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Kang EJ, Kim JH, Kim YE, Lee H, Jung KB, Chang DH, Lee Y, Park S, Lee EY, Lee EJ, Kang HB, Rhyoo MY, Seo S, Park S, Huh Y, Go J, Choi JH, Choi YK, Lee IB, Choi DH, Seo YJ, Noh JR, Kim KS, Hwang JH, Jeong JS, Kwon HJ, Yoo HM, Son MY, Kim YG, Lee DH, Kim TY, Kwon HJ, Kim MH, Kim BC, Kim YH, Kang D, Lee CH. The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation. Nat Commun 2024; 15:2983. [PMID: 38582860 PMCID: PMC10998920 DOI: 10.1038/s41467-024-47275-8] [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: 10/03/2023] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
Akkermansia muciniphila has received great attention because of its beneficial roles in gut health by regulating gut immunity, promoting intestinal epithelial development, and improving barrier integrity. However, A. muciniphila-derived functional molecules regulating gut health are not well understood. Microbiome-secreted proteins act as key arbitrators of host-microbiome crosstalk through interactions with host cells in the gut and are important for understanding host-microbiome relationships. Herein, we report the biological function of Amuc_1409, a previously uncharacterised A. muciniphila-secreted protein. Amuc_1409 increased intestinal stem cell (ISC) proliferation and regeneration in ex vivo intestinal organoids and in vivo models of radiation- or chemotherapeutic drug-induced intestinal injury and natural aging with male mice. Mechanistically, Amuc_1409 promoted E-cadherin/β-catenin complex dissociation via interaction with E-cadherin, resulting in the activation of Wnt/β-catenin signaling. Our results demonstrate that Amuc_1409 plays a crucial role in intestinal homeostasis by regulating ISC activity in an E-cadherin-dependent manner and is a promising biomolecule for improving and maintaining gut health.
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Affiliation(s)
- Eun-Jung Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Veterinary Pathology, College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jae-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Livestock Products Analysis Division, Division of Animal health, Daejeon Metropolitan City Institute of Health and Environment, Daejeon, 34146, Republic of Korea
| | - Young Eun Kim
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
- School of Earth Sciences & Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hana Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kwang Bo Jung
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Dong-Ho Chang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Youngjin Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Shinhye Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eun-Ji Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ho Bum Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Moon-Young Rhyoo
- Laboratory Animal Resource Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seungwoo Seo
- School of Earth Sciences & Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Sohee Park
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bio-Molecular Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Yubin Huh
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bio-Molecular Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Jun Go
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung Hyeon Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Young-Keun Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - In-Bok Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Dong-Hee Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yun Jeong Seo
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Ran Noh
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kyoung-Shim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Jung Hwan Hwang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Ji-Seon Jeong
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
- Department of Measurement Science, Korea Research Institute of Standards and Science (KRISS) School of Precision Measurement, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Ha-Jeong Kwon
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
| | - Hee Min Yoo
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
- Department of Measurement Science, Korea Research Institute of Standards and Science (KRISS) School of Precision Measurement, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Mi-Young Son
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bio-Molecular Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Applied Biological Engineering, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Biosystems and Bioengineering, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Tae-Young Kim
- School of Earth Sciences & Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hyo-Jung Kwon
- Department of Veterinary Pathology, College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Byoung-Chan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- HealthBiome Inc., Daejeon, 34141, Republic of Korea
| | - Yong-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
| | - Dukjin Kang
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea.
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
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Dávalos AL, Rivera Echeverri JD, Favaro DC, Junio de Oliveira R, Penteado Battesini Carretero G, Lacerda C, Midea Cuccovia I, Cangussu Cardoso MV, Farah CS, Kopke Salinas R. Uncovering the Association Mechanism between Two Intrinsically Flexible Proteins. ACS Chem Biol 2024; 19:669-686. [PMID: 38486495 DOI: 10.1021/acschembio.3c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The understanding of protein-protein interaction mechanisms is key to the atomistic description of cell signaling pathways and for the development of new drugs. In this context, the mechanism of intrinsically disordered proteins folding upon binding has attracted attention. The VirB9 C-terminal domain (VirB9Ct) and the VirB7 N-terminal motif (VirB7Nt) associate with VirB10 to form the outer membrane core complex of the Type IV Secretion System injectisome. Despite forming a stable and rigid complex, VirB7Nt behaves as a random coil, while VirB9Ct is intrinsically dynamic in the free state. Here we combined NMR, stopped-flow fluorescence, and computer simulations using structure-based models to characterize the VirB9Ct-VirB7Nt coupled folding and binding mechanism. Qualitative data analysis suggested that VirB9Ct preferentially binds to VirB7Nt by way of a conformational selection mechanism at lower temperatures. However, at higher temperatures, energy barriers between different VirB9Ct conformations are more easily surpassed. Under these conditions the formation of non-native initial encounter complexes may provide alternative pathways toward the native complex conformation. These observations highlight the intimate relationship between folding and binding, calling attention to the fact that the two molecular partners must search for the most favored intramolecular and intermolecular interactions on a rugged and funnelled conformational energy landscape, along which multiple intermediates may lead to the final native state.
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Affiliation(s)
- Angy Liseth Dávalos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | | | - Denize C Favaro
- Department of Organic Chemistry, State University of Campinas, Campinas, 13083-862, Brazil
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York 10031, United States
| | - Ronaldo Junio de Oliveira
- Department of Physics, Institute of Exact, Natural and Educational Sciences, Federal University of Triângulo Mineiro, Uberaba, 38064-200, Brazil
| | | | - Caroline Lacerda
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Iolanda Midea Cuccovia
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | | | - Chuck S Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Roberto Kopke Salinas
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
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3
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Moretti AIS, Baksheeva VE, Roman AY, De Bessa TC, Devred F, Kovacic H, Tsvetkov PO. Exploring the Influence of Zinc Ions on the Conformational Stability and Activity of Protein Disulfide Isomerase. Int J Mol Sci 2024; 25:2095. [PMID: 38396772 PMCID: PMC10889200 DOI: 10.3390/ijms25042095] [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: 11/28/2023] [Revised: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
The interplay between metal ion binding and the activity of thiol proteins, particularly within the protein disulfide isomerase family, remains an area of active investigation due to the critical role that these proteins play in many vital processes. This research investigates the interaction between recombinant human PDIA1 and zinc ions, focusing on the subsequent implications for PDIA1's conformational stability and enzymatic activity. Employing isothermal titration calorimetry and differential scanning calorimetry, we systematically compared the zinc binding capabilities of both oxidized and reduced forms of PDIA1 and assessed the structural consequences of this interaction. Our results demonstrate that PDIA1 can bind zinc both in reduced and oxidized states, but with significantly different stoichiometry and more pronounced conformational effects in the reduced form of PDIA1. Furthermore, zinc binding was observed to inhibit the catalytic activity of reduced-PDIA1, likely due to induced alterations in its conformation. These findings unveil a potential regulatory mechanism in PDIA1, wherein metal ion binding under reductive conditions modulates its activity. Our study highlights the potential role of zinc in regulating the catalytic function of PDIA1 through conformational modulation, suggesting a nuanced interplay between metal binding and protein stability in the broader context of cellular redox regulation.
