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Blázquez-Martín A, Bonardd S, Verde-Sesto E, Arbe A, Pomposo JA. Trimethylsilanol Cleaves Stable Azaylides As Revealed by Unfolding of Robust "Staudinger" Single-Chain Nanoparticles. ACS Polym Au 2024; 4:140-148. [PMID: 38618005 PMCID: PMC11010256 DOI: 10.1021/acspolymersau.3c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 04/16/2024]
Abstract
Herein, we disclose a unique and selective reagent for the cleavage of stable azaylides prepared by the nonhydrolysis Staudinger reaction, enabling the on-demand unfolding of robust single-chain nanoparticles (SCNPs). SCNPs with promising use in catalysis, nanomedicine, and sensing are obtained through intrachain folding of discrete synthetic polymer chains. The unfolding of SCNPs involving reversible interactions triggered by a variety of external stimuli (e.g., pH, temperature, light, and redox potential) or substances (e.g., competitive reagents, solvents, and anions) is well known. Conversely, methods for the unfolding (i.e., intrachain disassembly) of SCNPs with stronger covalent interactions are scarce. We show that trimethylsilanol (Me3SiOH) triggers the efficient unfolding of robust "Staudinger" SCNPs with stable azaylide (-N=P-) moieties as intrachain cross-linking units showing exceptional stability toward water, air, and CS2, a standard reagent for azaylides. As a consequence, Me3SiOH arises as a rare, exceptional, and valuable reagent for the cleavage of stable azaylides prepared by the nonhydrolysis Staudinger reaction.
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Affiliation(s)
- Agustín Blázquez-Martín
- Centro
de Física de Materiales (CSIC - UPV/EHU) − Materials
Physics Center MPC, P°
Manuel Lardizabal 5, E-20018 Donostia, Spain
| | - Sebastián Bonardd
- Centro
de Física de Materiales (CSIC - UPV/EHU) − Materials
Physics Center MPC, P°
Manuel Lardizabal 5, E-20018 Donostia, Spain
- Departamento
de Polímeros y Materiales Avanzados: Física, Química
y Tecnología,University of the Basque
Country (UPV/EHU), P°
Manuel Lardizabal 3, E-20800 Donostia, Spain
| | - Ester Verde-Sesto
- Centro
de Física de Materiales (CSIC - UPV/EHU) − Materials
Physics Center MPC, P°
Manuel Lardizabal 5, E-20018 Donostia, Spain
- IKERBASQUE
− Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Arantxa Arbe
- Centro
de Física de Materiales (CSIC - UPV/EHU) − Materials
Physics Center MPC, P°
Manuel Lardizabal 5, E-20018 Donostia, Spain
| | - José A. Pomposo
- Centro
de Física de Materiales (CSIC - UPV/EHU) − Materials
Physics Center MPC, P°
Manuel Lardizabal 5, E-20018 Donostia, Spain
- Departamento
de Polímeros y Materiales Avanzados: Física, Química
y Tecnología,University of the Basque
Country (UPV/EHU), P°
Manuel Lardizabal 3, E-20800 Donostia, Spain
- IKERBASQUE
− Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
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Vera JF, Roldán-Nofuentes JA. A two-step log-linear procedure for graphical representation and inference of associations in cross-classified data for disease diagnosis. Stat Med 2023; 42:4897-4916. [PMID: 37621084 DOI: 10.1002/sim.9854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023]
Abstract
Biometrical sciences and disease diagnosis in particular, are often concerned with the analysis of associations for cross-classified data, for which distance association models give us a graphical interpretation for non-sparse matrices with a low number of categories. In this framework, usually binary exploratory and response variables are present, with analysis based on individual profiles being of great interest. For saturated models, we show the usual linear relationship for log-linear models is preserved in full dimension for the distance association parameterization. This enables a two-step procedure to facilitate the analysis and the interpretation of associations in terms of unfolding after the overall and main effects are removed. The proposed procedure can deal with cross-classified data for profiles by binary variables, and it is easy to implement using traditional statistical software. For disease diagnosis, the problems of a degenerate solution in the unfolding representation, and that of determining significant differences between the profile locations are addressed. A hypothesis test of independence based on odds ratio is considered. Furthermore, a procedure is proposed to determine the causes of the significance of the test, avoiding the problem of error propagation. The equivalence between a test for equality of odds ratio pairs and the test for equality of location for two profiles in the unfolding representation in the disease diagnosis is shown. The results have been applied to a real example on the diagnosis of coronary disease, relating the odds ratios with performance parameters of the diagnostic test.
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Affiliation(s)
- J Fernando Vera
- Department of Statistics and O.R., University of Granada, Granada, Spain
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3
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Khan S, Khan M, Lohani M, Ahmad S, Sherwani S, Bhagwath S, Khan MWA, Wahid M, Aqil F, Haque S. NADP/H binding nearly doubles the stability of a Mycobacterium drug target: an unfolding study. J Biomol Struct Dyn 2023; 41:8018-8025. [PMID: 36166625 DOI: 10.1080/07391102.2022.2127910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
Mycobacterium Aspartate beta semialdehyde dehydrogenase (ASADH) was studied using various spectroscopic techniques and size exclusion chromatography to examine the unfolding of free (apo) and NADP/H-bound (holo) forms of ASADH. Non-cooperative guanidinium chloride (GdnHCl)-induced unfolding of the apo ASADH was discovered, and no partially folded intermediate structures were stabilized. On the other hand, it was observed that GdnHCl's unfolding of holoenzyme was a cooperative process without any stable intermediate structure. The native form of holoenzyme is found to be stable against the lower concentration of GdnHCl only (namely up to 1.25 M GdnHCl). The tryptophan environment appears to unfold cooperatively in case of the holoenzyme and is in well coordination with the overall unfolding of the holoenzyme. The presence of NADP/H shows a stabilizing effect on the tryptophan environment as well as on the native NADP/H-bound enzyme. Δ G Solvent o values reveal nearly two-fold (∼1.9) conformationally more stable folded holoenzyme compared to its native apo state. The Cm for the apo and holo forms of ASADH are 1.3 and 1.9 M, respectively. Novel drug leads targeting the NADP/H binding domain of ASADH could offer promising drugs against extremely infective Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Mahvish Khan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saheem Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Subuhi Sherwani
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Sundeep Bhagwath
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Mohd Wajid A Khan
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Farrukh Aqil
- Department of Medicine and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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Gaikwad HK, Jaswandkar SV, Katti KS, Haage A, Katti DR. Molecular basis of conformational changes and mechanics of integrins. Philos Trans A Math Phys Eng Sci 2023; 381:20220243. [PMID: 37211038 DOI: 10.1098/rsta.2022.0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/13/2023] [Indexed: 05/23/2023]
Abstract
Integrin, as a mechanotransducer, establishes the mechanical reciprocity between the extracellular matrix (ECM) and cells at integrin-mediated adhesion sites. This study used steered molecular dynamics (SMD) simulations to investigate the mechanical responses of integrin αvβ3 with and without 10th type III fibronectin (FnIII10) binding for tensile, bending and torsional loading conditions. The ligand-binding integrin confirmed the integrin activation during equilibration and altered the integrin dynamics by changing the interface interaction between β-tail, hybrid and epidermal growth factor domains during initial tensile loading. The tensile deformation in integrin molecules indicated that fibronectin ligand binding modulates its mechanical responses in the folded and unfolded conformation states. The bending deformation responses of extended integrin models reveal the change in behaviour of integrin molecules in the presence of Mn2+ ion and ligand based on the application of force in the folding and unfolding directions of integrin. Furthermore, these SMD simulation results were used to predict the mechanical properties of integrin underlying the mechanism of integrin-based adhesion. The evaluation of integrin mechanics provides new insights into understanding the mechanotransmission (force transmission) between cells and ECM and contributes to developing an accurate model for integrin-mediated adhesion. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Hanmant K Gaikwad
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| | - Sharad V Jaswandkar
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| | - Kalpana S Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| | - Amanda Haage
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Dinesh R Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
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Baklanov AV, Kiselev VG. The Nature of the Enthalpy-Entropy Compensation and "Exotic" Arrhenius Parameters in the Denaturation Kinetics of Proteins. Int J Mol Sci 2023; 24:10630. [PMID: 37445807 DOI: 10.3390/ijms241310630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Protein unfolding is a ubiquitous process responsible for the loss of protein functionality (denaturation), which, in turn, can be accompanied by the death of cells and organisms. The nature of enthalpy-entropy compensation (EEC) in the kinetics of protein unfolding is a subject of debate. In order to investigate the nature of EEC, the "completely loose" transition state (TS) model has been applied to calculate the Arrhenius parameters for the unfolding of polyglycine dimers as a model process. The calculated Arrhenius parameters increase with increasing dimer length and demonstrate enthalpy-entropy compensation. It is shown that EEC results from the linear correlations of enthalpy and entropy of activation with dimer length, which are derived directly from the properties of the transition state. It is shown that EEC in solvated (hydrated, etc.) proteins is a direct consequence of EEC in proteins themselves. The suggested model allows us also to reproduce and explain "exotic" very high values of the pre-exponential factor measured for the proteins unfolding, which are drastically higher than those known for unimolecular reactions of organic molecules. A similar approach can be applied to analyzing the nature of EEC phenomena observed in other areas of chemistry.
