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Martinez JC, Ruiz-Sanz J, Resina MJ, Montero F, Camara-Artigas A, Luque I. A calorimetric and structural analysis of cooperativity in the thermal unfolding of the PDZ tandem of human Syntenin-1. Int J Biol Macromol 2023; 242:124662. [PMID: 37119899 DOI: 10.1016/j.ijbiomac.2023.124662] [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: 02/03/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Syntenin-1 is a multidomain protein containing a central tandem of two PDZ domains flanked by two unnamed domains. Previous structural and biophysical studies show that the two PDZ domains are functional both isolated and in tandem, occurring a gain in their respective binding affinities when joined through its natural short linker. To get insight into the molecular and energetic reasons of such a gain, here, the first thermodynamic characterization of the conformational equilibrium of Syntenin-1 is presented, with special focus on its PDZ domains. These studies include the thermal unfolding of the whole protein, the PDZ-tandem construct and the two isolated PDZ domains using circular dichroism, differential scanning fluorimetry and differential scanning calorimetry. The isolated PDZ domains show low stability (ΔG < 10 kJ·mol-1) and poor cooperativity compared to the PDZ-tandem, which shows higher stability (20-30 kJ·mol-1) and a fully cooperative behaviour, with energetics similar to that previously described for archetypical PDZ domains. The high-resolution structures suggest that this remarkable increase in cooperativity is associated to strong, water-mediated, interactions at the interface between the PDZ domains, associated to nine conserved hydration regions. The low Tm value (45 °C), the anomalously high unfolding enthalpy (>400 kJ·mol-1), and native heat capacity values (above 40 kJ·K-1·mol-1), indicate that these interfacial buried waters play a relevant role in Syntenin-1 folding energetics.
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Affiliation(s)
- Jose C Martinez
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - María J Resina
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Fernando Montero
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain.
| | - Irene Luque
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
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2
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Gautier C, Gianni S. A short structural extension dictates the early stages of folding of a PDZ domain. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140852. [PMID: 36055518 DOI: 10.1016/j.bbapap.2022.140852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
PDZ domains are highly abundant protein-protein interaction modules in human. One of the most extensively characterized PDZ domain, the third PDZ domain from PSD-95 (PDZ3), contains an α-helical C-terminal extension that has a key role in the function of the domain. Here we compared the folding of PDZ3 with a truncated variant (PDZ3Δα3), lacking the additional helix, by means of the so-called Φ-value analysis, an experimental technique that allows inferring the structure of folding transition states. Experiments reveal subtle but detectable differences in the folding of PDZ3Δα3 versus PDZ3, as probed by structural characterization of the folding transition states. These differences appear more remarkable in the early stages of folding, with a detectable shift of the folding nucleus. The presented results allow demonstrating that the native state exerts a weak bias at the early stages of folding, which appear to be characterized by alternative pathways.
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Affiliation(s)
- Candice Gautier
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
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3
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Cobos ES, Sánchez IE, Chemes LB, Martinez JC, Murciano-Calles J. A Thermodynamic Analysis of the Binding Specificity between Four Human PDZ Domains and Eight Host, Viral and Designed Ligands. Biomolecules 2021; 11:biom11081071. [PMID: 34439737 PMCID: PMC8393326 DOI: 10.3390/biom11081071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 02/01/2023] Open
Abstract
PDZ domains are binding modules mostly involved in cell signaling and cell–cell junctions. These domains are able to recognize a wide variety of natural targets and, among the PDZ partners, viruses have been discovered to interact with their host via a PDZ domain. With such an array of relevant and diverse interactions, PDZ binding specificity has been thoroughly studied and a traditional classification has grouped PDZ domains in three major specificity classes. In this work, we have selected four human PDZ domains covering the three canonical specificity-class binding mode and a set of their corresponding binders, including host/natural, viral and designed PDZ motifs. Through calorimetric techniques, we have covered the entire cross interactions between the selected PDZ domains and partners. The results indicate a rather basic specificity in each PDZ domain, with two of the domains that bind their cognate and some non-cognate ligands and the two other domains that basically bind their cognate partners. On the other hand, the host partners mostly bind their corresponding PDZ domain and, interestingly, the viral ligands are able to bind most of the studied PDZ domains, even those not previously described. Some viruses may have evolved to use of the ability of the PDZ fold to bind multiple targets, with resulting affinities for the virus–host interactions that are, in some cases, higher than for host–host interactions.