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Affiliation(s)
- Ana Iochabel Soares Moretti
- Vascular Biology Laboratory (LIM64), School of Medicine, Heart Institute (InCor), Cardiopneumology Department, University of São Paulo, Campus Sao Paulo, Sao Paulo 05403-000, Brazil
| | - Viktoria E. Baksheeva
- Aix Marseille Univ, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Sciences Médicales et Paramédicales, 13005 Marseille, France (F.D.); (H.K.)
| | - Andrei Yu. Roman
- Aix Marseille Univ, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Sciences Médicales et Paramédicales, 13005 Marseille, France (F.D.); (H.K.)
| | - Tiphany Coralie De Bessa
- Vascular Biology Laboratory (LIM64), School of Medicine, Heart Institute (InCor), Cardiopneumology Department, University of São Paulo, Campus Sao Paulo, Sao Paulo 05403-000, Brazil
| | - François Devred
- Aix Marseille Univ, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Sciences Médicales et Paramédicales, 13005 Marseille, France (F.D.); (H.K.)
| | - Hervé Kovacic
- Aix Marseille Univ, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Sciences Médicales et Paramédicales, 13005 Marseille, France (F.D.); (H.K.)
| | - Philipp O. Tsvetkov
- Aix Marseille Univ, CNRS, UMR 7051, INP, Inst Neurophysiopathol, Fac Sciences Médicales et Paramédicales, 13005 Marseille, France (F.D.); (H.K.)
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Tammara V, Angrover R, Sirur D, Das A. Flagellar motor protein-targeted search for the druggable site of Helicobacter pylori. Phys Chem Chem Phys 2024; 26:2111-2126. [PMID: 38131449 DOI: 10.1039/d3cp05024f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The deleterious impact of Helicobacter pylori (H. pylori) on human health is contingent upon its ability to create and sustain colony structure, which in turn is dictated by the effective performance of flagella - a multi-protein rotary nanodevice. Hence, to design an effective therapeutic strategy against H. pylori, we here conducted a systematic search for an effective druggable site by focusing on the structure-dynamics-energetics-stability landscape of the junction points of three 1 : 1 protein complexes (FliFC-FliGN, FliGM-FliMM, and FliYC-FliNC) that contribute mainly to the rotary motion of the flagella via the transformation of information along the junctions over a wide range of pH values operative in the stomach (from neutral to acidic). We applied a gamut of physiologically relevant perturbations in the form of thermal scanning and mechanical force to sample the entire quasi - and non-equilibrium conformational spaces available for the protein complexes under neutral and acidic pH conditions. Our perturbation-induced magnification of conformational distortion approach identified pH-independent protein sequence-specific evolution of precise thermally labile segments, which dictate the specific thermal unfolding mechanism of each complex and this complex-specific pH-independent structural disruption notion remains consistent under mechanical stress as well. Complementing the above observations with the relative rank-ordering of estimated equilibrium binding free energies between two protein sequences of a specific complex quantifies the extent of structure-stability modulation due to pH alteration, rationalizes the exceptional stability of H. pylori under acidic pH conditions, and identifies the pH-independent complex-sequence-segment-residue diagram for targeted drug design.
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Affiliation(s)
- Vaishnavi Tammara
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ruchika Angrover
- The Departments of the University Institute of Biotechnology, Chandigarh University, NH-05, Ludhiana - Chandigarh State Highway, Punjab 140413, India
| | - Disha Sirur
- School of Physical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India
| | - Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Seelig J, Seelig A. Chemical Protein Unfolding - A Simple Cooperative Model. J Phys Chem B 2023; 127:8296-8304. [PMID: 37735883 PMCID: PMC10561279 DOI: 10.1021/acs.jpcb.3c03558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/08/2023] [Indexed: 09/23/2023]
Abstract
Chemical unfolding with guanidineHCl or urea is a common method to study the conformational stability of proteins. The analysis of unfolding isotherms is usually performed with an empirical linear extrapolation method (LEM). A large positive free energy is assigned to the native protein, which is usually considered to be a minimum of the free energy. The method thus contradicts common expectations. Here, we present a multistate cooperative model that addresses specifically the binding of the denaturant to the protein and the cooperativity of the protein unfolding equilibrium. The model is based on a molecular statistical-mechanical partition function of the ensemble, but simple solutions for the calculation of the binding isotherm and the associated free energy are presented. The model is applied to 23 published unfolding isotherms of small and large proteins. For a given denaturant, the binding constant depends on temperature and pH but shows little protein specificity. Chemical unfolding is less cooperative than thermal unfolding. The cooperativity parameter σ is at least 2 orders of magnitude larger than that of thermal unfolding. The multistate cooperative model predicts zero free energy for the native protein, which becomes strongly negative beyond the midpoint concentration of unfolding. The free energy to unfold a cooperative unit corresponds exactly to the diffusive energy of the denaturant concentration gradient necessary for unfolding. The temperature dependence of unfolding isotherms yields the denaturant-induced unfolding entropy and, in turn, the unfolding enthalpy. The multistate cooperative model provides molecular insight and is as simple to apply as the LEM but avoids the conceptual difficulties of the latter.
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Affiliation(s)
- Joachim Seelig
- Biozentrum, University
of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
| | - Anna Seelig
- Biozentrum, University
of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
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6
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Cun X, Jansman MMT, Liu X, Boureau V, Thulstrup PW, Hosta-Rigau L. Hemoglobin-stabilized gold nanoclusters displaying oxygen transport ability, self-antioxidation, auto-fluorescence properties and long-term storage potential. RSC Adv 2023; 13:15540-15553. [PMID: 37228685 PMCID: PMC10203863 DOI: 10.1039/d3ra00689a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
The development of hemoglobin (Hb)-based oxygen carriers (HBOCs) holds a lot of potential to overcome important drawbacks of donor blood such as a short shelf life or the potential risk of infection. However, a crucial limitation of current HBOCs is the autoxidation of Hb into methemoglobin (metHb), which lacks oxygen-carrying capacity. Herein, we address this challenge by fabricating a Hb and gold nanoclusters (AuNCs) composite (Hb@AuNCs) which preserves the exceptional features of both systems. Specifically, the Hb@AuNCs retain the oxygen-transporting properties of Hb, while the AuNCs provide antioxidant functionality as shown by their ability to catalytically deplete harmful reactive oxygen species (ROS). Importantly, these ROS-scavenging properties translate into antioxidant protection by minimizing the autoxidation of Hb into non-functional metHb. Furthermore, the AuNCs render Hb@AuNCs with auto-fluorescence properties which could potentially allow them to be monitored once administered into the body. Last but not least, these three features (i.e., oxygen transport, antioxidant and fluorescence properties) are well maintained following storage as a freeze-dried product. Thus, overall, the as-prepared Hb@AuNCs hold the potential to be used as a multifunctional blood surrogate in the near future.