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Affiliation(s)
- Alexey V Baklanov
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Street, 630090 Novosibirsk, Russia
| | - Vitaly G Kiselev
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Street, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 1 Pirogova Street, 630090 Novosibirsk, Russia
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Nobili G, Botticelli S, La Penna G, Morante S, Rossi G, Salina G. Probing protein stability: towards a computational atomistic, reliable, affordable, and improvable model. Front Mol Biosci 2023; 10:1122269. [PMID: 37325476 PMCID: PMC10267363 DOI: 10.3389/fmolb.2023.1122269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
We present an improved application of a recently proposed computational method designed to evaluate the change of free energy as a function of the average value of a suitably chosen collective variable in proteins. The method is based on a full atomistic description of the protein and its environment. The goal is to understand how the protein melting temperature changes upon single-point mutations, because the sign of the temperature variation will allow us to discriminate stabilizing vs. destabilizing mutations in protein sequences. In this refined application the method is based on altruistic well-tempered metadynamics, a variant of multiple-walkers metadynamics. The resulting metastatistics is then modulated by the maximal constrained entropy principle. The latter turns out to be especially helpful in free-energy calculations as it is able to alleviate the severe limitations of metadynamics in properly sampling folded and unfolded configurations. In this work we apply the computational strategy outlined above in the case of the bovine pancreatic trypsin inhibitor, a well-studied small protein, which is a reference for computer simulations since decades. We compute the variation of the melting temperature characterizing the folding-unfolding process between the wild-type protein and two of its single-point mutations that are seen to have opposite effect on the free energy changes. The same approach is used for free energy difference calculations between a truncated form of frataxin and a set of five of its variants. Simulation data are compared to in vitro experiments. In all cases the sign of the change of melting temperature is reproduced, under the further approximation of using an empirical effective mean-field to average out protein-solvent interactions.
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Affiliation(s)
- Germano Nobili
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Simone Botticelli
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Giovanni La Penna
- CNR-Istituto di Chimica Dei Composti Organometallici, Firenze, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Silvia Morante
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- CNR-Istituto di Chimica Dei Composti Organometallici, Firenze, Italy
| | - Giancarlo Rossi
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Roma, Italy
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Shityakov S, Skorb EV, Nosonovsky M. Folding- unfolding asymmetry and a RetroFold computational algorithm. R Soc Open Sci 2023; 10:221594. [PMID: 37153361 PMCID: PMC10154942 DOI: 10.1098/rsos.221594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process as the driving force is opposed by damping. Protein folding takes two orders of magnitude longer than unfolding. We suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modelling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns, while unfolding (denaturation) takes only about 5.0 ns and, therefore, fewer computational resources are needed for its simulation. This RetroFold approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.
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Affiliation(s)
- Sergey Shityakov
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova Street, St. Petersburg 191002, Russia
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova Street, St. Petersburg 191002, Russia
| | - Michael Nosonovsky
- Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova Street, St. Petersburg 191002, Russia
- College of Engineering and Applied Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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Ruane S, Li Z, Hollowell P, Hughes A, Warwicker J, Webster JRP, van der Walle CF, Kalonia C, Lu JR. Investigating the Orientation of an Interfacially Adsorbed Monoclonal Antibody and Its Fragments Using Neutron Reflection. Mol Pharm 2023; 20:1643-1656. [PMID: 36795985 PMCID: PMC9996827 DOI: 10.1021/acs.molpharmaceut.2c00864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Interfacial adsorption is a molecular process occurring during the production, purification, transport, and storage of antibodies, with a direct impact on their structural stability and subsequent implications on their bioactivities. While the average conformational orientation of an adsorbed protein can be readily determined, its associated structures are more complex to characterize. Neutron reflection has been used in this work to investigate the conformational orientations of the monoclonal antibody COE-3 and its Fab and Fc fragments at the oil/water and air/water interfaces. Rigid body rotation modeling was found to be suitable for globular and relatively rigid proteins such as the Fab and Fc fragments but less so for relatively flexible proteins such as full COE-3. Fab and Fc fragments adopted a 'flat-on' orientation at the air/water interface, minimizing the thickness of the protein layer, but they adopted a substantially tilted orientation at the oil/water interface with increased layer thickness. In contrast, COE-3 was found to adsorb in tilted orientations at both interfaces, with one fragment protruding into the solution. This work demonstrates that rigid-body modeling can provide additional insights into protein layers at various interfaces relevant to bioprocess engineering.
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Affiliation(s)
- Sean Ruane
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester, Oxford Road, Schuster Building, Manchester M13 9PL, U.K
| | - Zongyi Li
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester, Oxford Road, Schuster Building, Manchester M13 9PL, U.K
| | - Peter Hollowell
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester, Oxford Road, Schuster Building, Manchester M13 9PL, U.K
| | - Arwel Hughes
- ISIS Neutron Facility, STFC, Chilton, Didcot OX11 0QZ, U.K
| | - Jim Warwicker
- Division of Molecular and Cellular Function, Manchester Institute of Biotechnology, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | | | | | - Cavan Kalonia
- Dosage Form Design and Development, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jian R Lu
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester, Oxford Road, Schuster Building, Manchester M13 9PL, U.K
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Mizuno F, Aoki S, Matsugami A, Hayashi F, Nishimura C. The Residual Structure of Unfolded Proteins was Elucidated from the Standard Deviation of NMR Intensity Differences. Protein Pept Lett 2023; 30:103-107. [PMID: 36600624 DOI: 10.2174/0929866530666230104140830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Sensitive methods are necessary to identify the residual structure in an unfolded protein, which may be similar to the functionally native structure. Signal intensity in NMR experiments is useful for analyzing the line width for a dynamic structure; however, another contribution is contained. METHODS Here, the signal-intensity difference along the sequence was used for probability to calculate the standard deviation. RESULTS The relative values of the standard deviations were 0.57, 0.57, and 0.66 for alpha-synuclein wild-type, A53T, and A30P, respectively. This revealed that the flexible region was mainly in the Cterminal region of alpha-synuclein at higher temperatures as observed by the amide-proton exchange studies. CONCLUSION In particular, the flexible structure was induced by the A30P mutation.
