1
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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [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: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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2
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Martínez-Rodríguez S, Cámara-Artigas A, Gavira JA. First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family. Biochem Biophys Res Commun 2023; 682:85-90. [PMID: 37804591 DOI: 10.1016/j.bbrc.2023.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Acylphosphatase (AcP, EC 3.6.1.7) is a small model protein conformed by a ferredoxin-like fold, profoundly studied to get insights into protein folding and aggregation processes. Numerous studies focused on the aggregation and/or amyloidogenic properties of AcPs suggest the importance of edge-β-strands in the process. In this work, we present the first crystallographic structure of Escherichia coli AcP (EcoAcP), showing notable differences with the only available NMR structure for this enzyme. EcoAcP is crystalised as an intertwined dimer formed by replacing a single C-terminal β-strand between two protomers, suggesting a flexible character of the C-terminal edge of EcoAcP. Despite numerous works where AcP from different sources have been used as a model system for protein aggregation, our domain-swapped EcoAcP structure is the first 3-D structural evidence of native-like aggregated species for any AcP reported to date, providing clues on molecular determinants unleashing aggregation.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Avenida de La Investigación 11, Granada, 18071, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Centro de Investigación en Agrosistemas Intensivos Mediterráneos y Biotecnología Agroalimentaria (CIAMBITAL), Carretera de Sacramento S/n, Almería, 04120, Spain
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain
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3
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Huang Z, Cui X, Xia Y, Zhao K, Zhang G. Pathfinder: Protein folding pathway prediction based on conformational sampling. PLoS Comput Biol 2023; 19:e1011438. [PMID: 37695768 PMCID: PMC10513300 DOI: 10.1371/journal.pcbi.1011438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/21/2023] [Accepted: 08/17/2023] [Indexed: 09/13/2023] Open
Abstract
The study of protein folding mechanism is a challenge in molecular biology, which is of great significance for revealing the movement rules of biological macromolecules, understanding the pathogenic mechanism of folding diseases, and designing protein engineering materials. Based on the hypothesis that the conformational sampling trajectory contain the information of folding pathway, we propose a protein folding pathway prediction algorithm named Pathfinder. Firstly, Pathfinder performs large-scale sampling of the conformational space and clusters the decoys obtained in the sampling. The heterogeneous conformations obtained by clustering are named seed states. Then, a resampling algorithm that is not constrained by the local energy basin is designed to obtain the transition probabilities of seed states. Finally, protein folding pathways are inferred from the maximum transition probabilities of seed states. The proposed Pathfinder is tested on our developed test set (34 proteins). For 11 widely studied proteins, we correctly predicted their folding pathways and specifically analyzed 5 of them. For 13 proteins, we predicted their folding pathways to be further verified by biological experiments. For 6 proteins, we analyzed the reasons for the low prediction accuracy. For the other 4 proteins without biological experiment results, potential folding pathways were predicted to provide new insights into protein folding mechanism. The results reveal that structural analogs may have different folding pathways to express different biological functions, homologous proteins may contain common folding pathways, and α-helices may be more prone to early protein folding than β-strands.
