonclassical nucleation mechanism. The combination of computational methods developed in our present work offers a feasible and general solution to quantitatively and systematically study ion associations and crystal nucleation/growth in an aqueous solution at the atomic level, which are normally inaccessible to most of the existing experimental acquisitions.
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Affiliation(s)
- Xiao Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, China.
| | - Mingzhu Wang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, China.
| | - Yang Yang
- Department of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, PA 18015, USA
| | - Beiliang Cui
- Network Information Center, Nanjing Tech University, Nanjing 210009, China
| | - Zhijun Xu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, China.
| | - Xiaoning Yang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 210009, China.
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Niemann T, Zaitsau D, Strate A, Villinger A, Ludwig R. Cationic clustering influences the phase behaviour of ionic liquids. Sci Rep 2018; 8:14753. [PMID: 30283059 PMCID: PMC6170405 DOI: 10.1038/s41598-018-33176-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/19/2018] [Indexed: 11/17/2022] Open
Abstract
“Unlike charges attract, but like charges repel”. This conventional wisdom has been recently challenged for ionic liquids. It could be shown that like-charged ions attract each other despite the powerful opposing electrostatic forces. In principle, cooperative hydrogen bonding between ions of like-charge can overcome the repulsive Coulomb interaction while pushing the limits of chemical bonding. The key challenge of this solvation phenomenon is to establish design principles for the efficient formation of clusters of like-charged ions in ionic liquids. This is realised here for a set of well-suited ionic liquids including the same hydrophobic anion but different cations all equipped with hydroxyethyl groups for possible H-bonding. The formation of H-bonded cationic clusters can be controlled by the delocalization of the positive charge on the cations. Strongly localized charge results in cation-anion interaction, delocalized charge leads to the formation of cationic clusters. For the first time we can show, that the cationic clusters influence the properties of ILs. ILs comprising these clusters can be supercooled and form glasses. Crystalline structures are obtained only, if the ILs are dominantly characterized by the attraction between opposite-charged ions resulting in conventional ion pairs. That may open a new path for controlling glass formation and crystallization. The glass temperatures and the phase transitions of the ILs are observed by differential scanning calorimetry (DSC) and infrared (IR) spectroscopy.
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Affiliation(s)
- Thomas Niemann
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr. -Lorenz-Weg 2, 18059, Rostock, Germany
| | - Dimitri Zaitsau
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr. -Lorenz-Weg 2, 18059, Rostock, Germany
| | - Anne Strate
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr. -Lorenz-Weg 2, 18059, Rostock, Germany
| | - Alexander Villinger
- Universität Rostock, Institut für Chemie, Abteilung für Anorganische Chemie, Albert-Einstein-Str. 3a, 18059, Rostock, Germany
| | - Ralf Ludwig
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr. -Lorenz-Weg 2, 18059, Rostock, Germany. .,Department Life, Light & Matter, University of Rostock, 18051, Rostock, Germany. .,Leibniz-Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein-Str. 29a, 18059, Rostock, Germany.
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13
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Association of κ-carrageenan subjected to deep alkaline hydrolysis. Biopolymers 2018; 109:e23236. [DOI: 10.1002/bip.23236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/16/2018] [Accepted: 08/19/2018] [Indexed: 11/07/2022]
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14
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Nguyen D, Chen C, Pettitt BM, Iwahara J. NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics. Methods Enzymol 2018; 615:285-332. [PMID: 30638532 DOI: 10.1016/bs.mie.2018.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
NMR spectroscopy is a powerful tool for studying protein dynamics. Conventionally, NMR studies on protein dynamics have probed motions of protein backbone NH, side-chain aromatic, and CH3 groups. Recently, there has been remarkable progress in NMR methodologies that can characterize motions of cationic groups in protein side chains. These NMR methods allow investigations of the dynamics of positively charged lysine (Lys) and arginine (Arg) side chains and their hydrogen bonds as well as their electrostatic interactions important for protein function. Here, describing various practical aspects, we provide an overview of the NMR methods for dynamics studies of Lys and Arg side chains. Some example data on protein-DNA complexes are shown. We will also explain how molecular dynamics (MD) simulations can facilitate the interpretation of the NMR data on these basic side chains. Studies combining NMR and MD have revealed the highly dynamic nature of short-range electrostatic interactions via ion pairs, especially those involving Lys side chains.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Chuanying Chen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States.