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Affiliation(s)
- Fuko Mizuno
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo, Japan
| | - Saeko Aoki
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center (RSC) Yokohama, Kanagawa, 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center (RSC) Yokohama, Kanagawa, 230-0045, Japan
| | - Chiaki Nishimura
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo, Japan
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Ermakova E, Makshakova O, Zuev Y, Sedov I. Beta-rich intermediates in denaturation of lysozyme: accelerated molecular dynamics simulations. J Biomol Struct Dyn 2022; 40:13953-13964. [PMID: 34751100 DOI: 10.1080/07391102.2021.1997823] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Amyloid fibrillar aggregates play a critical role in many neurodegenerative disorders. Conversion of globular proteins into fibrils is associated with global conformational rearrangement and involves the transformation of α-helices to β-sheets. In the present work, the accelerated molecular dynamics technique was applied to study the unfolding of hen egg-white lysozyme at elevated temperatures, and the transformation of the native structure to a disordered one was analyzed. The influence of the disulfide bonds on the conformational dynamics and the energy landscape of denaturation process was considered. Our results show that formation of the metastable β-enriched conformers of individual protein molecules may precede the aggregation process. These β-rich intermediates can play a role of bricks making up fibrils.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elena Ermakova
- FRC Kazan Scientific Center of RAS, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia.,Sirius University of Science and Technology, Sochi, Russia
| | - Olga Makshakova
- FRC Kazan Scientific Center of RAS, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia.,Sirius University of Science and Technology, Sochi, Russia
| | - Yuriy Zuev
- FRC Kazan Scientific Center of RAS, Kazan Institute of Biochemistry and Biophysics, Kazan, Russia
| | - Igor Sedov
- Sirius University of Science and Technology, Sochi, Russia.,Kazan Federal University, Kazan, Russia
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Vera JF. Distance-based logistic model for cross-classified categorical data. Br J Math Stat Psychol 2022; 75:466-492. [PMID: 35080009 DOI: 10.1111/bmsp.12264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Logistic regression models are a powerful research tool for the analysis of cross-classified data in which a categorical response variable is involved. In a logistic model, the effect of a covariate refers to odds, and the simple relationship between the coefficients and the odds ratio often makes these the parameters of interest due to their easy interpretation. In this article we present a distance-based logistic model that allows a simple graphical interpretation of the association coefficients using the odds ratio in a contingency table. Two configurations are estimated, one for the rows and one for the columns, as the categories of a polytomous predictor and a nominal response variable respectively, such that the local odds ratio and the distances between the predictor and response categories are inversely related. The associations in terms of the odds ratios, or the ratios of the odds to their geometric means, are interpreted through distances for the most common coding schemes of the predictor variable, and the relationship between the distances related to different codings is investigated in its full dimension. The performance of the estimation procedure is analysed with a Monte Carlo experiment. The interpretation of the model and its performance, as well as its comparison with a two-step procedure involving first a logistic regression and then unfolding, is illustrated using real data sets.
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Affiliation(s)
- José Fernando Vera
- Department of Statistics and O.R. Faculty of Sciences, University of Granada, Spain
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12
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Islam S, Do M, Frank BS, Hom GL, Wheeler S, Fujioka H, Wang B, Minocha G, Sell DR, Fan X, Lampi KJ, Monnier VM. α-Crystallin chaperone mimetic drugs inhibit lens γ-crystallin aggregation: potential role for cataract prevention. J Biol Chem 2022; 298:102417. [PMID: 36037967 PMCID: PMC9525908 DOI: 10.1016/j.jbc.2022.102417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Γ-Crystallins play a major role in age-related lens transparency. Their destabilization by mutations and physical chemical insults are associated with cataract formation. Therefore, drugs that increase their stability should have anticataract properties. To this end, we screened 2560 Federal Drug Agency–approved drugs and natural compounds for their ability to suppress or worsen H2O2 and/or heat-mediated aggregation of bovine γ-crystallins. The top two drugs, closantel (C), an antihelminthic drug, and gambogic acid (G), a xanthonoid, attenuated thermal-induced protein unfolding and aggregation as shown by turbidimetry fluorescence spectroscopy dynamic light scattering and electron microscopy of human or mouse recombinant crystallins. Furthermore, binding studies using fluorescence inhibition and hydrophobic pocket–binding molecule bis-8-anilino-1-naphthalene sulfonic acid revealed static binding of C and G to hydrophobic sites with medium-to-low affinity. Molecular docking to HγD and other γ-crystallins revealed two binding sites, one in the “NC pocket” (residues 50–150) of HγD and one spanning the “NC tail” (residues 56–61 to 168–174 in the C-terminal domain). Multiple binding sites overlap with those of the protective mini αA-crystallin chaperone MAC peptide. Mechanistic studies using bis-8-anilino-1-naphthalene sulfonic acid as a proxy drug showed that it bound to MAC sites, improved Tm of both H2O2 oxidized and native human gamma D, and suppressed turbidity of oxidized HγD, most likely by trapping exposed hydrophobic sites. The extent to which these drugs act as α-crystallin mimetics and reduce cataract progression remains to be demonstrated. This study provides initial insights into binding properties of C and G to γ-crystallins.
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Affiliation(s)
- Sidra Islam
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Michael Do
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Brett S Frank
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Grant L Hom
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Samuel Wheeler
- Dept of Integrative Biosciences, Oregon Health & Sciences University, Portland, OR 97239
| | - Hisashi Fujioka
- Cryo-EM Core Facility, School of Medicine, Case Western Reserve University, Case Western Reserve University, Cleveland, OH 44016
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Dept of Nutrition, Case Western Reserve University, Cleveland, OH 44106
| | - Geeta Minocha
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - David R Sell
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Xingjun Fan
- Dept of Cell Biology and Anatomy, Augusta University, Georgia, GA 30912
| | - Kirsten J Lampi
- Dept of Integrative Biosciences, Oregon Health & Sciences University, Portland, OR 97239
| | - Vincent M Monnier
- Dept of Pathology and Biochemistry, Case Western Reserve University, Cleveland, OH 44106; Dept of Biochemistry, Case Western Reserve University, Cleveland OH 44106.
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13
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Sagar V, Wistow G. Acquired disorder and asymmetry in a domain-swapped model for γ-crystallin aggregation. J Mol Biol 2022; 434:167559. [PMID: 35341744 PMCID: PMC9050881 DOI: 10.1016/j.jmb.2022.167559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/19/2022]
Abstract
Misfolding and aggregation of proteins occur in many pathological states. Because of the inherent disorder involved, these processes are difficult to study. We attempted to capture aggregation intermediates of γ S-crystallin, a highly stable, internally symmetrical monomeric protein, by crystallization under mildly acidic and oxidizing conditions. Here we describe novel oligomerization through strained domain-swapping and partial intermolecular disulfide formation. This forms an octamer built from asymmetric tetramers, each of which comprises an asymmetric pair of twisted, domain-swapped dimers. Each tetramer shows patterns of acquired disorder among subunits, ranging from local loss of secondary structure to regions of intrinsic disorder. The octamer ring is tied together by partial intermolecular disulfide bonds, which may contribute to strain and disorder in the octamer. Oligomerization in this structure is self-limited by the distorted octamer ring. In a more heterogeneous environment, the disordered regions could serve as seeds for cascading interactions with other proteins. Indeed, solubilized protein from crystals retain many features observed in the crystal and are prone to further oligomerization and precipitation. This structure illustrates modes of loss of organized structure and aggregation that are relevant for cataract and for other disorders involving deposition of formerly well-folded proteins.
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Affiliation(s)
- Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Davari N, Bakhtiary N, Khajehmohammadi M, Sarkari S, Tolabi H, Ghorbani F, Ghalandari B. Protein-Based Hydrogels: Promising Materials for Tissue Engineering. Polymers (Basel) 2022; 14:986. [PMID: 35267809 PMCID: PMC8914701 DOI: 10.3390/polym14050986] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
The successful design of a hydrogel for tissue engineering requires a profound understanding of its constituents' structural and molecular properties, as well as the proper selection of components. If the engineered processes are in line with the procedures that natural materials undergo to achieve the best network structure necessary for the formation of the hydrogel with desired properties, the failure rate of tissue engineering projects will be significantly reduced. In this review, we examine the behavior of proteins as an essential and effective component of hydrogels, and describe the factors that can enhance the protein-based hydrogels' structure. Furthermore, we outline the fabrication route of protein-based hydrogels from protein microstructure and the selection of appropriate materials according to recent research to growth factors, crucial members of the protein family, and their delivery approaches. Finally, the unmet needs and current challenges in developing the ideal biomaterials for protein-based hydrogels are discussed, and emerging strategies in this area are highlighted.