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Affiliation(s)
- Eva S. Cobos
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Ignacio E. Sánchez
- Laboratorio de Fisiología de Proteínas, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, 1428 Buenos Aires, Argentina;
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, 1650 Buenos Aires, Argentina;
| | - Jose C. Martinez
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Javier Murciano-Calles
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
- Correspondence:
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4
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Bousova K, Bednarova L, Zouharova M, Vetyskova V, Postulkova K, Hofbauerová K, Petrvalska O, Vanek O, Tripsianes K, Vondrasek J. The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization. Protein Sci 2021; 30:1653-1666. [PMID: 33969912 DOI: 10.1002/pro.4107] [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: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/09/2022]
Abstract
Most of the structural proteins known today are composed of domains that carry their own functions while keeping their structural properties. It is supposed that such domains, when taken out of the context of the whole protein, can retain their original structure and function to a certain extent. Information on the specific functional and structural characteristics of individual domains in a new context of artificial fusion proteins may help to reveal the rules of internal and external domain communication. Moreover, this could also help explain the mechanism of such communication and address how the mutual allosteric effect plays a role in a such multi-domain protein system. The simple model system of the two-domain fusion protein investigated in this work consisted of a well-folded PDZ3 domain and an artificially designed small protein domain called Tryptophan Cage (TrpCage). Two fusion proteins with swapped domain order were designed to study their structural and functional features as well as their biophysical properties. The proteins composed of PDZ3 and TrpCage, both identical in amino acid sequence but different in composition (PDZ3-TrpCage, TrpCage-PDZ3), were studied using circualr dichroism (CD) spectrometry, analytical ultracentrifugation, and molecular dynamic simulations. The biophysical analysis uncovered different structural and denaturation properties of both studied proteins, revealing their different unfolding pathways and dynamics.
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Affiliation(s)
- Kristyna Bousova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Lucie Bednarova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Monika Zouharova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Second Faculty of Medicine, Charles University, Prague 5, Czech Republic
| | - Veronika Vetyskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague 6, Czech Republic
| | - Klara Postulkova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Second Faculty of Medicine, Charles University, Prague 5, Czech Republic
| | - Kateřina Hofbauerová
- Faculty of Mathematics and Physics, Charles University, Prague 2, Czech Republic.,Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Olivia Petrvalska
- Department of Structural Biology of Signalling Proteins, Division BIOCEV, Institute of Physiology, Vestec, Czech Republic
| | - Ondrej Vanek
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | | | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
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5
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The Conformational Plasticity Vista of PDZ Domains. Life (Basel) 2020; 10:life10080123. [PMID: 32726937 PMCID: PMC7460260 DOI: 10.3390/life10080123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/19/2020] [Accepted: 07/25/2020] [Indexed: 02/01/2023] Open
Abstract
The PDZ domain (PSD95-Discs large-ZO1) is a widespread modular domain present in the living organisms. A prevalent function in the PDZ family is to serve as scaffolding and adaptor proteins connecting multiple partners in signaling pathways. An explanation of the flexible functionality in this domain family, based just on a static perspective of the structure-activity relationship, might fall short. More dynamic and conformational aspects in the protein fold can be the reasons for such functionality. Folding studies indeed showed an ample and malleable folding landscape for PDZ domains where multiple intermediate states were experimentally detected. Allosteric phenomena that resemble energetic coupling between residues have also been found in PDZ domains. Additionally, several PDZ domains are modulated by post-translational modifications, which introduce conformational switches that affect binding. Altogether, the ability to connect diverse partners might arise from the intrinsic plasticity of the PDZ fold.