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Affiliation(s)
- Zhaohong Huang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xinyue Cui
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuhao Xia
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
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4
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Miret NV, Zárate LV, Díaz FE, Agustina Leguizamón M, Pontillo CA, Chiappini FA, Ceballos L, Geffner J, Randi AS. Extracellular acidosis stimulates breast cancer cell motility through aryl hydrocarbon receptor and c-Src kinase activation. J Cell Biochem 2022; 123:1197-1206. [PMID: 35538691 DOI: 10.1002/jcb.30275] [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: 02/10/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 01/18/2023]
Abstract
A reduction in extracellular pH (pHe) is a characteristic of most malignant tumors. The aryl hydrocarbon receptor (AhR) is a transcription factor localized in a cytosolic complex with c-Src, which allows it to trigger non-genomic effects through c-Src. Considering that the slightly acidic tumor microenvironment promotes breast cancer progression in a similar way to the AhR/c-Src axis, our aim was to evaluate whether this pathway could be activated by low pHe. We examined the effect of pHe 6.5 on AhR/c-Src axis using two breast cancer cell lines (MDA-MB-231 and LM3) and mammary epithelial cells (NMuMG) and found that acidosis increased c-Src phosphorylation only in tumor cells. Moreover, the presence of AhR inhibitors prevented c-Src activation. Low pHe reduced intracellular pH (pHi), while amiloride treatment, which is known to reduce pHi, induced c-Src phosphorylation through AhR. Analyses were conducted on cell migration and metalloproteases (MMP)-2 and -9 activities, with results showing an acidosis-induced increase in MDA-MB-231 and LM3 cell migration and MMP-9 activity, but no changes in NMuMG cells. Moreover, all these effects were blocked by AhR and c-Src inhibitors. In conclusion, acidosis stimulates the AhR/c-Src axis only in breast cancer cells, increasing cell migration and MMP-9 activity. Although the AhR activation mechanism still remains elusive, a reduction in pHi may be thought to be involved. These findings suggest a critical role for the AhR/c-Src axis in breast tumor progression stimulated by an acidic microenvironment. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Noelia V Miret
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
| | - Lorena V Zárate
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
| | - Fernando Erra Díaz
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (CONICET), Paraguay 2155, 11° piso, (CP 1121), Buenos Aires, Argentina
| | - M Agustina Leguizamón
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
| | - Carolina A Pontillo
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
| | - Florencia A Chiappini
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
| | - Leandro Ceballos
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
| | - Jorge Geffner
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (CONICET), Paraguay 2155, 11° piso, (CP 1121), Buenos Aires, Argentina
| | - Andrea S Randi
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Bioquímica Humana, Laboratorio de Efectos Biológicos de Contaminantes Ambientales, Paraguay 2155, 5° piso, (CP 1121), Buenos Aires, Argentina
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5
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Salinas-Garcia MC, Plaza-Garrido M, Camara-Artigas A. The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain. Acta Crystallogr D Struct Biol 2021; 77:854-866. [PMID: 34076598 PMCID: PMC8171063 DOI: 10.1107/s2059798321004344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 03/26/2023] Open
Abstract
Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.
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Affiliation(s)
- M. Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
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6
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Mondal B, Nagesh J, Reddy G. Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. J Phys Chem B 2021; 125:1705-1715. [PMID: 33566611 DOI: 10.1021/acs.jpcb.0c07833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human γD (HγD) and γC (HγC) are two-domain crystallin (Crys) proteins expressed in the nucleus of the eye lens. Structural perturbations in the protein often trigger aggregation, which eventually leads to cataract. To decipher the underlying molecular mechanism, it is important to characterize the partially unfolded conformations, which are aggregation-prone. Using a coarse grained protein model and molecular dynamics simulations, we studied the role of on-pathway folding intermediates in the early stages of aggregation. The multidimensional free energy surface revealed at least three different folding pathways with the population of partially structured intermediates. The two dominant pathways confirm sequential folding of the N-terminal [Ntd] and the C-terminal domains [Ctd], while the third, least favored, pathway involves intermediates where both the domains are partially folded. A native-like intermediate (I*), featuring the folded domains and disrupted interdomain contacts, gets populated in all three pathways. I* forms domain swapped dimers by swapping the entire Ntds and Ctds with other monomers. Population of such oligomers can explain the increased resistance to unfolding resulting in hysteresis observed in the folding experiments of HγD Crys. An ensemble of double domain swapped dimers are also formed during refolding, where intermediates consisting of partially folded Ntds and Ctds swap secondary structures with other monomers. The double domain swapping model presented in our study provides structural insights into the early events of aggregation in Crys proteins and identifies the key secondary structural swapping elements, where introducing mutations will aid in regulating the overall aggregation propensity.
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Affiliation(s)
- Balaka Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka, India 560012
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7
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Stadmiller SS, Aguilar JS, Parnham S, Pielak GJ. Protein–Peptide Binding Energetics under Crowded Conditions. J Phys Chem B 2020; 124:9297-9309. [DOI: 10.1021/acs.jpcb.0c05578] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jhoan S. Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stuart Parnham
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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8
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Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG. Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain. J Biol Chem 2020; 295:7849-7864. [PMID: 32317279 PMCID: PMC7278359 DOI: 10.1074/jbc.ra120.012788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3ϵ that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3ϵ interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3ϵ interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (ζ chain of T cell receptor–associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro. Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3ϵ. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3ϵ, possibly representing an inactive form of Nck in cells.