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Affiliation(s)
- Niyousha Davari
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 143951561, Iran;
| | - Negar Bakhtiary
- Burn Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran;
- Department of Biomaterials, Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran 14115114, Iran
| | - Mehran Khajehmohammadi
- Department of Mechanical Engineering, Faculty of Engineering, Yazd University, Yazd 8174848351, Iran;
- Medical Nanotechnology and Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd 8916877391, Iran
| | - Soulmaz Sarkari
- Department of Biomedical Engineering, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran;
| | - Hamidreza Tolabi
- New Technologies Research Center (NTRC), Amirkabir University of Technology, Tehran 158754413, Iran;
- Department of Biomedical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran 158754413, Iran
| | - Farnaz Ghorbani
- Institute of Biomaterials, Department of Material Science and Engineering, University of Erlangen-Nuremberg, Cauerstraße 6, 91058 Erlangen, Germany
| | - Behafarid Ghalandari
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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15
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Ji Z, Li H, Peterle D, Paulo JA, Ficarro SB, Wales TE, Marto JA, Gygi SP, Engen JR, Rapoport TA. Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase. Mol Cell 2022; 82:570-584.e8. [PMID: 34951965 PMCID: PMC8818041 DOI: 10.1016/j.molcel.2021.11.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/30/2021] [Accepted: 11/24/2021] [Indexed: 02/05/2023]
Abstract
The hexameric Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactor Ufd1/Npl4 to extract polyubiquitinated proteins from membranes or macromolecular complexes for degradation by the proteasome. Here, we clarify how the Cdc48 complex unfolds its substrates and translocates polypeptides with branchpoints. The Cdc48 complex recognizes primarily polyubiquitin chains rather than the attached substrate. Cdc48 and Ufd1/Npl4 cooperatively bind the polyubiquitin chain, resulting in the unfolding of one ubiquitin molecule (initiator). Next, the ATPase pulls on the initiator ubiquitin and moves all ubiquitin molecules linked to its C terminus through the central pore of the hexameric double ring, causing transient ubiquitin unfolding. When the ATPase reaches the isopeptide bond of the substrate, it can translocate and unfold both N- and C-terminal segments. Ubiquitins linked to the branchpoint of the initiator dissociate from Ufd1/Npl4 and move outside the central pore, resulting in the release of unfolded, polyubiquitinated substrate from Cdc48.
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Affiliation(s)
- Zhejian Ji
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.,Corresponding authors: Zhejian Ji and Tom Rapoport, Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA., and
| | - Hao Li
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Scott B. Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jarrod A. Marto
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.,Corresponding authors: Zhejian Ji and Tom Rapoport, Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA., and
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16
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Olia AS, Tsybovsky Y, Chen SJ, Liu C, Nazzari AF, Ou L, Wang L, Kong WP, Leung K, Liu T, Stephens T, Teng IT, Wang S, Yang ES, Zhang B, Zhang Y, Zhou T, Mascola JR, Kwong PD. SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity. J Biol Chem 2021; 297:101127. [PMID: 34461095 PMCID: PMC8393506 DOI: 10.1016/j.jbc.2021.101127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
The SARS-CoV-2 spike is the primary target of virus-neutralizing antibodies and critical to the development of effective vaccines against COVID-19. Here, we demonstrate that the prefusion-stabilized two-proline "S2P" spike-widely employed for laboratory work and clinical studies-unfolds when stored at 4 °C, physiological pH, as observed by electron microscopy (EM) and differential scanning calorimetry, but that its trimeric, native-like conformation can be reacquired by low pH treatment. When stored for approximately 1 week, this unfolding does not significantly alter antigenic characteristics; however, longer storage diminishes antibody binding, and month-old spike elicits virtually no neutralization in mice despite inducing high ELISA-binding titers. Cryo-EM structures reveal the folded fraction of spike to decrease with aging; however, its structure remains largely similar, although with varying mobility of the receptor-binding domain. Thus, the SARS-CoV-2 spike is susceptible to unfolding, which affects immunogenicity, highlighting the need to monitor its integrity.
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Affiliation(s)
- Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Steven J Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexandra F Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kwan Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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17
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Coscia F, Löwe J. Cryo-EM structure of the full-length Lon protease from Thermus thermophilus. FEBS Lett 2021; 595:2691-2700. [PMID: 34591981 PMCID: PMC8835725 DOI: 10.1002/1873-3468.14199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/30/2022]
Abstract
In bacteria, Lon is a large hexameric ATP‐dependent protease that targets misfolded and also folded substrates, some of which are involved in cell division and survival of cellular stress. The N‐terminal domain of Lon facilitates substrate recognition, but how the domains confer such activity has remained unclear. Here, we report the full‐length structure of Lon protease from Thermus thermophilus at 3.9 Å resolution in a substrate‐engaged state. The six N‐terminal domains are arranged in three pairs, stabilized by coiled‐coil segments and forming an additional channel for substrate sensing and entry into the AAA+ ring. Sequence conservation analysis and proteolysis assays confirm that this architecture is required for the degradation of both folded and unfolded substrates in bacteria.
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Affiliation(s)
- Francesca Coscia
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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18
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Duarte Neto JMW, Silva JDC, Sousa F, Gonçalves OSL, Wanderley MCDA, Sarmento B, Lima CDA, Neves-Petersen MT, Porto ALF. Structural and functional analysis of broad pH and thermal stable protease from Penicillium aurantiogriseum URM 4622. Prep Biochem Biotechnol 2021; 52:578-589. [PMID: 34533419 DOI: 10.1080/10826068.2021.1972429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This study aimed to better characterize a recently purified stable extracellular alkaline peptidase produced by Penicillium aurantiogriseum (URM 4622) through fluorescence spectroscopy, far-UV circular dichroism, kinetic and thermodynamic models to understand its' structure-activity and denaturation. Fluorescence data showed that changing pH leads to tryptophan residues exposure to more hydrophilic environments at optimum activity pH 9.0 and 10.0. When thermally treated, it displayed less unfolding at these pH values, along with 4-fold less photoproducts formation than at neutral pH. Different pH CD spectra showed more β-sheet (21.5-43.0%) than α-helix (1-6.2%). At pH9.0, more than 2-fold higher α-helix content than any other pH. The melting temperature (Tm) was observed between 50 and 60 °C at all pH studied, with lower Tm at pH 9.0-11.0 (54.9-50.3 °C). The protease displayed two phase transition, with two energies of denaturation, and a 4-fold higher thermal stability (ΔH°m) than reports for other microorganism's proteases. An irreversible folding transition occurs between 50 and 60 °C. It displayed energies of denaturation suggesting higher thermal stability than reported for other microorganism's proteases. These results help elucidating the applicability of this new stable protease.
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Affiliation(s)
| | | | - Flávia Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | | | | | - Bruno Sarmento
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | | | - Maria Teresa Neves-Petersen
- Department of Health Science and Technology, Aalborg University, Aalborg Ø, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Ana Lúcia Figueiredo Porto
- Keizo Asami Immunopathology Laboratory (LIKA), Federal University of Pernambuco (UFPE), Recife, PE, Brazil.,Department of Morphology and Physiology, Federal Rural University of Pernambuco, UFRPE, Recife, PE, Brasil
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19
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Hanson JR, Walker SI. Formalizing falsification for theories of consciousness across computational hierarchies. Neurosci Conscious 2021; 2021:niab014. [PMID: 34377534 PMCID: PMC8339439 DOI: 10.1093/nc/niab014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 11/23/2022] Open
Abstract
The scientific study of consciousness is currently undergoing a critical transition in the form of a rapidly evolving scientific debate regarding whether or not currently proposed theories can be assessed for their scientific validity. At the forefront of this debate is Integrated Information Theory (IIT), widely regarded as the preeminent theory of consciousness because it quantified subjective experience in a scalar mathematical measure called Φ that is in principle measurable. Epistemological issues in the form of the "unfolding argument" have provided a concrete refutation of IIT by demonstrating how it permits functionally identical systems to have differences in their predicted consciousness. The implication is that IIT and any other proposed theory based on a physical system's causal structure may already be falsified even in the absence of experimental refutation. However, so far many of these arguments surrounding the epistemological foundations of falsification arguments, such as the unfolding argument, are too abstract to determine the full scope of their implications. Here, we make these abstract arguments concrete, by providing a simple example of functionally equivalent machines realizable with table-top electronics that take the form of isomorphic digital circuits with and without feedback. This allows us to explicitly demonstrate the different levels of abstraction at which a theory of consciousness can be assessed. Within this computational hierarchy, we show how IIT is simultaneously falsified at the finite-state automaton level and unfalsifiable at the combinatorial-state automaton level. We use this example to illustrate a more general set of falsification criteria for theories of consciousness: to avoid being already falsified, or conversely unfalsifiable, scientific theories of consciousness must be invariant with respect to changes that leave the inference procedure fixed at a particular level in a computational hierarchy.