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Affiliation(s)
- Xingli Cun
- DTU Health Tech, Center for Nanomedicine and Theranostics, Technical University of Denmark Nils Koppels Allé, Building 423 2800 Kgs. Lyngby Denmark
| | - Michelle M T Jansman
- DTU Health Tech, Center for Nanomedicine and Theranostics, Technical University of Denmark Nils Koppels Allé, Building 423 2800 Kgs. Lyngby Denmark
| | - Xiaoli Liu
- DTU Health Tech, Center for Nanomedicine and Theranostics, Technical University of Denmark Nils Koppels Allé, Building 423 2800 Kgs. Lyngby Denmark
| | - Victor Boureau
- Interdisciplinary Center for Electron Microscopy (CIME), École Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Leticia Hosta-Rigau
- DTU Health Tech, Center for Nanomedicine and Theranostics, Technical University of Denmark Nils Koppels Allé, Building 423 2800 Kgs. Lyngby Denmark
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7
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Seelig J, Seelig A. Protein Stability─Analysis of Heat and Cold Denaturation without and with Unfolding Models. J Phys Chem B 2023; 127:3352-3363. [PMID: 37040567 PMCID: PMC10123674 DOI: 10.1021/acs.jpcb.3c00882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Protein stability is important in many areas of life sciences. Thermal protein unfolding is investigated extensively with various spectroscopic techniques. The extraction of thermodynamic properties from these measurements requires the application of models. Differential scanning calorimetry (DSC) is less common, but is unique as it measures directly a thermodynamic property, that is, the heat capacity Cp(T). The analysis of Cp(T) is usually performed with the chemical equilibrium two-state model. This is not necessary and leads to incorrect thermodynamic consequences. Here we demonstrate a straightforward model-independent evaluation of heat capacity experiments in terms of protein unfolding enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T)). This now allows the comparison of the experimental thermodynamic data with the predictions of different models. We critically examined the standard chemical equilibrium two-state model, which predicts a positive free energy for the native protein, and diverges distinctly from the experimental temperature profiles. We propose two new models which are equally applicable to spectroscopy and calorimetry. The ΘU(T)-weighted chemical equilibrium model and the statistical-mechanical two-state model provide excellent fits of the experimental data. They predict sigmoidal temperature profiles for enthalpy and entropy, and a trapezoidal temperature profile for the free energy. This is illustrated with experimental examples for heat and cold denaturation of lysozyme and β-lactoglobulin. We then show that the free energy is not a good criterion to judge protein stability. More useful parameters are discussed, including protein cooperativity. The new parameters are embedded in a well-defined thermodynamic context and are amenable to molecular dynamics calculations.
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Affiliation(s)
- Joachim Seelig
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
| | - Anna Seelig
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
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8
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Seelig J, Seelig A. Protein Unfolding—Thermodynamic Perspectives and Unfolding Models. Int J Mol Sci 2023; 24:ijms24065457. [PMID: 36982534 PMCID: PMC10049513 DOI: 10.3390/ijms24065457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
We review the key steps leading to an improved analysis of thermal protein unfolding. Thermal unfolding is a dynamic cooperative process with many short-lived intermediates. Protein unfolding has been measured by various spectroscopic techniques that reveal structural changes, and by differential scanning calorimetry (DSC) that provides the heat capacity change Cp(T). The corresponding temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) have thus far been evaluated using a chemical equilibrium two-state model. Taking a different approach, we demonstrated that the temperature profiles of enthalpy ΔH(T), entropy ΔS(T), and free energy ΔG(T) can be obtained directly by a numerical integration of the heat capacity profile Cp(T). DSC thus offers the unique possibility to assess these parameters without resorting to a model. These experimental parameters now allow us to examine the predictions of different unfolding models. The standard two-state model fits the experimental heat capacity peak quite well. However, neither the enthalpy nor entropy profiles (predicted to be almost linear) are congruent with the measured sigmoidal temperature profiles, nor is the parabolic free energy profile congruent with the experimentally observed trapezoidal temperature profile. We introduce three new models, an empirical two-state model, a statistical–mechanical two-state model and a cooperative statistical-mechanical multistate model. The empirical model partially corrects for the deficits of the standard model. However, only the two statistical–mechanical models are thermodynamically consistent. The two-state models yield good fits for the enthalpy, entropy and free energy of unfolding of small proteins. The cooperative statistical–mechanical multistate model yields perfect fits, even for the unfolding of large proteins such as antibodies.
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9
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Izumi Y, Matsuo K, Yokoya A. Secondary structural analyses of histone H2A-H2B proteins extracted from heated cells. Chirality 2023; 35:165-171. [PMID: 36578136 DOI: 10.1002/chir.23529] [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: 10/31/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022]
Abstract
Histone proteins, building blocks of chromatins, participate in enzymatic reactions in cells heated at around 45°C though in vitro the denaturation of histones significantly proceeds at a similar temperature. It implies that unidentified mechanisms prevent thermal denaturation of histones in vivo. However, studies on the histone structures in the heated cells have been scarce. Here, we analyzed the secondary structures of histone H2A-H2B proteins originating from the heated cells using circular dichroism spectroscopy. The secondary structure contents of the H2A-H2B extracted from the heated cells differed from those of H2A-H2B both native and denatured in vitro but reverted to the native structures by incubating the heated cells at 37°C within 2 h. Such structural flexibility may play a role in protecting genomic functions governed by chromatin structures from heat stresses.
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Affiliation(s)
- Yudai Izumi
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Ibaraki, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Research Center (HiSOR), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Ibaraki, Japan
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10
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Tran M, Signorelli RL, Yamaguchi A, Chen E, Holinstat M, Iavarone AT, Offenbacher AR, Holman T. Biochemical and hydrogen-deuterium exchange studies of the single nucleotide polymorphism Y649C in human platelet 12-lipoxygenase linked to a bleeding disorder. Arch Biochem Biophys 2023; 733:109472. [PMID: 36442529 PMCID: PMC9888433 DOI: 10.1016/j.abb.2022.109472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Human platelet 12-lipoxygenase (h12-LOX) is responsible for the formation of oxylipin products that play an important role in platelet aggregation. Single nucleotide polymorphisms (SNPs) of h12-LOX have been implicated in several diseases. In this study, we investigate the structural, dynamical, and functional impact of a h12-LOX SNP that generates a tyrosine-to-cysteine mutation at a buried site (Y649C h12-LOX) and was previously ascribed with reduced levels of 12(S)-hydroxyeicosatetraenoic acid (12S-HETE) production in isolated platelets. Herein, in vitro Michaelis-Menten kinetics show reduced catalytic rates for Y649C compared to WT h12-LOX at physiological or lower temperatures. Both proteins exhibited similar melting temperatures, metal content, and oligomerization state. Liposome binding for both proteins was also dependent upon the presence of calcium, temperature, and liposome composition; however, the Y649C variant was found to have lowered binding capacity to liposomes compared to WT at physiological temperatures. Further, hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments revealed a regional defined enhancement in the peptide mobility caused by the mutation. This increased instability for the mutation stemmed from a change in an interaction with an arched helix that lines the substrate binding site, located ≥15 Å from the mutation site. Finally, differential scanning calorimetry demonstrated a reduced protein (un)folding enthalpy, consistent with the HDX results. Taken together, these results demonstrate remarkable similarity between the mutant and WT h12-LOX, and yet, subtle changes in activity, membrane affinity and protein stability may be responsible for the significant physiological changes that the Y649C SNP manifests in platelet biology.