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15
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Lysines and Arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions. Sci Rep 2018; 8:12289. [PMID: 30115951 PMCID: PMC6095893 DOI: 10.1038/s41598-018-30697-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/02/2018] [Indexed: 12/26/2022] Open
Abstract
Glycosaminoglycans (GAGs) bind a large array of proteins and mediate fundamental and diverse roles in human physiology. Ion pair interactions between protein lysines/arginines and GAG sulfates/carboxylates mediate binding. Neutrophil-activating chemokines (NAC) are GAG-binding proteins, and their sequences reveal high selectivity for lysines over arginines indicating they are functionally not equivalent. NAC binding to GAGs impacts gradient formation, receptor functions, and endothelial activation, which together regulate different components of neutrophil migration. We characterized the consequence of mutating lysine to arginine in NAC CXCL8, a well-characterized GAG-binding protein. We chose three lysines — two highly conserved lysines (K20 and K64) and a CXCL8-specific lysine (K67). Interestingly, the double K64R/K20R and K64R/K67R mutants are highly impaired in recruiting neutrophils in a mouse model. Further, both the mutants bind GAG heparin with higher affinity but show similar receptor activity. NMR and MD studies indicate that the structures are essentially identical to the WT, but the mutations alter the network of intramolecular ion pair interactions. These observations collectively indicate that the reduced in vivo recruitment is due to altered GAG interactions, higher GAG binding affinity can be detrimental, and specificity of lysines fine-tunes in vivo GAG interactions and function.
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16
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Mohorič T, Bren U. Microwave irradiation affects ion pairing in aqueous solutions of alkali halide salts. J Chem Phys 2018; 146:044504. [PMID: 28147548 DOI: 10.1063/1.4974759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water's rotational motion on the ion pairing of ionic solutes in aqueous solutions. The situation with rotational temperature higher than the translational one, Trot>Ttrs, is mimicking the non-equilibrium effects of microwaves on model solutions of alkali halide salts. The simulations reveal that an increase in the rotational temperature at constant translational temperature exerts significant changes in the structure of the solution. The latter are reflected in increased pairing of the oppositely charged ions, which can be explained by the weaker ability of rotationally excited water to screen and separate the opposite charges. It seems that Collins' law of matching water affinities retains its validity also in the non-equilibrium situation where the rotational temperature exceeds the translational one. On the other hand, the equilibrium effect (i.e., an increase in the solution's overall temperature T≡Trot = Ttrs) favors the formation of small-small (NaCl), while it has a little effect on large-large (CsI) ion pairs. This is in accordance with water becoming less polar solvent upon a temperature increase. Furthermore, we investigated the effects of excited translational motion of water (and ions) on the ion pairing by increasing the translational temperature, while keeping the rotational one unchanged (i.e., Ttrs>Trot). Interestingly, in certain cases the faster translational motion causes an increase in correlations. The temperature variations in the like-ion association constants, Kas++ and Kas--, are also examined. Here the situation is more complex but, in most cases, a decrease in the ion pairing is observed.
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Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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17
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Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M. Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations. Biochemistry 2018; 57:2796-2813. [PMID: 29664630 DOI: 10.1021/acs.biochem.8b00195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics and may, therefore, play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain/DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a nonconsensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.
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Affiliation(s)
- Jamie M Baird-Titus
- Department of Chemistry and Physical Sciences , Mount St. Joseph University , Cincinnati , Ohio 45233 , United States
| | - Mahendra Thapa
- Department of Physics , University of Cincinnati , Cincinnati , Ohio 45220 , United States
| | - Thomas Doerdelmann
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| | - Kelly A Combs
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
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18
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Affiliation(s)
| | - Shenda M. Baker
- Synedgen Inc.; 1420 N. Claremont Blvd., Suite 105D Claremont CA 91711 USA
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19
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Strate A, Overbeck V, Lehde V, Neumann J, Bonsa AM, Niemann T, Paschek D, Michalik D, Ludwig R. The influence of like-charge attraction on the structure and dynamics of ionic liquids: NMR chemical shifts, quadrupole coupling constants, rotational correlation times and failure of Stokes–Einstein–Debye. Phys Chem Chem Phys 2018; 20:5617-5625. [DOI: 10.1039/c7cp06454c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of clusters of like-charge influences the structure and dynamics of ionic liquids.