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Affiliation(s)
- Jake R Hanson
- School of Earth and Space Exploration, Arizona State University, 550 East Tyler Mall, Tempe, AZ 85287, USA
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, P.O. Box 870506, Tempe, AZ 85287, USA
| | - Sara I Walker
- School of Earth and Space Exploration, Arizona State University, 550 East Tyler Mall, Tempe, AZ 85287, USA
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, P.O. Box 870506, Tempe, AZ 85287, USA
- ASU–SFI Center for Biosocial Complex Systems, Arizona State University, 1031 S. Palm Walk Tempe, AZ 85281-2701, USA
- Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
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20
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Qian GY, Lim G, Yin SJ, Yang JM, Lee J, Park YD. Biochemical Study of Fibrinolytic Protease from Euphausia superba Possessing Multifunctional Serine Protease Activity. Protein Pept Lett 2021; 28:651-664. [PMID: 33183186 DOI: 10.2174/0929866527666201112123714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Fibrinolytic protease from Euphausia superba (EFP) was isolated. OBJECTIVE Biochemical distinctions, regulation of the catalytic function, and the key residues of EFP were investigated. METHODS The serial inhibition kinetic evaluations coupled with measurements of fluorescence spectra in the presence of 4-(2-aminoethyl) benzene sulfonyl fluoride hydrochloride (AEBSF) was conducted. The computational molecular dynamics (MD) simulations were also applied for a comparative study. RESULTS The enzyme behaved as a monomeric protein with a molecular mass of about 28.6 kD with Km BApNA = 0.629 ± 0.02 mM and kcat/Km BApNA = 7.08 s-1/mM. The real-time interval measurements revealed that the inactivation was a first-order reaction, with the kinetic processes shifting from a monophase to a biphase. Measurements of fluorescence spectra showed that serine residue modification by AEBSF directly caused conspicuous changes of the tertiary structures and exposed hydrophobic surfaces. Some osmolytes were applied to find protective roles. These results confirmed that the active region of EFP is more flexible than the overall enzyme molecule and serine, as the key residue, is associated with the regional unfolding of EFP in addition to its catalytic role. The MD simulations were supportive to the kinetics data. CONCLUSION Our study indicated that EFP has an essential serine residue for its catalyst function and associated folding behaviors. Also, the functional role of osmolytes such as proline and glycine that may play a role in defense mechanisms from environmental adaptation in a krill's body was suggested.
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Affiliation(s)
- Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Gyutae Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro, Yuseonggu, Daejeon, 34141, Korea
| | - Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Jun-Mo Yang
- Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul 135-710, Korea
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro, Yuseonggu, Daejeon, 34141, Korea
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
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21
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Mao Z, Ahmed S, Graham C, Kind P. The Unfolding Method to Explore Health-Related Quality of Life Constructs in a Chinese General Population. Value Health 2021; 24:846-854. [PMID: 34119083 DOI: 10.1016/j.jval.2020.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/29/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Health-related quality of life (HRQOL) is a complicated concept that can be measured using multiple health items. Although HRQOL is closely associated with people's subjective assessment of their own health, a limited number of studies have investigated which health items are considered most important and relevant by the general population. Even fewer empirical studies have investigated how HRQOL is understood in non-Western populations. This study used multidimensional unfolding analysis in a Chinese general population to explore the constructs of HRQOL. METHODS A scoping review of Chinese generic HRQOL measures and a series of qualitative interviews produced a list of 42 potentially important health items in a Chinese cultural setting; 110 Chinese participants in face-to-face interviews ranked the health items from most important to least important. Responses were coded into a rectangular 110 × 42 matrix, and multidimensional unfolding was conducted to analyze participants' preferences for health items. RESULTS It was found that demographic characteristics and one's health condition affected views of HRQOL. Meanwhile, 3 health items were considered to be most important across the whole sample: sleep quality, body constitution, and spiritual appearance. CONCLUSION This study used a novel approach to explore how people coming from a Chinese cultural setting may perceive HRQOL and which aspects of HRQOL are most important to them. The study shows that multidimensional unfolding is a feasible approach to assess preferences in a general population. Future studies using this approach are recommended to further explore the constructs of HRQOL in other general populations.
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Affiliation(s)
- Zhuxin Mao
- School of Insurance, Southwestern University of Finance and Economics, Sichuan, China.
| | - Shenaz Ahmed
- Institute of Health Sciences, University of Leeds, Leeds, England, UK
| | - Christopher Graham
- Department of Psychology, Queen's University Belfast, Belfast, England, UK
| | - Paul Kind
- Institute of Health Sciences, University of Leeds, Leeds, England, UK
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22
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Chakraborty T, Polley S, Sinha D, Seal S, Sinha D, Mitra SK, Hazra J, Sau K, Pal M, Sau S. Structurally distinct unfolding intermediates formed from a staphylococcal capsule-producing enzyme retained NADPH binding activity. J Biomol Struct Dyn 2021; 40:9126-9143. [PMID: 33977860 DOI: 10.1080/07391102.2021.1924269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CapF, a capsule-producing enzyme expressed by Staphylococcus aureus, binds NADPH and exists as a dimer in the aqueous solution. Many other capsule-producing virulent bacteria also express CapF orthologs. To understand the folding-unfolding mechanism of S. aureus CapF, herein a recombinant CapF (rCapF) was individually investigated using urea and guanidine hydrochloride (GdnCl). Unfolding of rCapF by both the denaturants was reversible but proceeded via the synthesis of a different number of intermediates. While two dimeric intermediates (rCapF4 and rCapF5) were formed at 0.5 M and 1.5 M GdnCl, three dimeric intermediates (rCapF1, rCapF2, and rCapF3) were produced at 1 M, 2 M, and 3 M urea, respectively. rCapF5 showed 3.6 fold less NADPH binding activity, whereas other intermediates retained full NADPH binding activity. Compared to rCapF, all of the intermediates (except rCapF3) had a compressed shape. Conversely, rCapF3 possessed a native protein-like shape. The maximum shape loss was in rCapF4 though its secondary structure remained unperturbed. Additionally, the tertiary structure and hydrophobic surface area of the intermediates neither matched with each other nor with those of the native rCapF. Of the four Trp residues in rCapF, one or more Trp residues in the intermediates may have higher solvent accessibility. Using sequence alignment and a tertiary structural model of CapF, we have demonstrated that the region around Trp 137 of CapF may be most sensitive to unfolding, whereas the NADPH binding motif carrying region at the N-terminal end of this protein may be resistant to unfolding, particularly at the low denaturant concentrations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Sudip K Mitra
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Joyita Hazra
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Mahadeb Pal
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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23
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Shahbazi Dastjerdeh M, Shokrgozar MA, Rahimi H, Golkar M. Potential aggregation hot spots in recombinant human keratinocyte growth factor: a computational study. J Biomol Struct Dyn 2021; 40:8169-8184. [PMID: 33843469 DOI: 10.1080/07391102.2021.1908912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The recombinant human keratinocyte growth factor (rhKGF) is a highly aggregation-prone therapeutic protein. The high aggregation liability of rhKGF is manifested by loss of the monomeric state, and accumulation of the aggregated species even at moderate temperatures. Here, we analyzed the rhKGF for its vulnerability toward aggregation by detection of aggregation-prone regions (APRs) using several sequence-based computational tools including TANGO, ZipperDB, AGGRESCAN, Zyggregator, Camsol, PASTA, SALSA, WALTZ, SODA, Amylpred, AMYPDB, and structure-based tools including SolubiS, CamSol structurally corrected, Aggrescan3D and spatial aggregation propensity (SAP) algorithm. The sequence-based prediction of APRs in rhKGF indicated that they are mainly located at positions 10-30, 40-60, 61-66, 88-120, and 130-140. Mapping on the rhKGF structure revealed that most of these residues including F16-R25, I43, E45, R47-I56, F61, Y62, N66, L88-E91, E108-F110, A112, N114, T131, and H133-T140 are surface-exposed in the native state which can promote aggregation without major unfolding event, or the conformational change may occur in the oligomers. The other regions are buried in the native state and their contribution to non-native aggregation is mediated by a preceding unfolding event. The structure-based prediction of APRs using the SAP tool limited the number of identified APRs to the dynamically-exposed hydrophobic residues including V12, A50, V51, L88, I89, L90, I118, L135, and I139 mediating the native-state aggregation. Our analysis of APRs in rhKGF identified the regions determining the intrinsic aggregation propensity of the rhKGF which are the candidate positions for engineering the rhKGF to reduce its aggregation tendency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Golkar
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
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24
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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25
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March D, Bianco V, Franzese G. Protein Unfolding and Aggregation near a Hydrophobic Interface. Polymers (Basel) 2021; 13:polym13010156. [PMID: 33401542 PMCID: PMC7795562 DOI: 10.3390/polym13010156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 01/29/2023] Open
Abstract
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we study how the presence of a hydrophobic surface affects this course of events. To this goal, we use a coarse-grained model of proteins and study by simulations their folding and aggregation near an ideal hydrophobic surface in an aqueous environment by changing parameters such as temperature and hydrophobic strength, related, e.g., to ions concentration. We show that the hydrophobic surface, as well as the other parameters, affect both the protein unfolding and aggregation. We discuss the interpretation of these results and define future lines for further analysis, with their possible implications in neurodegenerative diseases.