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Affiliation(s)
- Michelle Tran
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Adriana Yamaguchi
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eefie Chen
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Michael Holinstat
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA,Corresponding author. (A.R. Offenbacher)
| | - Theodore Holman
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA,Corresponding author. (T. Holman)
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11
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Zhang Y, Zhang W, Snow T, Ju Y, Liu Y, Smith AJ, Prabakar S. Minimising Chemical Crosslinking for Stabilising Collagen in Acellular Bovine Pericardium: Mechanistic Insights via Structural Characterisations. Acta Biomater 2022; 152:113-123. [DOI: 10.1016/j.actbio.2022.08.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/01/2022]
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12
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Garg A, Sinha S. Doxorubicin induced aggregation of α-synuclein: Insights into the mechanism of drug induced Parkinsonism. Colloids Surf B Biointerfaces 2022; 212:112371. [PMID: 35131711 DOI: 10.1016/j.colsurfb.2022.112371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022]
Abstract
The aggregation of α-synuclein is a prominent feature of Parkinson's disease. It is induced by factors such as genetic mutations and presence of metal salts leading to Parkinson's like symptoms. Existing case studies show that patients undergoing cancer chemotherapeutics are also prone to developing Parkinson's like symptoms. However, the underlying cause behind onset of these symptoms is not understood. It is not clear whether the administration of chemotherapeutic drugs alter the structural stability of α-synuclein. In the present study, we address this question by looking into the effect of chemotherapeutic drug namely doxorubicin on the α-synuclein stability. Using complementary spectroscopic, molecular docking and imaging techniques, we observe that doxorubicin interacted with central aggregation prone region of α-synuclein and induces destabilization leading to aggregation. We also show that the combination of doxorubicin and L-DOPA drugs impedes the α-synuclein aggregation. This may explain the reason behind the effectiveness of using L-DOPA against Parkinson's like symptoms.
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Affiliation(s)
- Ankush Garg
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Knowledge City, Sahibzada Ajit Singh Nagar, Punjab 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Knowledge City, Sahibzada Ajit Singh Nagar, Punjab 140306, India.
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13
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Seelig J, Seelig A. Molecular understanding of calorimetric protein unfolding experiments. BIOPHYSICAL REPORTS 2022; 2:100037. [PMID: 36425081 PMCID: PMC9680786 DOI: 10.1016/j.bpr.2021.100037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/02/2021] [Indexed: 06/16/2023]
Abstract
Testing and predicting protein stability gained importance because proteins, including antibodies, became pharmacologically relevant in viral and cancer therapies. Isothermal scanning calorimetry is the principle method to study protein stability. Here, we use the excellent experimental heat capacity Cp(T) data from the literature for a critical inspection of protein unfolding as well as for the test of a new cooperative model. In the relevant literature, experimental temperature profiles of enthalpy, Hcal(T), entropy, Scal(T), and free energy, Gcal(T) are missing. First, we therefore calculate the experimental Hcal(T), Scal(T), and Gcal(T) from published Cp(T) thermograms. Considering only the unfolding transition proper, the heat capacity and all thermodynamic functions are zero in the region of the native protein. In particular, the free energy of the folded proteins is also zero and Gcal(T) displays a trapezoidal temperature profile when cold denaturation is included. Second, we simulate the DSC-measured thermodynamic properties with a new molecular model based on statistical-mechanical thermodynamics. The model quantifies the protein cooperativity and predicts the aggregate thermodynamic variables of the system with molecular parameters only. The new model provides a perfect simulation of all thermodynamic properties, including the observed trapezoidal Gcal(T) temperature profile. Importantly, the new cooperative model can be applied to a broad range of protein sizes, including antibodies. It predicts not only heat and cold denaturation but also provides estimates of the unfolding kinetics and allows a comparison with molecular dynamics calculations and quasielastic neutron scattering experiments.
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Affiliation(s)
| | - Anna Seelig
- Biozentrum, University of Basel, Basel, Switzerland
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14
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Expanding the toolbox for predictive parameters describing antibody stability considering thermodynamic and kinetic determinants. Pharm Res 2021; 38:2065-2089. [PMID: 34904201 DOI: 10.1007/s11095-021-03120-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 10/03/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Introduction of the activation energy (Ea) as a kinetic parameter to describe and discriminate monoclonal antibody (mAb) stability. METHODS Ea is derived from intrinsic fluorescence (IF) unfolding thermograms. An apparent irreversible three-state fit model based on the Arrhenius integral is developed to determine Ea of respective unfolding transitions. These activation energies are compared to the thermodynamic parameter of van´t Hoff enthalpies (∆Hvh). Using a set of 34 mAbs formulated in four different formulations, both the apparent thermodynamic and kinetic parameters together with apparent melting temperatures are correlated collectively with each other to storage stabilities to evaluate its predictive power with respect to long-term effects potentially reflected in shelf-life. RESULTS Ea allows for the discrimination of (i) different parent mAbs, (ii) different variants that originate from parent mAbs, and (iii) different formulations. Interestingly, we observed that the Ea of the CH2 unfolding transition shows strongest correlations with monomer and aggregate content after storage at accelerated and stress conditions when collectively compared to ∆Hvh and Tm of the CH2 transition. Moreover, the predictive parameters determined for the CH2 domain show generally stronger correlations with monomer and aggregate content than those derived for the Fab. Qualitative assessment by ranking Ea of the Fab domain showed good agreement with monomer content in storage stabilities of individual mAb sub-sets. CONCLUSION Ea from IF unfolding transitions can be used in addition to other commonly used thermodynamic predictive parameters to discriminate and characterize thermal stability of different mAbs in different formulations. Hence, it shows great potential for antibody engineering and formulation scientists.
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15
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Zhang W, Liu M, Yu L, Mo S, Deng Z, Liu S, Yang Y, Wang C, Wang C. Perturbation effect of single polar group substitution on the Self-Association of amphiphilic peptide helices. J Colloid Interface Sci 2021; 610:1005-1014. [PMID: 34887062 DOI: 10.1016/j.jcis.2021.11.154] [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: 08/26/2021] [Revised: 10/18/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
As an important attempt towards creating hierarchical structures more like nature, the peptide is employed as a building block to build supramolecular architectures. An emerging question is whether the molecular mechanism of self-assembly obtained from the small molecule system, e.g., the driving forces of assembly are conventionally regarded as pairwise-additive, can be manifested in the self-association of biologically relevant amphiphilic peptides. A peptide, KRT-R, was derived from the 120-144 segment of keratin 14. The single cation-to-cation substitution with KRT-R at the site of 125 from arginine (R) to either lysine (K) or histidine (H) results in the peptide helices, KRT-K and KRT-H, sharing 96% sequence identity. These KRT-derived peptides possess similarities in the folding structures but exhibit divergent self-assembled structures. KRT-R and KRT-K self-assemble into sheets and fibrils, respectively. Whereas KRT-H associates into heterogeneous structures, including sheets, particles, and branched networks. The intrinsic tyrosine fluorescence spectroscopy measurements with the KRT-derived peptides within a temperature range of 25 °C to 95 °C reveal that the heating-triggered structural transitions of KRT-derived peptides are divergent. The alternation of single cationic residue changes the thermodynamic signature of peptide assemblies upon heating. A chemical denaturation experiment with KRT-derived peptides indicates that the intermolecular interactions that govern the supramolecular architectures formed by peptides are distinct. Overall, our work demonstrates the contribution of the interplay among various noncovalent interactions to supramolecular assembly.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Zhun Deng
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Shuli Liu
- Department of Clinical Laboratory, Peking University Civil Aviation School of Clinical Medicine, Beijing 100123, China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
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16
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Pal S, Banerjee S, Prabhakaran EN. α-Helices propagating from stable nucleators exhibit unconventional thermal folding. FEBS Lett 2021; 595:2942-2949. [PMID: 34716991 DOI: 10.1002/1873-3468.14216] [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: 09/03/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/07/2022]
Abstract
Although the effect of thermal perturbations on protein structure has long been modeled in helical peptides, several details, such as the relation between the thermal stabilities of the propagating and nucleating segments of helices, remain elusive. We had earlier reported on the helix-nucleating propensities of covalent H-bond surrogate-constrained α-turns. Here, we analyze the thermal stabilities of helices that propagate along peptides appended to these α-helix nucleators using their NMR and far-UV CD spectra. Unconventional thermal folding of these helix models reveals that the helical fold in propagating backbones resists thermal perturbations as long as their nucleating template is intact. The threshold temperature of such resistance is also influenced by the extent of similarity between the natures of helical folds in the nucleating and propagating segments. Correlations between helicities and rigidities of helix-nucleating and helix-propagating segments reveal subtle interdependence, which explains cooperativity and residual helix formation during protein folding.