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Affiliation(s)
- Anne Strate
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Viviane Overbeck
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Viktoria Lehde
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Jan Neumann
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Anne-Marie Bonsa
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Thomas Niemann
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Dietmar Paschek
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Dirk Michalik
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
| | - Ralf Ludwig
- University of Rostock
- Institute for Chemistry
- Physical and Theoretical Chemistry
- Rostock
- Germany
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20
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Nguyen D, Hoffpauir ZA, Iwahara J. Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States. Biochemistry 2017; 56:5866-5869. [PMID: 29045141 PMCID: PMC5682595 DOI: 10.1021/acs.biochem.7b00885] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Basic side chains play crucial roles in protein-DNA interactions. In this study, using NMR spectroscopy, we investigated the dynamics of Arg and Lys side chains of the fruit fly Antennapedia homeodomain in the free state and in the complex with target DNA. We measured 15N relaxation for Arg and Lys side chains at two magnetic fields, from which generalized order parameters for the cationic groups were determined. Mobility of the R5 side chain, which makes hydrogen bonds with a thymine base in the DNA minor groove, was greatly dampened. Several Lys and Arg side chains that form intermolecular ion pairs with DNA phosphates were found to retain high mobility with the order parameter being <0.6 in the DNA-bound state. Interestingly, some of the interfacial cationic groups in the complex were more mobile than in the free protein. The retained or enhanced mobility of the Arg and Lys side chains in the complex should mitigate the overall loss of conformational entropy in the protein-DNA association and allow dynamic molecular recognition.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Zoe A. Hoffpauir
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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21
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Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein. J Mol Model 2017; 23:298. [PMID: 28956172 DOI: 10.1007/s00894-017-3471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
Abstract
Protein stability is known to be influenced by the presence of Hofmeister active ions in the solution. In addition to direct ion-protein interactions, this influence manifests through the local alterations of the interfacial water structure induced by the anions and cations present in this region. In our earlier works it was pointed out that the effects of Hofmeister active salts on the stability of Trp-cage miniprotein can be modeled qualitatively using non-polarizable force fields. These simulations reproduced the structure-stabilization and structure-destabilization effects of selected kosmotropic and chaotropic salts, respectively. In the present study we use the same model system to elucidate atomic processes behind the chaotropic destabilization and kosmotropic stabilization of the miniprotein. We focus on changes of the local hydration environment of the miniprotein upon addition of NaClO4 and NaF salts to the solution. The process is separated into two parts. In the first, 'promotion' phase, the protein structure is fixed, and the local hydration properties induced by the simultaneous presence of protein and ions are investigated, with a special focus on the interaction of Hofmeister active anions with the charged and polar sites. In the second, 'rearrangement' phase we follow changes of the hydration of ions and the protein, accompanying the conformational relaxation of the protein. We identify significant factors of an enthalpic and entropic nature behind the ion-induced free energy changes of the protein-water system, and also propose a possible atomic mechanism consistent with the Collins's rule, for the chaotropic destabilization and kosmotropic stabilization of protein conformation.
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22
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Nguyen D, Lokesh GLR, Volk DE, Iwahara J. A Unique and Simple Approach to Improve Sensitivity in 15N-NMR Relaxation Measurements for NH₃⁺ Groups: Application to a Protein-DNA Complex. Molecules 2017; 22:molecules22081355. [PMID: 28809801 PMCID: PMC5602601 DOI: 10.3390/molecules22081355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/11/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
NMR spectroscopy is a powerful tool for research on protein dynamics. In the past decade, there has been significant progress in the development of NMR methods for studying charged side chains. In particular, NMR methods for lysine side-chain NH₃⁺ groups have been proven to be powerful for investigating the dynamics of hydrogen bonds or ion pairs that play important roles in biological processes. However, relatively low sensitivity has been a major practical issue in NMR experiments on NH₃⁺ groups. In this paper, we present a unique and simple approach to improve sensitivity in 15N relaxation measurements for NH₃⁺ groups. In this approach, the efficiency of coherence transfers for the desired components are maximized, whereas undesired anti-phase or multi-spin order components are purged through pulse schemes and rapid relaxation. For lysine side-chain NH₃⁺ groups of a protein-DNA complex, we compared the data obtained with the previous and new pulse sequences under the same conditions and confirmed that the 15N relaxation parameters were consistent for these datasets. While retaining accuracy in measuring 15N relaxation, our new pulse sequences for NH₃⁺ groups allowed an 82% increase in detection sensitivity of 15N longitudinal and transverse relaxation measurements.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Ganesh L R Lokesh
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
| | - David E Volk
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
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23
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Kyne C, Jordon K, Filoti DI, Laue TM, Crowley PB. Protein charge determination and implications for interactions in cell extracts. Protein Sci 2017; 26:258-267. [PMID: 27813264 PMCID: PMC5275725 DOI: 10.1002/pro.3077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/24/2016] [Accepted: 10/27/2016] [Indexed: 01/30/2023]
Abstract
Decades of dilute-solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behavior under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ∼2-fold lower than predicted from primary structure analysis. Cytochrome c charge was tuned by sulfate binding and was rendered anionic in E. coli extracts due to interactions with macroanions. Mutants in which three or four cationic residues were replaced with glutamate were charge-neutral and "inert" in extracts. A comparison of the interaction propensities of cytochrome c and the mutants emphasizes the role of negative charge in stabilizing physiological environments. Charge-charge repulsion and preferential hydration appear to prevent aggregation. The implications for molecular organization in vivo are discussed.