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Affiliation(s)
- David March
- Secció de Física Estadística i Interdisciplinària—Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
| | - Valentino Bianco
- Chemical Physics Department, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040 Madrid, Spain
- Correspondence: (V.B.); (G.F.)
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària—Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
- Correspondence: (V.B.); (G.F.)
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26
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Haun A, Tsuchiya N. Reasonable criteria for functionalists; scarce criteria from phenomenological perspective. Cogn Neurosci 2020; 12:95-96. [PMID: 33280493 DOI: 10.1080/17588928.2020.1838473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In their article, Doerig et al suggest a set of criteria for evaluating theories of consciousness. Naturally, their criteria are situated in their own particular perspective on consciousness science, which we have critiqued in the past. Their first criterion is likely to be the one that is most productive and least contentious: if the field can agree to a family of paradigm cases for consciousness, this would be an important endeavor for the field.
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Affiliation(s)
- Andrew Haun
- Department of Psychiatry, University of Wisconsin-Madison, Madison, USA
| | - Naotsugu Tsuchiya
- Turner Institute for Brain and Mental Health & School of Psychological Sciences, Faculty of Medicine, Nursing, and Health Sciences, Monash University,Melbourne, Victoria, Australia
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Abstract
α-Lactalbumin (α-LA) is a small (Mr 14,200), acidic (pI 4–5), Ca2+-binding protein. α-LA is a regulatory component of lactose synthase enzyme system functioning in the lactating mammary gland. The protein possesses a single strong Ca2+-binding site, which can also bind Mg2+, Mn2+, Na+, K+, and some other metal cations. It contains several distinct Zn2+-binding sites. Physical properties of α-LA strongly depend on the occupation of its metal binding sites by metal ions. In the absence of bound metal ions, α-LA is in the molten globule-like state. The binding of metal ions, and especially of Ca2+, increases stability of α-LA against the action of heat, various denaturing agents and proteases, while the binding of Zn2+ to the Ca2+-loaded protein decreases its stability and causes its aggregation. At pH 2, the protein is in the classical molten globule state. α-LA can associate with membranes at neutral or slightly acidic pH at physiological temperatures. Depending on external conditions, α-LA can form amyloid fibrils, amorphous aggregates, nanoparticles, and nanotubes. Some of these aggregated states of α-LA can be used in practical applications such as drug delivery to tissues and organs. α-LA and some of its fragments possess bactericidal and antiviral activities. Complexes of partially unfolded α-LA with oleic acid are cytotoxic to various tumor and bacterial cells. α-LA in the cytotoxic complexes plays a role of a delivery carrier of cytotoxic fatty acid molecules into tumor and bacterial cells across the cell membrane. Perhaps in the future the complexes of α-LA with oleic acid will be used for development of new anti-cancer drugs.
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Sereno MI, Diedrichsen J, Tachrount M, Testa-Silva G, d'Arceuil H, De Zeeuw C. The human cerebellum has almost 80% of the surface area of the neocortex. Proc Natl Acad Sci U S A 2020; 117:19538-43. [PMID: 32723827 DOI: 10.1073/pnas.2002896117] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The cerebellum has long been recognized as a partner of the cerebral cortex, and both have expanded greatly in human evolution. The thin cerebellar cortex is even more tightly folded than the cerebral cortex. By scanning a human cerebellum specimen at ultra-high magnetic fields, we were able to computationally reconstruct its surface down to the level of the smallest folds, revealing that the cerebellar cortex has almost 80% of the surface area of the cerebral cortex. By performing the same procedure on a monkey brain, we found that the surface area of the human cerebellum has expanded even more than that of the human cerebral cortex, suggesting a role in characteristically human behaviors, such as toolmaking and language. The surface of the human cerebellar cortex is much more tightly folded than the cerebral cortex. It was computationally reconstructed for the first time to the level of all individual folia from multicontrast high-resolution postmortem MRI scans. Its total shrinkage-corrected surface area (1,590 cm2) was larger than expected or previously reported, equal to 78% of the total surface area of the human neocortex. The unfolded and flattened surface comprised a narrow strip 10 cm wide but almost 1 m long. By applying the same methods to the neocortex and cerebellum of the macaque monkey, we found that its cerebellum was relatively much smaller, approximately 33% of the total surface area of its neocortex. This suggests a prominent role for the cerebellum in the evolution of distinctively human behaviors and cognition.
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Kamenik AS, Hofer F, Handle PH, Liedl KR. Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1. Front Mol Biosci 2020; 7:18. [PMID: 32154264 PMCID: PMC7045072 DOI: 10.3389/fmolb.2020.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Proteolytic susceptibility during endolysosomal degradation is decisive for allergic sensitization. In the major birch pollen allergen Bet v 1 most protease cleavage sites are located within its secondary structure elements, which are inherently inaccessible to proteases. The allergen thus must unfold locally, exposing the cleavage sites to become susceptible to proteolysis. Hence, allergen cleavage rates are presumed to be linked to their fold stability, i.e., unfolding probability. Yet, these locally unfolded structures have neither been captured in experiment nor simulation due to limitations in resolution and sampling time, respectively. Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of Bet v 1a and two variants with higher and lower cleavage rates. Already at the nanosecond-timescale we observe a significantly higher flexibility for the destabilized variant compared to Bet v 1a and the proteolytically stabilized mutant. Estimating the thermodynamics and kinetics of local unfolding around an initial cleavage site, we find that the Bet v 1 variant with the highest cleavage rate also shows the highest probability for local unfolding. For the stabilized mutant on the other hand we only find minimal unfolding probability. These results strengthen the link between the conformational dynamics of allergen proteins and their stability during endolysosomal degradation. The presented approach further allows atomistic insights in the conformational ensemble of allergen proteins and provides probability estimates below experimental detection limits.
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Affiliation(s)
| | | | | | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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30
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Zhang CM, Tan YB, Zhou HH, Ge ZB, Feng JR, Lv GB, Sun ZY, Fu Y, Wang MY. Intra-subunit Disulfide Determines the Conversion and Structural Stability of CRP Isoforms. Inflammation 2019; 43:466-477. [PMID: 31760526 DOI: 10.1007/s10753-019-01130-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
C-reactive protein (CRP) is a major human acute-phase reactant that is composed of five identical subunits. CRP dissociates into subunits at inflammatory loci forming monomeric CRP (mCRP) with substantially enhanced activities, which can be further activated by reducing the intra-subunit disulfide bond. However, conformational changes underlying the activation process of CRP are less well understood. Conformational changes accompanying the conversion of CRP to mCRP with or without reduction were examined with circular dichroism spectroscopy, fluorescence spectroscopy, electron microscopy, size-exclusion chromatography, and neoepitope expression. The conversion of CRP to mCRP follows a two-stage process. In the first stage, CRP dissociates into molten globular subunits characterized by intact secondary structure elements with greatly impaired tertiary packing. In the second stage, these intermediates completely lose their native subunit conformation and assemble into high-order aggregates. The inclusion of reductant accelerates the formation of molten globular subunits in the first step and promotes the formation of more compact aggregates in the second stage. We further show a significant contribution of electrostatic interactions to the stabilization of native CRP. The conformational features of dissociated subunits and the aggregation of mCRP may have a key impact on their activities.