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Affiliation(s)
- Kirsten Richter
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Arne C Rufer
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Magali Muller
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dominique Burger
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Fabio Casagrande
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tabea Grossenbacher
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sylwia Huber
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melanie N Hug
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Philipp Koldewey
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andrea D'Osualdo
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Daniel Schlatter
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Theodor Stoll
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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Plaza-Garrido M, Salinas-García MC, Martínez JC, Cámara-Artigas A. The effect of an engineered ATCUN motif on the structure and biophysical properties of the SH3 domain of c-Src tyrosine kinase. J Biol Inorg Chem 2020; 25:621-634. [PMID: 32279137 DOI: 10.1007/s00775-020-01785-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/22/2020] [Indexed: 10/24/2022]
Abstract
Metal binding to sites engineered in proteins can provide an increase in their stability and facilitate new functions. Besides the sites introduced in purpose, sometimes they are present accidentally as a consequence of the expression system used to produce the protein. This happens with the copper- and nickel-binding (ATCUN) motif generated by the amino-terminal residues Gly-Ser-His. This ATCUN motif is fortuitously present in many proteins, but how it affects the structural and biophysical characterization of the proteins has not been studied. In this work, we have compared the structure and biophysical properties of a small modular domain, the SH3 domain of the c-Src tyrosine kinase, cloned with and without an ATCUN motif at the N terminus. At pH 7.0, the SH3 domain with the ATCUN motif binds nickel with a binding constant Ka = 28.0 ± 3.0 mM-1. The formation of the nickel complex increases the thermal and chemical stability of the SH3 domain. A comparison of the crystal structures of the SH3 domain with and without the ATCUN motif shows that the binding of nickel does not affect the overall structure of the SH3 domain. In all crystal structures analyzed, residues Gly-Ser-His in complex with Ni2+ show a square planar geometry. The CD visible spectrum of the nickel complex shows that this geometry is also present in the solution. Therefore, our results not only show that the ATCUN motif might influence the biophysical properties of the protein, but also points to an advantageous stabilization of the protein with potential biotechnological applications.
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Affiliation(s)
- Marina Plaza-Garrido
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence ceiA3 and CIAMBITAL, 04120, Almería, Spain
| | - Mª Carmen Salinas-García
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence ceiA3 and CIAMBITAL, 04120, Almería, Spain
| | - José C Martínez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence ceiA3 and CIAMBITAL, 04120, Almería, Spain.
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10
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Mondal B, Reddy G. Cosolvent Effects on the Growth of Protein Aggregates Formed by a Single Domain Globular Protein and an Intrinsically Disordered Protein. J Phys Chem B 2019; 123:1950-1960. [DOI: 10.1021/acs.jpcb.8b11128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Balaka Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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11
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Takács K, Varga B, Grolmusz V. PDB_Amyloid: an extended live amyloid structure list from the PDB. FEBS Open Bio 2018; 9:185-190. [PMID: 30652085 PMCID: PMC6325586 DOI: 10.1002/2211-5463.12524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 12/24/2022] Open
Abstract
The Protein Data Bank (PDB) contains more than 135 000 entries at present. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, most amyloid structures deposited in the PDB are in the form of solid state NMR data. Based on the geometric analysis of these deposited structures, we have prepared an automatically updated web server, which generates a list of the deposited amyloid structures, and also entries of globular proteins that have amyloid‐like substructures of given size and characteristics. We have found that by applying only appropriately selected geometric conditions, it is possible to identify deposited amyloid structures and a number of globular proteins with amyloid‐like substructures. We have analyzed these globular proteins and have found proof in the literature that many of them form amyloids more easily than many other globular proteins. Our results relate to the method of Stanković et al. [Stanković I et al. (2017) IPSI BgD Tran Int Res 13, 47–51], who applied a hybrid textual‐search and geometric approach for finding amyloids in the PDB. If one intends to identify a subset of the PDB for certain applications, the identification algorithm needs to be re‐run periodically, since in 2017 on average 30 new entries per day were deposited in the data bank. Our web server is updated regularly and automatically, and the identified amyloid and partial amyloid structures can be viewed or their list can be downloaded from the following website https://pitgroup.org/amyloid.