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Affiliation(s)
- Ciara Kyne
- School of ChemistryNational University of IrelandGalway, University RoadGalwayIreland
| | - Kiara Jordon
- Spin Analytical468 Portland StreetBerwickMaine03901
| | - Dana I. Filoti
- Centre to Advance Macromolecular Interaction Sciences University of New HampshireDurhamNew Hampshire03824
| | - Thomas M. Laue
- Spin Analytical468 Portland StreetBerwickMaine03901
- Centre to Advance Macromolecular Interaction Sciences University of New HampshireDurhamNew Hampshire03824
| | - Peter B. Crowley
- School of ChemistryNational University of IrelandGalway, University RoadGalwayIreland
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24
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BIKKINA SWETHA, BHATI AGASTYAP, PADHI SILADITYA, PRIYAKUMAR UDEVA. Temperature Dependence of the Stability of Ion Pair Interactions, and its Implications on the Thermostability of Proteins from Thermophiles. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1231-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Ferjaoui Z, Schneider R, Meftah A, Gaffet E, Alem H. Functional responsive superparamagnetic core/shell nanoparticles and their drug release properties. RSC Adv 2017. [DOI: 10.1039/c7ra02437a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Folic acid functionalized responsive core/shell superparamagnetic iron oxide nanoparticles were successfully synthesized for further application in cancer therapy. Their cancer drug loading and release performances were demonstrated.
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Affiliation(s)
- Zied Ferjaoui
- Institut Jean Lamour (IJL)
- Université de Lorraine
- Department N2EV
- UMR CNRS 7198
- 54011 Nancy
| | - Raphaël Schneider
- Laboratoire Réactions et Génie des Procédés (LRGP)
- Université de Lorraine
- UMR CNRS 7274
- 54001 Nancy
- France
| | - Abdelaziz Meftah
- Unite Nanamatériaux et Photonique
- Faculty of Sciences of Tunis
- Tunis El-Manar University
- 2092 Tunis
- Tunisia
| | - Eric Gaffet
- Institut Jean Lamour (IJL)
- Université de Lorraine
- Department N2EV
- UMR CNRS 7198
- 54011 Nancy
| | - Halima Alem
- Institut Jean Lamour (IJL)
- Université de Lorraine
- Department N2EV
- UMR CNRS 7198
- 54011 Nancy
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26
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Strate A, Niemann T, Ludwig R. Controlling the kinetic and thermodynamic stability of cationic clusters by the addition of molecules or counterions. Phys Chem Chem Phys 2017; 19:18854-18862. [DOI: 10.1039/c7cp02227a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We discuss the stability of cationic clusters when adding molecules or counterions, and predict their occurrence in gas phase experiments.
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Affiliation(s)
- Anne Strate
- Universität Rostock
- Institut für Chemie
- Abteilung für Physikalische Chemie
- Rostock
- Germany
| | - Thomas Niemann
- Universität Rostock
- Institut für Chemie
- Abteilung für Physikalische Chemie
- Rostock
- Germany
| | - Ralf Ludwig
- Universität Rostock
- Institut für Chemie
- Abteilung für Physikalische Chemie
- Rostock
- Germany
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27
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Gindt YM, Edani BH, Olejnikova A, Roberts AN, Munshi S, Stanley RJ. The Missing Electrostatic Interactions Between DNA Substrate and Sulfolobus solfataricus DNA Photolyase: What is the Role of Charged Amino Acids in Thermophilic DNA Binding Proteins? J Phys Chem B 2016; 120:10234-10242. [PMID: 27626127 DOI: 10.1021/acs.jpcb.6b07201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA photolyase can be used to study how a protein with its required cofactor has adapted over a large temperature range. The enzymatic activity and thermodynamics of substrate binding for protein from Sulfolobus solfataricus were directly compared to protein from Escherichia coli. Turnover numbers and catalytic activity were virtually identical, but organic cosolvents may be necessary to maintain activity of the thermophilic protein at higher temperatures. UV-damaged DNA binding to the thermophilic protein is less favorable by ∼2 kJ/mol. The enthalpy of binding is ∼10 kJ/mol less exothermic for the thermophile, but the amount and type of surface area buried upon DNA binding appears to be somewhat similar. The most important finding was observed when ionic strength studies were used to separate binding interactions into electrostatic and nonelectrostatic contributions; DNA binding to the thermophilic protein appears to lack the electrostatic contributions observed with the mesophilic protein.