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Affiliation(s)
- Sunit Pal
- Department of Chemistry, Indian Institute of Science, Bangalore, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, India
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17
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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins. Commun Chem 2021; 4:57. [PMID: 36697562 PMCID: PMC9814862 DOI: 10.1038/s42004-021-00499-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.
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19
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Lindorff-Larsen K, Teilum K. Linking thermodynamics and measurements of protein stability. Protein Eng Des Sel 2021; 34:6173616. [PMID: 33724431 DOI: 10.1093/protein/gzab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/21/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible folding/unfolding transitions and the experimental methods that are available for extracting thermodynamic parameters. We highlight the importance of modelling both how the folding equilibrium depends on a perturbing variable such as temperature or denaturant concentration, and the importance of modelling the baselines in the experimental observables.
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Affiliation(s)
- Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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20
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Patel AY, Jonnalagadda KS, Paradis N, Vaden TD, Wu C, Caputo GA. Effects of Ionic Liquids on Metalloproteins. Molecules 2021; 26:514. [PMID: 33478102 PMCID: PMC7835893 DOI: 10.3390/molecules26020514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/28/2023] Open
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
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Affiliation(s)
- Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | | | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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21
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Konar M, Sahoo H. Exploring the chemistry behind protein-glycosaminoglycan conjugate: A steady-state and kinetic spectroscopy based approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118726. [PMID: 32745937 DOI: 10.1016/j.saa.2020.118726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
The impact of glycosaminoglycan (chondroitin sulphate, CS) on bone morphogenetic protein - 2 (BMP - 2) structure, stability (thermal and chemical), association kinetics and conformation was monitored by multiple spectroscopic techniques (UV-Visible, fluorescence and circular dichroism). The absorbance in peptide region and fluorescence intensity of BMP - 2 was quenched in presence of CS; thus, confirming the formation of a ground-state complex. As there was an increase in Stern-Volmer constant observed as a function of temperature, idea of dynamic quenching was established. However, the negligible changes in lifetime indicated static quenching; thus, making the process a combination of static-dynamic quenching. Basically, the protein - glycan interaction was driven by entropy of the system and mediated by hydrophobic interactions. Secondary structure (CD spectroscopy) of native protein was significantly affected (intensity became more negative) in presence of CS, thus, introducing more compactness in the protein. CS infused thermal and chemical stability into BMP - 2 via alteration in its conformation. The rate of association was inversely proportional to concentration of quencher (CS), which confirmed the correlation between large size (~ 5 times the size of protein) and structural complexity of CS with fewer binding sites present in BMP - 2. The rate of association in presence of urea, suggested a decrease in association rate as a function of urea concentration for 15 μM CS. Experimental evidences suggested an interaction between protein and glycan mediated by hydrophobic interactions, which deciphers structural, thermal and chemical stability into protein.
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Affiliation(s)
- Monidipa Konar
- Biophysical Chemistry Lab, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Harekrushna Sahoo
- Biophysical Chemistry Lab, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India.
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22
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Ulisse S, Iorio M, Armillotta G, Laguardia C, Testa L, Capista S, Centorame P, Traini S, Serroni A, Monaco F, Caporale M, Mercante MT, Di Ventura M. Production and Easy One-Step Purification of Bluetongue Recombinant VP7 from Infected Sf9 Supernatant for an Immunoenzymatic Assay (ELISA). Mol Biotechnol 2020; 63:40-52. [PMID: 33078348 PMCID: PMC7820184 DOI: 10.1007/s12033-020-00282-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 01/06/2023]
Abstract
Bluetongue (BT) is non-contagious, vector-borne viral disease of domestic and wild ruminants, transmitted by midges (Culicoides spp.) and is caused by Bluetongue virus (BTV). BTV is the type species of the Orbivirus genus within the Reoviridae family and possesses a genome consisting of 10 double-stranded RNA segments encoding 7 structural and 4 nonstructural proteins. Viral Protein 7 (VP7) is the major sera group-specific protein and is a good antigen candidate for immunoenzymatic assays for the BT diagnosis. In our work, BTV-2 recombinant VP7 (BTV-2 recVP7), expressed in Spodoptera frugiperda (Sf9) cells using a baculovirus system, was produced and purified by affinity chromatography from the supernatant of infected cell culture. The use of the supernatant allowed us to obtain a high quantity of recombinant protein with high purity level by an easy one-step procedure, rather than the multistep purification from the pellet. RecVP7-BTV2 was detected using a MAb anti-BTV in Western blot and it was used to develop an immunoenzymatic assay.
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Affiliation(s)
- S Ulisse
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - M Iorio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy.
| | - G Armillotta
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - C Laguardia
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - L Testa
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - S Capista
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - P Centorame
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - S Traini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - A Serroni
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - F Monaco
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - M Caporale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - M T Mercante
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - M Di Ventura
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
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23
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Daso R, Osborn LJ, Thomas MF, Banerjee IA. Development of Nanoscale Hybrids from Ionic Liquid-Peptide Amphiphile Assemblies as New Functional Materials. ACS OMEGA 2020; 5:14543-14554. [PMID: 32596592 PMCID: PMC7315584 DOI: 10.1021/acsomega.0c01254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/25/2020] [Indexed: 05/11/2023]
Abstract
Over the years, ionic liquids (ILs) have gained tremendous importance because of their unique properties and plethora of applications. In this work, we have developed a new nanoscale hybrid gel consisting of 1-ethyl-3-methylimidazolium dimethyl phosphate, [C2mim][dmp], and self-assembled peptide nanoassemblies. The peptide nanoassemblies were formed by self-assembly of a newly synthesized peptide bolaamphiphile bis(N-α-amido-threonine) 1,7 heptane dicarboxylate (ThrC7). Upon mild heating and sonication of the IL and ThrC7 nanoassemblies, ThrC7-IL nanocomposites were formed. We explored the formation of nanohybrids by varying the ratio of IL to ThrC7 assemblies. While at lower IL ratios, a gelatinous matrix was formed, at higher IL ratios, highly ordered multilayered structures were observed by atomic force microscopy (AFM) imaging. The interactions between the ThrC7 nanofibers and [C2mim][dmp] IL were probed by Fourier transform infrared spectroscopy, transmission electron microscopy, and AFM imaging. Differential scanning calorimetry and thermogravimetric analysis showed that the nanohybrids illustrated distinct thermal phase changes due to changes in hydrogen bonding interactions and unfolding of the nanoassemblies. The viscoelastic behavior of the nanohybrids indicated that the materials displayed higher storage modulus upon incorporation of the ThrC7 nanoassemblies when compared to the IL. Furthermore, the nanohybrids were found to adhere to and promote proliferation of human dermal fibroblasts, while cytotoxicity was observed toward MCF-7 breast cancer cells. Thus, for the first time, we have developed peptide-based nanohybrids with an imidazolium-based IL with unique structural properties that may open new avenues for exploring potential biological applications.