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Affiliation(s)
- Kristóf Takács
- PIT Bioinformatics Group Eötvös University Budapest Hungary
| | - Bálint Varga
- PIT Bioinformatics Group Eötvös University Budapest Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group Eötvös University Budapest Hungary.,Uratim Ltd. Budapest Hungary
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12
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Hu HQ, Johnson RC, Merrell DS, Maroney MJ. Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori. Biochemistry 2017; 56:1105-1116. [PMID: 28177601 DOI: 10.1021/acs.biochem.6b00912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The human pathogen Helicobacter pylori requires nickel for colonization of the acidic environment of the stomach. HypA, a Ni metallochaperone that is typically associated with hydrogenase maturation, is also required for urease maturation and acid survival of H. pylori. There are two proposed Ni site structures for HypA; one is a paramagnetic six-coordinate site characterized by X-ray absorption spectroscopy (XAS) in unmodified HypA, while another is a diamagnetic four-coordinate planar site characterized by solution nuclear magnetic resonance in an N-terminally modified HypA construct. To determine the role of the N-terminal amine in Ni binding of HypA, an N-terminal extension variant, L2*-HypA, in which a leucine residue was inserted into the second position of the amino acid sequence in the proposed Ni-binding motif, was characterized in vitro and in vivo. Structural characterization of the Ni site using XAS showed a coordination change from six-coordinate in wild-type HypA (WT-HypA) to five-coordinate pyramidal in L2*-HypA, which was accompanied by the loss of two N/O donor protein ligands and the addition of an exogenous bromide ligand from the buffer. The magnetic properties of the Ni sites in WT-HypA compared to those of the Ni sites in L2*-HypA confirmed that a spin-state change from high to low spin accompanied this change in structure. The L2*-HypA H. pylori strain was shown to be acid sensitive and deficient in urease activity in vivo. In vitro characterization showed that L2*-HypA did not disrupt the HypA-UreE interaction that is essential for urease maturation but was at least 20-fold weaker in Ni binding than WT-HypA. Characterization of the L2*-HypA variant clearly demonstrates that the N-terminal amine of HypA is involved in proper Ni coordination and is necessary for urease activity and acid survival.
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Affiliation(s)
- Heidi Q Hu
- Department of Chemistry and Program of Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Ryan C Johnson
- Microbiology and Immunology, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
| | - D Scott Merrell
- Microbiology and Immunology, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
| | - Michael J Maroney
- Department of Chemistry and Program of Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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13
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Muttathukattil AN, Reddy G. Osmolyte Effects on the Growth of Amyloid Fibrils. J Phys Chem B 2016; 120:10979-10989. [DOI: 10.1021/acs.jpcb.6b09215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Aswathy N. Muttathukattil
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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14
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Camara-Artigas A, Ortiz-Salmeron E, Andujar-Sánchez M, Bacarizo J, Martin-Garcia JM. The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase. Acta Crystallogr F Struct Biol Commun 2016; 72:707-12. [PMID: 27599862 PMCID: PMC5012211 DOI: 10.1107/s2053230x16012310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/29/2016] [Indexed: 01/05/2023] Open
Abstract
Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in the class II complexes. The structures suggest a role of these water molecules in facilitating conformational changes in the SH3 domain to allow the binding of the class I or II peptides. In the third binding pocket these changes modify the cation-π and salt-bridge interactions that determine the affinity of the binding. Comparison of the water molecules involved in the binding of the peptides with previous reported hydration spots suggests a different pattern for the SH3 domains of the Src tyrosine kinase family.
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Affiliation(s)
- Ana Camara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
| | - Emilia Ortiz-Salmeron
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
| | - Montserrrat Andujar-Sánchez
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
| | - Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento, 04120 Almeria, Spain
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15
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Tsutsui Y, Deredge D, Wintrode PL, Hays FA. Imatinib binding to human c-Src is coupled to inter-domain allostery and suggests a novel kinase inhibition strategy. Sci Rep 2016; 6:30832. [PMID: 27480221 PMCID: PMC4969603 DOI: 10.1038/srep30832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022] Open
Abstract
Imatinib (Gleevec), a non-receptor tyrosine kinase inhibitor (nRTKI), is one of the most successful anti-neoplastic drugs in clinical use. However, imatinib-resistant mutations are increasingly prevalent in patient tissues and driving development of novel imatinib analogs. We present a detailed study of the conformational dynamics, in the presence and absence of bound imatinib, for full-length human c-Src using hydrogen-deuterium exchange and mass spectrometry. Our results demonstrate that imatinib binding to the kinase domain effects dynamics of proline-rich or phosphorylated peptide ligand binding sites in distal c-Src SH3 and SH2 domains. These dynamic changes in functional regulatory sites, distal to the imatinib binding pocket, show similarities to structural transitions involved in kinase activation. These data also identify imatinib-sensitive, and imatinib-resistant, mutation sites. Thus, the current study identifies novel c-Src allosteric sites associated with imatinib binding and kinase activation and provide a framework for follow-on development of TKI binding modulators.