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Affiliation(s)
- Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Ban H Edani
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Antonia Olejnikova
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Ariana N Roberts
- Department of Chemistry and Biochemistry, Montclair State University , 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Sudipto Munshi
- Department of Chemistry, Temple University , 1801 N Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University , 1801 N Broad Street, Philadelphia, Pennsylvania 19122, United States
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28
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Etheve L, Martin J, Lavery R. Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors. Nucleic Acids Res 2016; 44:9990-10002. [PMID: 27658967 PMCID: PMC5175364 DOI: 10.1093/nar/gkw841] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/14/2022] Open
Abstract
We have studied the dynamics of three transcription factor-DNA complexes using all-atom, microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond interactions formed at the protein-DNA interface are found to be dynamic, with lifetimes typically in the range of tens to hundreds of picoseconds, although some interactions, notably those involving specific binding to DNA bases, can be a hundred times longer lived. Depending on the complex studied, this dynamics may or may not lead to the existence of distinct conformational substates. Using a sequence threading technique, it has been possible to determine whether DNA sequence recognition is sensitive or not to such conformational changes, and, in one case, to show that recognition appears to be locally dependent on protein-mediated cation distributions.
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Affiliation(s)
- Loïc Etheve
- MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Juliette Martin
- MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
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29
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Nguyen D, Zandarashvili L, White MA, Iwahara J. Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity. Chembiochem 2016; 17:1636-42. [PMID: 27271797 DOI: 10.1002/cbic.201600265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 02/05/2023]
Abstract
Oxygen-to-sulfur substitutions in DNA phosphate often enhance affinity for DNA-binding proteins. Our previous studies have suggested that this effect of sulfur substitution of both OP1 and OP2 atoms is due to an entropic gain associated with enhanced ion pair dynamics. In this work, we studied stereospecific effects of single sulfur substitution of either the OP1 or OP2 atom in DNA phosphate at the Lys57 interaction site of the Antennapedia homeodomain-DNA complex. Using crystallography, we obtained structural information on the RP and SP diastereomers of the phosphoromonothioate and their interaction with Lys57. Using fluorescence-based assays, we found significant affinity enhancement upon sulfur substitution of the OP2 atom. Using NMR spectroscopy, we found significant mobilization of the Lys57 side-chain NH3 (+) group upon sulfur substitution of the OP2 atom. These data provide further mechanistic insights into the affinity enhancement by oxygen-to-sulfur substitution in DNA phosphate.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA.
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30
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Esadze A, Chen C, Zandarashvili L, Roy S, Pettitt BM, Iwahara J. Changes in conformational dynamics of basic side chains upon protein-DNA association. Nucleic Acids Res 2016; 44:6961-70. [PMID: 27288446 PMCID: PMC5001603 DOI: 10.1093/nar/gkw531] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/31/2016] [Indexed: 11/24/2022] Open
Abstract
Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.
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Affiliation(s)
- Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Chuanying Chen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Sourav Roy
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - B Montgometry Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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Zandarashvili L, Esadze A, Kemme CA, Chattopadhyay A, Nguyen D, Iwahara J. Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling. J Phys Chem Lett 2016; 7:820-4. [PMID: 26881297 PMCID: PMC4850060 DOI: 10.1021/acs.jpclett.6b00019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The residence times of molecular complexes in solution are important for understanding biomolecular functions and drug actions. We show that NMR data of intermolecular hydrogen-bond scalar couplings can yield information on the residence times of molecular complexes in solution. The molecular exchange of binding partners via the breakage and reformation of a complex causes self-decoupling of intermolecular hydrogen-bond scalar couplings, and this self-decoupling effect depends on the residence time of the complex. For protein-DNA complexes, we investigated the salt concentration dependence of intermolecular hydrogen-bond scalar couplings between the protein side-chain (15)N and DNA phosphate (31)P nuclei, from which the residence times were analyzed. The results were consistent with those obtained by (15)Nz-exchange spectroscopy. This self-decoupling-based kinetic analysis is unique in that it does not require any different signatures for the states involved in the exchange, whereas such conditions are crucial for kinetic analyses by typical NMR and other methods.
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