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6
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Murciano‐Calles J, Coello A, Cámara‐Artigas A, Martinez JC. PDZ/PDZ interaction between PSD‐95 and nNOS neuronal proteins. J Mol Recognit 2019; 33:e2826. [DOI: 10.1002/jmr.2826] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/14/2019] [Accepted: 11/04/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Javier Murciano‐Calles
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of SciencesUniversity of Granada Granada Spain
| | - Andrea Coello
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of SciencesUniversity of Granada Granada Spain
| | - Ana Cámara‐Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3), Research Centre for Mediterranean Intensive Agriculture and Food Biotechnology (CIAMBITAL)University of Almería Almería Spain
| | - Jose C. Martinez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of SciencesUniversity of Granada Granada Spain
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7
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Liu Z, Thirumalai D. Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain. J Phys Chem B 2018; 122:1408-1416. [PMID: 29303586 DOI: 10.1021/acs.jpcb.7b11408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although we understand many aspects of how small proteins (number of residues less than about hundred) fold, it is a major challenge to quantitatively describe how large proteins self-assemble. To partially overcome this challenge, we performed simulations using the self-organized polymer model with side chains (SOP-SC) in guanidinium chloride (GdmCl), using the molecular transfer model (MTM), to describe the folding of the 110-residue PDZ3 domain. The simulations reproduce the folding thermodynamics accurately including the melting temperature (Tm), the stability of the folded state with respect to the unfolded state. We show that the calculated dependence of ln kobs (kobs is the relaxation rate) has the characteristic chevron shape. The slopes of the chevron plots are in good agreement with experiments. We show that PDZ3 folds by four major pathways populating two metastable intermediates, in accord with the kinetic partitioning mechanism. The structure of one of the intermediates, populated after polypeptide chain collapse, is structurally similar to an equilibrium intermediate. Surprisingly, the connectivities between the intermediates and hence, the fluxes through the pathways depend on the concentration of GdmCl. The results are used to predict possible outcomes for unfolding of PDZ domain subject to mechanical forces. Our study demonstrates that, irrespective of the size or topology, simulations based on MTM and SOP-SC offer a theoretical framework for describing the folding of proteins, mimicking precisely the conditions used in experiments.
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Affiliation(s)
- Zhenxing Liu
- Department of Physics, Beijing Normal University , Beijing 100875, China
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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8
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Addressing the role of the α-helical extension in the folding of the third PDZ domain from PSD-95. Sci Rep 2017; 7:12593. [PMID: 28974728 PMCID: PMC5626748 DOI: 10.1038/s41598-017-12827-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/14/2017] [Indexed: 01/22/2023] Open
Abstract
PDZ domains are one of the most important protein-protein interaction domains in human. While presenting a conserved three dimensional structure, a substantial number of PDZ domains display structural extensions suggested to be involved in their folding and binding mechanisms. The C-terminal α-helix extension (α3) of the third PDZ domain from PSD-95 (PDZ3) has been reported to have a role in function of the domain as well as in the stabilization of the native fold. Here we report an evaluation of the effect of the truncation of this additional helix on the folding and unfolding kinetics of PDZ3. Fluorescent variants of full length and truncated PDZ3 were produced and stopped-flow fluorescence measurements were made under different experimental conditions (pH, ionic strength and temperature) to investigate the folding kinetics of the respective variant. The results show that folding of PDZ3 is robust and that the mechanism is only marginally affected by the truncation, which contributes to a destabilization of the native state, but otherwise do not change the overall observed kinetics. Furthermore, the increase in the unfolding rate constants, but not the folding rate constant upon deletion of α3 suggests that the α-helical extension is largely unstructured in the folding transition state.
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