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Affiliation(s)
- Yuko Tsutsui
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
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16
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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17
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Camara-Artigas A, Plaza-Garrido M, Martinez-Rodriguez S, Bacarizo J. New crystal form of human ubiquitin in the presence of magnesium. Acta Crystallogr F Struct Biol Commun 2016; 72:29-35. [PMID: 26750481 PMCID: PMC4708047 DOI: 10.1107/s2053230x15023390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/05/2015] [Indexed: 01/07/2023] Open
Abstract
Ubiquitin is a small globular protein that has a considerable number of lysine residues on its surface. This results in a high surface entropy that precludes the formation of crystal-packing interactions. To date, only a few structures of the native form of ubiquitin have been solved, and most of the crystals that led to these structures were obtained in the presence of different divalent metal cations. In this work, a new crystallographic structure of human ubiquitin solved from crystals grown in the presence of magnesium is presented. The crystals belonged to a triclinic space group, with unit-cell parameters a = 29.96, b = 30.18, c = 41.41 Å, α = 88.52, β = 79.12, γ = 67.37°. The crystal lattice is composed of stacked layers of human ubiquitin molecules with a large hydrophobic interface and a smaller polar interface in which the magnesium ion lies at the junction between adjacent layers in the crystal. The metal ion appears in a hexa-aquo coordination, which is key to facilitating the crystallization of the protein.
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Affiliation(s)
- Ana Camara-Artigas
- Department of Chemistry and Physics, University of Almeria, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento (s/n), 04120 Almeria, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, University of Almeria, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento (s/n), 04120 Almeria, Spain
| | - Sergio Martinez-Rodriguez
- Department of Physical Chemistry, University of Granada, Avdenida de Fuentenueva s/n, 18071 Granada, Spain
| | - Julio Bacarizo
- Department of Chemistry and Physics, University of Almeria, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento (s/n), 04120 Almeria, Spain
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18
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Wu H, Shi Y, Deng X, Su Y, Du C, Wei J, Ren Y, Wu M, Hou Y, Duan H. Inhibition of c-Src/p38 MAPK pathway ameliorates renal tubular epithelial cells apoptosis in db/db mice. Mol Cell Endocrinol 2015; 417:27-35. [PMID: 26363223 DOI: 10.1016/j.mce.2015.09.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/05/2015] [Accepted: 09/08/2015] [Indexed: 01/08/2023]
Abstract
Renal tubular epithelial cells (RTEC) apoptosis, which plays a key role in the pathogenesis and progression of diabetic nephropathy (DN), is believed to be contributive to the hyperglycemia-induced kidney failure, though the exact mechanisms remain elusive. In this study, we investigated how inhibition of c-Src/p38 MAPK pathway would affect RTEC apoptosis. The c-Src inhibitor PP2 i.p. administered every other day for 8 weeks to diabetic db/db mice significantly reduced their kidney weights, daily urinary volumes, blood glucose, blood urea nitrogen, serum creatinine, triglyceride and urine albumin excretion, whereas deactivation of c-Src and p38 MAPK were also observed, along with decreases in both Bax/Bcl-2 ratio and cleaved caspase-3 level in the kidneys. In vitro, exposure of HK-2 cells (a human RTEC line), to high glucose (HG) promoted phosphorylation of c-Src and p38 MAPK, and subsequently, as revealed by western blotting, TUNEL assay and flow cytometry, increased cell death, which can be inhibited by PP2. Especially, a specific p38 MAPK inhibitor, SB203580, that both attenuated HG-induced c-Src activation and abrogated the expression of PPARγ and CHOP, also reduced apoptosis. Taken together, PP2 inhibits c-Src and therefore reduces apoptosis in RTEC, which at least in part, is due to suppressed p38 MAPK activation in diabetic kidney.