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Affiliation(s)
- Rachel
E. Daso
- Department
of Chemistry, Fordham University, 441 East Fordham Road, Bronx, New York 10458, United States
| | - Luke J. Osborn
- Department
of Natural Science, Fordham College at Lincoln
Center, 113 W. 60th Street, New York, New York 10023, United States
| | - Marie F. Thomas
- Department
of Natural Science, Fordham College at Lincoln
Center, 113 W. 60th Street, New York, New York 10023, United States
| | - Ipsita A. Banerjee
- Department
of Chemistry, Fordham University, 441 East Fordham Road, Bronx, New York 10458, United States
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Li H, Wang Y, Ye M, Li S, Li D, Ren H, Wang M, Du L, Li H, Veglia G, Gao J, Weng Y. Dynamical and allosteric regulation of photoprotection in light harvesting complex II. Sci China Chem 2020; 63:1121-1133. [PMID: 33163014 DOI: 10.1007/s11426-020-9771-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Major light-harvesting complex of photosystem II (LHCII) plays a dual role in light-harvesting and excited energy dissipation to protect photodamage from excess energy. The regulatory switch is induced by increased acidity, temperature or both. However, the molecular origin of the protein dynamics at the atomic level is still unknown. We carried out temperature-jump time-resolved infrared spectroscopy and molecular dynamics simulations to determine the energy quenching dynamics and conformational changes of LHCII trimers. We found that the spontaneous formation of a pair of local α-helices from the 310-helix E/loop and the C-terminal coil of the neighboring monomer, in response to the increased environmental temperature and/or acidity, induces a scissoring motion of transmembrane helices A and B, shifting the conformational equilibrium to a more open state, with an increased angle between the associated carotenoids. The dynamical allosteric conformation change leads to close contacts between the first excited state of carotenoid lutein 1 and chlorophyll pigments, facilitating the fluorescence quenching. Based on these results, we suggest a unified mechanism by which the LHCII trimer controls the dissipation of excess excited energy in response to increased temperature and acidity, as an intrinsic result of intense sun light in plant photosynthesis.
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Affiliation(s)
- Hao Li
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Manping Ye
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shanshan Li
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Deyong Li
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Haisheng Ren
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mohan Wang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luchao Du
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Heng Li
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Gianluigi Veglia
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yuxiang Weng
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Structural and conformational behavior of MurE ligase from Salmonella enterica serovar Typhi at different temperature and pH conditions. Int J Biol Macromol 2020; 150:389-399. [DOI: 10.1016/j.ijbiomac.2020.01.306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 11/20/2022]
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26
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Melien R, Garidel P, Hinderberger D, Blech M. Thermodynamic Unfolding and Aggregation Fingerprints of Monoclonal Antibodies Using Thermal Profiling. Pharm Res 2020; 37:78. [DOI: 10.1007/s11095-020-02792-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023]
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27
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Garidel P, Eiperle A, Blech M, Seelig J. Thermal and Chemical Unfolding of a Monoclonal IgG1 Antibody: Application of the Multistate Zimm-Bragg Theory. Biophys J 2020; 118:1067-1075. [PMID: 32049058 PMCID: PMC7063443 DOI: 10.1016/j.bpj.2019.12.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 11/25/2022] Open
Abstract
The thermal unfolding of a recombinant monoclonal antibody IgG1 (mAb) was measured with differential scanning calorimetry (DSC). The DSC thermograms reveal a pretransition at 72°C with an unfolding enthalpy of ΔHcal ∼200-300 kcal/mol and a main transition at 85°C with an enthalpy of ∼900-1000 kcal/mol. In contrast to small single-domain proteins, mAb unfolding is a complex reaction that is analyzed with the multistate Zimm-Bragg theory. For the investigated mAb, unfolding is characterized by a cooperativity parameter σ ∼6 × 10-5 and a Gibbs free energy of unfolding of gnu ∼100 cal/mol per amino acid. The enthalpy of unfolding provides the number of amino acid residues ν participating in the unfolding reaction. On average, ν∼220 ± 50 amino acids are involved in the pretransition and ν∼850 ± 30 in the main transition, accounting for ∼90% of all amino acids. Thermal unfolding was further studied in the presence of guanidineHCl. The chemical denaturant reduces the unfolding enthalpy ΔHcal and lowers the midpoint temperature Tm. Both parameters depend linearly on the concentration of denaturant. The guanidineHCl concentrations needed to unfold mAb at 25°C are predicted to be 2-3 M for the pretransition and 5-7 M for the main transition, varying with pH. GuanidineHCl binds to mAb with an exothermic binding enthalpy, which partially compensates the endothermic mAb unfolding enthalpy. The number of guanidineHCl molecules bound upon unfolding is deduced from the DSC thermograms. The bound guanidineHCl-to-unfolded amino acid ratio is 0.79 for the pretransition and 0.55 for the main transition. The pretransition binds more denaturant molecules and is more sensitive to unfolding than the main transition. The current study shows the strength of the Zimm-Bragg theory for the quantitative description of unfolding events of large, therapeutic proteins, such as a monoclonal antibody.
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Affiliation(s)
- Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Biberach an der Riss, Germany.
| | - Andrea Eiperle
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Biberach an der Riss, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Biberach an der Riss, Germany
| | - Joachim Seelig
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, Switzerland.
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28
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Pal S, Pyne P, Samanta N, Ebbinghaus S, Mitra RK. Thermal stability modulation of the native and chemically-unfolded state of bovine serum albumin by amino acids. Phys Chem Chem Phys 2020; 22:179-188. [DOI: 10.1039/c9cp04887a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cells are crowded with various cosolutes including salts, osmolytes, nucleic acids, peptides and proteins.