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Affiliation(s)
- Chun-Miao Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yu-Bo Tan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hai-Hong Zhou
- Gansu Provincial Cancer Hospital, Lanzhou, 730050, People's Republic of China
| | - Zhong-Bo Ge
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jun-Rui Feng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Guang-Bo Lv
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Zhi-Yuan Sun
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yu Fu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Ming-Yu Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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31
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Sugimoto H, Nakajima Y, Motoyama A, Katagiri E, Watanabe T, Suzuki K. Unfolding of CBP21, a lytic polysaccharide monooxygenase, without dissociation of its copper ion cofactor. Biopolymers 2019; 111:e23339. [PMID: 31688961 DOI: 10.1002/bip.23339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 01/22/2023]
Abstract
Chitin-binding protein 21 (CBP21) from Serratia marcescens is a lytic polysaccharide monooxygenase that contains a copper ion as a cofactor. We aimed to elucidate the unfolding mechanism of CBP21 and the effects of Cu2+ on its structural stability at pH 5.0. Thermal unfolding of both apo- and holoCBP21 was reversible. ApoCBP21 unfolded in a simple two-state transition manner. The peak temperature of the DSC curve, tp , for holoCBP21 (74.4°C) was about nine degrees higher than that for apoCBP21 (65.6°C). The value of tp in the presence of excess Cu2+ was around 75°C, indicating that Cu2+ does not dissociate from the protein molecule during unfolding. The unfolding mechanism of holoCBP21 was considered to be as follows: N∙Cu2+ ⇌ U∙Cu2+ , where N and U represent the native and unfolded states, respectively. Urea-induced equilibrium unfolding analysis showed that holoCBP21 was stabilized by 35 kJ mol-1 in terms of the Gibbs energy change for unfolding (pH 5.0, 25°C), compared with apoCBP21. The increased stability of holoCBP21 was considered to result from the structural stabilization of the protein-Cu2+ complex itself.
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Affiliation(s)
- Hayuki Sugimoto
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Yuichi Nakajima
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Ayaka Motoyama
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Erina Katagiri
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Takeshi Watanabe
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kazushi Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan.,Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
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32
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Bhunia AK, Saha S, Kamilya T. Microscopic and spectroscopic study of the corona formation and unfolding of human haemoglobin in presence of ZnO nanoparticles. LUMINESCENCE 2019; 35:144-155. [PMID: 31514262 DOI: 10.1002/bio.3707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/11/2019] [Accepted: 08/21/2019] [Indexed: 12/23/2022]
Abstract
The interaction of zinc oxide nanoparticles (ZnO NPs) with human haemoglobin (Hb) is studied for the biologically safe application of ZnO NPs in the human body. The Hb corona is formed around the ZnO nanoparticles, directly observed from high-resolution transmission electron microscopy (HRTEM) images. Hb formed 'hard corona' on the surface of ZnO NPs from an exponential association mechanism over a very short duration, as well as unfolding of Hb that occurred over a long lifetime. Dynamic light scattering measurements demonstrated that the ZnO NPs were completely covered by Hb with shell thickness of c. 6 nm that formed a 'hard corona'. Zeta potential measurements represented that the ZnO NPs were fully covered by Hb molecules using an exponential association mechanism. Tryptophans (TRY), as well as heme-porphyrin moieties of Hb, are the major binding sites for ZnO NPs. The nature of the interaction between ZnO NPs and Hb was analysed from the fluorescence quenching of TRYs. Electrostatic interaction, along with the hydrophobic interaction between ZnO NPs and Hb, is responsible for the conformational change in Hb due to increase in the percentage of β-sheets together with a decrease in α-helices.
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Affiliation(s)
- A K Bhunia
- Department of Physics & Technophysics, Vidyasagar University, Paschim Medinipur, India.,Department of Physics, Government General Degree College at Gopiballavpur-II, Jhargram, India
| | - S Saha
- Department of Physics & Technophysics, Vidyasagar University, Paschim Medinipur, India
| | - T Kamilya
- Department of Physics, Narajole Raj College, Paschim Medinip, India
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Andrich D, Luo G. A Law of Comparative Preference: Distinctions Between Models of Personal Preference and Impersonal Judgment in Pair Comparison Designs. Appl Psychol Meas 2019; 43:181-194. [PMID: 31019355 PMCID: PMC6463346 DOI: 10.1177/0146621617738014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The pair comparison design for distinguishing between stimuli located on the same natural or hypothesized linear continuum is used both when the response is a personal preference and when it is an impersonal judgment. Appropriate models which complement the different responses have been proposed. However, the models most appropriate for impersonal judgments have also been described as modeling choice, which may imply personal preference. This leads to potential confusion in interpretation of scale estimates of the stimuli, in particular whether they reflect a substantive order on the variable or reflect a characteristic of the sample which is different from the substantive order on the variable. Using Thurstone's concept of a discriminal response when a person engages with each stimulus, this article explains the overlapping and distinctive relationships between models for pair comparison designs when used for preference and judgment. In doing so, it exploits the properties of the relatively new hyperbolic cosine model which is not only appropriate for modeling personal preferences but has an explicit mathematical relationship with models for impersonal judgments. The hyperbolic cosine model is shown to be a special case of a more general form, referred to in parallel with Thurstone's Law of Comparative Judgment, as a specific law of comparative preference. Analyses of two real data sets illustrate the differences between the models most appropriate for personal preferences and impersonal judgments in a pair comparison design.
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Affiliation(s)
- David Andrich
- The University of Western Australia, Perth, Australia
| | - Guanzhong Luo
- Hong Kong Examinations and Assessment Authority, Wan Chai, Hong Kong
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Abstract
Recently, some attitude researchers have argued that the traditional bipolar model of attitudes should be replaced, claiming that a bivariate model is superior in several ways, foremost of which is its ability to account for ambivalent attitudes. This study argues that ambivalence is not at odds with bipolarity per se, but rather the conventional view of bipolarity, and that the psychometric evidence supporting a bivariate interpretation has been flawed. To demonstrate this, a scale developed out of the bivariate approach was examined using a unidimensional unfolding item response theory model: general hyperbolic cosine model for polytomous responses. The results were consistent with a bipolar interpretation, providing support for the argument that ambivalent evaluations are the correct middle-point of a bipolar evaluative dimension. Thus, it is argued that attitudinal ambivalence does not necessitate moving beyond bipolarity, but rather, moving beyond the conventional conceptualization and assessment of attitudes.
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Hosseini SA, Esmaili Paeen Afrakoti I. Evaluation of a new neutron energy spectrum unfolding code based on an Adaptive Neuro-Fuzzy Inference System (ANFIS). J Radiat Res 2018; 59:436-441. [PMID: 29351656 PMCID: PMC6054179 DOI: 10.1093/jrr/rrx087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 10/09/2017] [Indexed: 06/07/2023]
Abstract
The purpose of the present study was to reconstruct the energy spectrum of a poly-energetic neutron source using an algorithm developed based on an Adaptive Neuro-Fuzzy Inference System (ANFIS). ANFIS is a kind of artificial neural network based on the Takagi-Sugeno fuzzy inference system. The ANFIS algorithm uses the advantages of both fuzzy inference systems and artificial neural networks to improve the effectiveness of algorithms in various applications such as modeling, control and classification. The neutron pulse height distributions used as input data in the training procedure for the ANFIS algorithm were obtained from the simulations performed by MCNPX-ESUT computational code (MCNPX-Energy engineering of Sharif University of Technology). Taking into account the normalization condition of each energy spectrum, 4300 neutron energy spectra were generated randomly. (The value in each bin was generated randomly, and finally a normalization of each generated energy spectrum was performed). The randomly generated neutron energy spectra were considered as output data of the developed ANFIS computational code in the training step. To calculate the neutron energy spectrum using conventional methods, an inverse problem with an approximately singular response matrix (with the determinant of the matrix close to zero) should be solved. The solution of the inverse problem using the conventional methods unfold neutron energy spectrum with low accuracy. Application of the iterative algorithms in the solution of such a problem, or utilizing the intelligent algorithms (in which there is no need to solve the problem), is usually preferred for unfolding of the energy spectrum. Therefore, the main reason for development of intelligent algorithms like ANFIS for unfolding of neutron energy spectra is to avoid solving the inverse problem. In the present study, the unfolded neutron energy spectra of 252Cf and 241Am-9Be neutron sources using the developed computational code were found to have excellent agreement with the reference data. Also, the unfolded energy spectra of the neutron sources as obtained using ANFIS were more accurate than the results reported from calculations performed using artificial neural networks in previously published papers.