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Affiliation(s)
- Haijiang Wu
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Yonghong Shi
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Xinna Deng
- Department of Oncology & Immunotherapy, Hebei General Hospital, Shijiazhuang, China
| | - Ye Su
- Mathew Mailing Centre for Translational Transplantation Studies, Lawson Health Research Institute, London Health Sciences Centre, Department of Medicine, and Pathology, University of Western Ontario, London, Ontario, Canada
| | - Chunyang Du
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Jinying Wei
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Yunzhuo Ren
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Ming Wu
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Yanjuan Hou
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China
| | - Huijun Duan
- Department of Pathology, Hebei Medical University, Shijiazhuang, China; Key Laboratory of Kidney Diseases of Hebei Province, Shijiazhufang, China.
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19
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Egge N, Muthusubramanian A, Cornwall GA. Amyloid properties of the mouse egg zona pellucida. PLoS One 2015; 10:e0129907. [PMID: 26043223 PMCID: PMC4456372 DOI: 10.1371/journal.pone.0129907] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/14/2015] [Indexed: 01/15/2023] Open
Abstract
The zona pellucida (ZP) surrounding the oocyte is an extracellular fibrillar matrix that plays critical roles during fertilization including species-specific gamete recognition and protection from polyspermy. The mouse ZP is composed of three proteins, ZP1, ZP2, and ZP3, all of which have a ZP polymerization domain that directs protein fibril formation and assembly into the three-dimensional ZP matrix. Egg coats surrounding oocytes in nonmammalian vertebrates and in invertebrates are also fibrillar matrices and are composed of ZP domain-containing proteins suggesting the basic structure and function of the ZP/egg coat is highly conserved. However, sequence similarity between ZP domains is low across species and thus the mechanism for the conservation of ZP/egg coat structure and its function is not known. Using approaches classically used to identify amyloid including conformation-dependent antibodies and dyes, X-ray diffraction, and negative stain electron microscopy, our studies suggest the mouse ZP is a functional amyloid. Amyloids are cross-β sheet fibrillar structures that, while typically associated with neurodegenerative and prion diseases in mammals, can also carry out functional roles in normal cells without resulting pathology. An analysis of the ZP domain from mouse ZP3 and ZP3 homologs from five additional taxa using the algorithm AmylPred 2 to identify amyloidogenic sites, revealed in all taxa a remarkable conservation of regions that were predicted to form amyloid. This included a conserved amyloidogenic region that localized to a stretch of hydrophobic amino acids previously shown in mouse ZP3 to be essential for fibril assembly. Similarly, a domain in the yeast protein α-agglutinin/Sag 1p, that possesses ZP domain-like features and which is essential for mating, also had sites that were predicted to be amyloidogenic including a hydrophobic stretch that appeared analogous to the critical site in mouse ZP3. Together, these studies suggest that amyloidogenesis may be a conserved mechanism for ZP structure and function across billions of years of evolution.
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Affiliation(s)
- Nathan Egge
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Archana Muthusubramanian
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Gail A. Cornwall
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- * E-mail:
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Bacarizo J, Martínez-Rodríguez S, Cámara-Artigas A. Structure of the c-Src-SH3 domain in complex with a proline-rich motif of NS5A protein from the hepatitis C virus. J Struct Biol 2014; 189:67-72. [PMID: 25447263 DOI: 10.1016/j.jsb.2014.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
The non-structural hepatitis C virus proteins NS5A and NS5B form a complex through interaction with the SH2 and SH3 domains of the non-receptor Src tyrosine kinase, which seems essential for viral replication. We have crystallized the complex between the SH3 domain of the c-Src tyrosine kinase and the C-terminal proline rich motif of the NS5A protein (A349PPIPPPRRKR359). Crystals obtained at neutral pH belong to the space group I41, with a single molecule of the SH3/NS5A complex at the asymmetric unit. The NS5A peptide is bound in a reverse orientation (class II) and the comparison of this structure with those of the high affinity synthetic peptides APP12 and VSL12 shows some important differences at the salt bridge that drives the peptide orientation. Further conformational changes in residues placed apart from the binding site also seem to play an important role in the binding orientation of this peptide. Our results show the interaction of the SH3 domain of the c-Src tyrosine kinase with a proline rich motif in the NS5A protein and point to their potential interaction in vivo.
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Affiliation(s)
- Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento s/n, Almería 04120, Spain
| | - Sergio Martínez-Rodríguez
- Department of Physical Chemistry, University of Granada, Avda. de Fuentenueva s/n, Granada 18071, Spain
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Carretera de Sacramento s/n, Almería 04120, Spain.
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