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Affiliation(s)
- Saikat Pal
- Department of Chemical
- Biological and Macromolecular Sciences
- S N Bose National Centre for Basic Sciences
- Kolkata 700106
- India
| | - Partha Pyne
- Department of Chemical
- Biological and Macromolecular Sciences
- S N Bose National Centre for Basic Sciences
- Kolkata 700106
- India
| | - Nirnay Samanta
- Institute for Physical and Theoretical Chemistry
- TU Braunschweig
- BRICS
- 56 D-38106 Braunschweig
- Germany
| | - Simon Ebbinghaus
- Institute for Physical and Theoretical Chemistry
- TU Braunschweig
- BRICS
- 56 D-38106 Braunschweig
- Germany
| | - Rajib Kumar Mitra
- Department of Chemical
- Biological and Macromolecular Sciences
- S N Bose National Centre for Basic Sciences
- Kolkata 700106
- India
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29
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Rodrigues RM, Claro B, Bastos M, Pereira RN, Vicente AA, Petersen SB. Multi-step thermally induced transitions of β-lactoglobulin – An in situ spectroscopy approach. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2019.104562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Li-Blatter X, Seelig J. Thermal and Chemical Unfolding of Lysozyme. Multistate Zimm-Bragg Theory Versus Two-State Model. J Phys Chem B 2019; 123:10181-10191. [PMID: 31686511 DOI: 10.1021/acs.jpcb.9b08816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Thermal and chemical unfolding of lysozyme in the presence of the guanidine HCl denaturant is a model system to compare the conventional two-state model of protein unfolding with the multistate Zimm-Bragg theory. The two-state model is shown to be the noncooperative limit of the Zimm-Bragg theory. In particular, the Zimm-Bragg theory provides a molecular interpretation of the empirical linear extrapolation method (LEM) of the two-state model. Differential scanning calorimetry (DSC) experiments reported in the literature are analyzed with both methods. Lysozyme unfolding is associated with a large endothermic enthalpy that decreases significantly upon addition of guanidine HCl. In contrast, the Gibbs free energy of unfolding is small, negative, and independent of the guanidine HCl concentration, contradicting, in part, the conclusions of the LEM. The unfolding enthalpy is compensated by an even larger entropy term. The multistate Zimm-Bragg theory predicts a larger conformational enthalpy and a smaller Gibbs free energy than the two-state model. The Zimm-Bragg theory provides the protein cooperativity parameter, the average length of independently folding protein domains, and the Gibbs free energy of unfolding of individual amino acid residues. Guanidine HCl binding to lysozyme is exothermic and counteracts the endothermic unfolding enthalpy. The number of bound denaturant molecules is determined from the decrease in enthalpy and is extrapolated to the guanidine HCl-to-amino acid stoichiometry at complete lysozyme unfolding. Chemical unfolding isotherms measured with circular dichroism (CD) spectroscopy are analyzed with both models. The chemical Zimm-Bragg theory is a cooperative molecular model, yielding the guanidine HCl binding constant and the protein cooperativity parameter. It allows a quantitative comparison between thermal and chemical protein unfolding. The two reactions have almost identical changes in Gibbs free energy. However, thermal unfolding is significantly more cooperative than chemical unfolding. Finally, distinct differences are observed in thermal unfolding between DSC and CD spectroscopy.
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Affiliation(s)
- Xiaochun Li-Blatter
- Biozentrum , University of Basel , Klingelbergstrasse 50/70 , CH-4056 Basel , Switzerland
| | - Joachim Seelig
- Biozentrum , University of Basel , Klingelbergstrasse 50/70 , CH-4056 Basel , Switzerland
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31
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The role of circular dichroism spectroscopy in the era of integrative structural biology. Curr Opin Struct Biol 2019; 58:191-196. [DOI: 10.1016/j.sbi.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022]
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32
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The Effect of Dimethyl Sulfoxide on the Lysozyme Unfolding Kinetics, Thermodynamics, and Mechanism. Biomolecules 2019; 9:biom9100547. [PMID: 31569484 PMCID: PMC6843525 DOI: 10.3390/biom9100547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
The thermal stability of proteins in the presence of organic solvents and the search for ways to increase this stability are important topics in industrial biocatalysis and protein engineering. The denaturation of hen egg-white lysozyme in mixtures of water with dimethyl sulfoxide (DMSO) with a broad range of compositions was studied using a combination of differential scanning calorimetry (DSC), circular dichroism (CD), and spectrofluorimetry techniques. In this study, for the first time, the kinetics of unfolding of lysozyme in DMSO–water mixtures was characterized. In the presence of DMSO, a sharp decrease in near-UV CD and an increase in the fluorescence signal were observed at lower temperatures than the DSC denaturation peak. It was found that differences in the temperatures of the CD and DSC signal changes increase as the content of DMSO increases. Changes in CD and fluorescence are triggered by a break of the tertiary contacts, leading to an intermediate state, while the DSC peak corresponds to a subsequent complete loss of the native structure. In this way, the commonly used two-state model was proven to be unsuitable to describe the unfolding of lysozyme in the presence of DMSO. In kinetic studies, it was found that even high concentrations of DMSO do not drastically change the activation energy of the initial stage of unfolding associated with a disruption of the tertiary structure, while the enthalpy of denaturation shows a significant dependence on DMSO content. This observation suggests that the structure of the transition state upon unfolding remains similar to the structure of the native state.
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33
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile. Int J Mol Sci 2019; 20:E1452. [PMID: 30909394 PMCID: PMC6470811 DOI: 10.3390/ijms20061452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/04/2022] Open
Abstract
Determining the effects of extreme conditions on proteins from "extremophilic" and mesophilic microbes is important for understanding how life adapts to living at extremes as well as how extreme conditions can be used for sterilization and food preservation. Previous molecular dynamics simulations of dihydrofolate reductase (DHFR) from a psychropiezophile (cold- and pressure-loving), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec), at various pressures and temperatures indicate that atomic fluctuations, which are important for enzyme function, increase with both temperature and pressure. Here, the factors that cause increases in atomic fluctuations in the simulations are examined. The fluctuations increase with temperature not only because of greater thermal energy and thermal expansion of the protein but also because hydrogen bonds between protein atoms are weakened. However, the increase in fluctuations with pressure cannot be due to thermal energy, which remains constant, nor the compressive effects of pressure, but instead, the hydrogen bonds are also weakened. In addition, increased temperature causes larger increases in fluctuations of the loop regions of MpDHFR than EcDHFR, and increased pressure causes both increases and decreases in fluctuations of the loops, which differ between the two.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
| | - Jocelyn M Rodgers
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
| | - Russell J Hemley
- Department of Civil and Environmental Engineering, George Washington University, Washington, DC 20052, USA.
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
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35
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Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Sci Rep 2019; 9:2650. [PMID: 30804351 PMCID: PMC6389909 DOI: 10.1038/s41598-018-37072-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 01/20/2023] Open
Abstract
Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Heinrich Roder
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology and Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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36
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Anbouhi TS, Esfidvajani EM, Nemati F, Haghighat S, Sari S, Attar F, Pakaghideh A, Sohrabi MJ, Mousavi SE, Falahati M. Albumin binding, anticancer and antibacterial properties of synthesized zero valent iron nanoparticles. Int J Nanomedicine 2018; 14:243-256. [PMID: 30643404 PMCID: PMC6314318 DOI: 10.2147/ijn.s188497] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Nanoparticles (NPs) have been emerging as potential players in modern medicine with clinical applications ranging from therapeutic purposes to antimicrobial agents. However, before applications in medical agents, some in vitro studies should be done to explore their biological responses. AIM In this study, protein binding, anticancer and antibacterial activates of zero valent iron (ZVFe) were explored. MATERIALS AND METHODS ZVFe nanoparticles were synthesized and fully characterized by X-ray diffraction, field-emission scanning electron microscope, and dynamic light scattering analyses. Afterward, the interaction of ZVFe NPs with human serum albumin (HSA) was examined using a range of techniques including intrinsic fluorescence, circular dichroism, and UV-visible spectroscopic methods. Molecular docking study was run to determine the kind of interaction between ZVFe NPs and HSA. The anticancer influence of ZVFe NPs on SH-SY5Y was examined by MTT and flow cytometry analysis, whereas human white blood cells were used as the control cell. Also, the antibacterial effect of ZVFe NPs was examined on Pseudomonas aeruginosa (ATCC 27853), Escherichia coli (ATCC 25922), and Staphylococcus aureus (ATCC 25923). RESULTS X-ray diffraction, transmission electron microscope, and dynamic light scattering analyses verified the synthesis of ZVFe NPs in a nanosized diameter. Fluorescence spectroscopy analysis showed that ZVFe NPs spontaneously formed a complex with HSA through hydrogen bonds and van der Waals interactions. Also, circular dichroism spectroscopy study revealed that ZVFe NPs did not change the secondary structure of HSA. Moreover, UV-visible data presented that melting temperature (Tm) of HSA in the absence and presence of ZVFe NPs was almost identical. Molecular dynamic study also showed that ZVFe NP came into contact with polar residues on the surface of HSA molecule. Cellular assays showed that ZVFe NPs can induce cell mortality in a dose-dependent manner against SH-SY5Y cells, whereas these NPs did not trigger significant cell mortality against normal white bloods in the concentration range studied (1-100 µg/mL). Antibacterial assays showed a noteworthy inhibition on both bacterial strains. CONCLUSION In conclusion, it was revealed that ZVFe NPs did not induce a substantial influence on the structure of protein and cytotoxicity against normal cell, whereas they derived significant anticancer and antibacterial effects.
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Affiliation(s)
- Tabassom Sedaghat Anbouhi
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Elnaz Mokhtari Esfidvajani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fahimeh Nemati
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soyar Sari
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry and Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Arezoo Pakaghideh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Pharmaceutical Science Branch, Islamic Azad University (IAUPS), Tehran, Iran
| | - Mohammad Javad Sohrabi
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran,
| | - Seyyedeh Elaheh Mousavi
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran,
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran,
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Nikoofard N, Mashaghi A. Implications of Molecular Topology for Nanoscale Mechanical Unfolding. J Phys Chem B 2018; 122:9703-9712. [PMID: 30351148 DOI: 10.1021/acs.jpcb.8b09454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biopolymer unfolding events are ubiquitous in biology and mechanical unfolding is an established approach to study the structure and function of biomolecules, yet whether and how mechanical unfolding processes depend on native state topology remain unexplored. Here, we investigate how the number of unfolding pathways via mechanical methods depends on the circuit topology of a folded chain, which categorizes the arrangement of intrachain contacts into parallel, crossing, and series. Three unfolding strategies, namely, threading through a pore, pulling from the ends, and pulling by threading, are compared. Considering that some contacts may be unbreakable within the relevant forces, we also study the dependence of the unfolding efficiency on the chain topology. Our analysis reveals that the number of pathways and the efficiency of unfolding are critically determined by topology in a manner that depends on the employed mechanical approach, a significant result for interpretation of the unfolding experiments.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology , University of Kashan , Kashan 51167-87317 , Iran
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research, Faculty of Science , Leiden University , Leiden 2333 CC , The Netherlands
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38
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Eckhardt D, Li-Blatter X, Schönfeld HJ, Heerklotz H, Seelig J. Cooperative unfolding of apolipoprotein A-1 induced by chemical denaturation. Biophys Chem 2018; 240:42-49. [DOI: 10.1016/j.bpc.2018.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 12/30/2022]
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39
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Effect of Technically Relevant X-Ray Doses on the Structure and Function of Alcohol Dehydrogenase and Hen Egg-White Lysozyme. Pharm Res 2018; 35:135. [DOI: 10.1007/s11095-018-2417-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/22/2018] [Indexed: 10/17/2022]
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40
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Self-homodimerization of an actinoporin by disulfide bridging reveals implications for their structure and pore formation. Sci Rep 2018; 8:6614. [PMID: 29700324 PMCID: PMC5920107 DOI: 10.1038/s41598-018-24688-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022] Open
Abstract
The Trp111 to Cys mutant of sticholysin I, an actinoporin from Stichodactyla helianthus sea anemone, forms a homodimer via a disulfide bridge. The purified dimer is 193 times less hemolytic than the monomer. Ultracentrifugation, dynamic light scattering and size-exclusion chromatography demonstrate that monomers and dimers are the only independent oligomeric states encountered. Indeed, circular dichroism and fluorescence spectroscopies showed that Trp/Tyr residues participate in homodimerization and that the dimer is less thermostable than the monomer. A homodimer three-dimensional model was constructed and indicates that Trp147/Tyr137 are at the homodimer interface. Spectroscopy results validated the 3D-model and assigned 85° to the disulfide bridge dihedral angle responsible for dimerization. The homodimer model suggests that alterations in the membrane/carbohydrate-binding sites in one of the monomers, as result of dimerization, could explain the decrease in the homodimer ability to form pores.
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41
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Suárez IP, Gauto DF, Hails G, Mascali FC, Crespo R, Zhao L, Wang J, Rasia RM. Conformational sampling of the intrinsically disordered dsRBD-1 domain from Arabidopsis thaliana DCL1. Phys Chem Chem Phys 2018; 20:11237-11246. [DOI: 10.1039/c7cp07908g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Partial folding and stability of DCL1-dsRBD1.
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Affiliation(s)
- Irina P. Suárez
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Diego F. Gauto
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Guillermo Hails
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Florencia C. Mascali
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Roberta Crespo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Lingzi Zhao
- College of Physics
- Jilin University
- Jilin
- China
| | - Jin Wang
- State University of New York at Stony Brook
- USA
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
- Área Biofísica
- Facultad de Ciencias Bioquímicas y Farmacéuticas
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Seelig J. Cooperative protein unfolding. A statistical-mechanical model for the action of denaturants. Biophys Chem 2017; 233:19-25. [PMID: 29232602 DOI: 10.1016/j.bpc.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 01/09/2023]
Abstract
Knowledge of protein stability is of utmost importance in various fields of biotechnology. Protein stability can be assessed in solution by increasing the concentration of denaturant and recording the structural changes with spectroscopic or thermodynamic methods. The standard interpretation of the experimental data is to assume a 2-state equilibrium between completely folded and completely unfolded protein molecules. Here we propose a cooperative model based on the statistical-mechanical Zimm-Bragg theory. In this model protein unfolding is driven by the weak binding of a rather small number of denaturant molecules, inducing the cooperative unfolding with multiple dynamic intermediates. The modified Zimm-Bragg theory is applied to published thermodynamic and spectroscopic data leading to the following conclusions. (i) The binding constant KD is correlated with the midpoint concentration, c0, of the unfolding reaction according to c0≅1/KD. The better the binding of denaturant the lower is the concentration to achieve unfolding. (ii) The binding constant KD agrees with direct thermodynamic measurements. A rather small number of bound denaturants suffices to induce the cooperative unfolding of the whole protein. (iii) Chemical unfolding occurs in the concentration range ΔcD=cend-cini. The theory predicts the unfolding energy per amino acid residue as gnu=RTKD(cend-cini). The Gibbs free energy of an osmotic gradient of the same size is ΔGDiff=-RTln(cend/cini). In all examples investigated ΔGDiff exactly balances the unfolding energy gnu. The total unfolding energy is thus close to zero. (iv) Protein cooperativity in chemical unfolding is rather low with cooperativity parameters σ≥3x10-3. As a consequence, the theory predicts a dynamic mixture of conformations during the unfolding reaction. The probabilities of individual conformations are easily accessible via the partition function Z(cD,σ).
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Affiliation(s)
- J Seelig
- Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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Characterization of physicochemical and structural properties of atmospheric cold plasma (ACP) modified zein. FOOD AND BIOPRODUCTS PROCESSING 2017. [DOI: 10.1016/j.fbp.2017.05.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sousa F, Sarmento B, Neves-Petersen MT. Biophysical study of bevacizumab structure and bioactivity under thermal and pH-stresses. Eur J Pharm Sci 2017; 105:127-136. [DOI: 10.1016/j.ejps.2017.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
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