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Abstract
Spectrins are cytoskeletal proteins located at the inner face of the plasma membrane, making connections between membrane anchors and the actin cortex, and between actin filaments. Spectrins share a common structure forming a bundle of 3 α-helices and play a major role during cell deformation. Here, we used high-speed force spectroscopy and steered molecular dynamics simulations to understand the mechanical stability of spectrin, revealing a molecular force buffering function. We find that spectrin acts as a soft spring at short extensions (70-100 Å). Under continuous external stretching, its α-helices unwind, leading to a viscous mechanical response over larger extensions (100-300 Å), represented by a constant-force plateau in force/extension curves. This viscous force buffering emerges from a quasi-equilibrium competition between disruption and re-formation of α-helical hydrogen bonds. Our results suggest that, in contrast to β-sheet proteins, which unfold in a catastrophic event, α-helical spectrins dominantly unwind, providing a viscous force buffer over extensions about 5 times their folded length.
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Affiliation(s)
- Hirohide Takahashi
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 Avenue de Luminy , 13009 Marseille , France
- Department of Anesthesiology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
- Departments of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Felix Rico
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 Avenue de Luminy , 13009 Marseille , France
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign , UMR 7565, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France, and Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana , Illinois 61801 , United States
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy , 163 Avenue de Luminy , 13009 Marseille , France
- Department of Anesthesiology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
- Departments of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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Valdés-García G, Millán-Pacheco C, Pastor N. Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants. Biopolymers 2018; 107. [PMID: 28509352 DOI: 10.1002/bip.23027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 12/30/2022]
Abstract
Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Both mutations make the germline protein unstable and speed up its ability to aggregate. To date, there is no molecular mechanism that explains how these differences in amyloidogenesis can arise from a single mutation. To look into the structural and dynamical differences in the native state of these proteins, we carried out molecular dynamics simulations at room temperature. Despite the structural similarity of the germline protein and the mutants, we found differences in their dynamical signatures that explain the mutants' increased tendency to form amyloids. The contact network alterations caused by the mutations, though different, converge in affecting two anti-aggregation motifs present in light chain variable domains, suggesting a different starting point for aggregation in lambda chains compared to kappa chains.
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Affiliation(s)
- Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - César Millán-Pacheco
- Facultad de Farmacia; Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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Trokter M, Waksman G. Translocation through the Conjugative Type IV Secretion System Requires Unfolding of Its Protein Substrate. J Bacteriol 2018; 200:e00615-17. [PMID: 29311273 DOI: 10.1128/JB.00615-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Bacterial conjugation, a mechanism of horizontal gene transfer, is the major means by which antibiotic resistance spreads among bacteria (1, 2). Conjugative plasmids are transferred from one bacterium to another through a type IV secretion system (T4SS) in the form of single-stranded DNA covalently attached to a protein called relaxase. The relaxase is fully functional both in a donor cell (prior to conjugation) and recipient cell (after conjugation). Here, we demonstrate that the protein substrate has to unfold for efficient translocation through the conjugative T4SS. Furthermore, we present various relaxase modifications that preserve the function of the relaxase but block substrate translocation. This study brings us a step closer to deciphering the complete mechanism of T4SS substrate translocation, which is vital for the development of new therapies against multidrug-resistant pathogenic bacteria. IMPORTANCE Conjugation is the principal means by which antibiotic resistance genes spread from one bacterium to another (1, 2). During conjugation, a covalent complex of single-stranded DNA and a protein termed relaxase is transported by a type IV secretion system. To date, it is not known whether the relaxase requires unfolding prior to transport. In this report, we use functional assays to monitor the transport of wild-type relaxase and variants containing unfolding-resistant domains and show that these domains reduce conjugation and protein transport dramatically. Mutations that lower the free energy of unfolding in these domains do not block translocation and can even promote it. We thus conclude that the unfolding of the protein substrate is required during transport.
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Castro IH, Ferrari A, Herrera MG, Noguera ME, Maso L, Benini M, Rufini A, Testi R, Costantini P, Santos J. Biophysical characterisation of the recombinant human frataxin precursor. FEBS Open Bio 2018; 8:390-405. [PMID: 29511616 PMCID: PMC5832983 DOI: 10.1002/2211-5463.12376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/25/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022] Open
Abstract
Friedreich's ataxia is a disease caused by a decrease in the levels of expression or loss of functionality of the mitochondrial protein frataxin (FXN). The development of an active and stable recombinant variant of FXN is important for protein replacement therapy. Although valuable data about the mature form FXN81-210 has been collected, not enough information is available about the conformation of the frataxin precursor (FXN1-210). We investigated the conformation, stability and function of a recombinant precursor variant (His6-TAT-FXN1-210), which includes a TAT peptide in the N-terminal region to assist with transport across cell membranes. His6-TAT-FXN1-210 was expressed in Escherichia coli and conditions were found for purifying folded protein free of aggregation, oxidation or degradation, even after freezing and thawing. The protein was found to be stable and monomeric, with the N-terminal stretch (residues 1-89) mostly unstructured and the C-terminal domain properly folded. The experimental data suggest a complex picture for the folding process of full-length frataxin in vitro: the presence of the N-terminal region increased the tendency of FXN to aggregate at high temperatures but this could be avoided by the addition of low concentrations of GdmCl. The purified precursor was translocated through cell membranes. In addition, immune response against His6-TAT-FXN1-210 was measured, suggesting that the C-terminal fragment was not immunogenic at the assayed protein concentrations. Finally, the recognition of recombinant FXN by cellular proteins was studied to evaluate its functionality. In this regard, cysteine desulfurase NFS1/ISD11/ISCU was activated in vitro by His6-TAT-FXN1-210. Moreover, the results showed that His6-TAT-FXN1-210 can be ubiquitinated in vitro by the recently identified frataxin E3 ligase RNF126, in a similar way as the FXN1-210, suggesting that the His6-TAT extension does not interfere with the ubiquitination machinery.
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Affiliation(s)
- Ignacio Hugo Castro
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Alejandro Ferrari
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - María Georgina Herrera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Martín Ezequiel Noguera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Lorenzo Maso
- Department of Biology University of Padova Italy
| | - Monica Benini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Alessandra Rufini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Roberto Testi
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | | | - Javier Santos
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
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Kudryashova E, Seveau SM, Kudryashov DS. Targeting and inactivation of bacterial toxins by human defensins. Biol Chem 2017; 398:1069-1085. [PMID: 28593905 DOI: 10.1515/hsz-2017-0106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/18/2017] [Indexed: 11/15/2022]
Abstract
Defensins, as a prominent family of antimicrobial peptides (AMP), are major effectors of the innate immunity with a broad range of immune modulatory and antimicrobial activities. In particular, defensins are the only recognized fast-response molecules that can neutralize a broad range of bacterial toxins, many of which are among the deadliest compounds on the planet. For a decade, the mystery of how a small and structurally conserved group of peptides can neutralize a heterogeneous group of toxins with little to no sequential and structural similarity remained unresolved. Recently, it was found that defensins recognize and target structural plasticity/thermodynamic instability, fundamental physicochemical properties that unite many bacterial toxins and distinguish them from the majority of host proteins. Binding of human defensins promotes local unfolding of the affected toxins, destabilizes their secondary and tertiary structures, increases susceptibility to proteolysis, and leads to their precipitation. While the details of toxin destabilization by defensins remain obscure, here we briefly review properties and activities of bacterial toxins known to be affected by or resilient to defensins, and discuss how recognized features of defensins correlate with the observed inactivation.
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41
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Montoliu-Gaya L, Murciano-Calles J, Martinez JC, Villegas S. Towards the improvement in stability of an anti-Aβ single-chain variable fragment, scFv-h3D6, as a way to enhance its therapeutic potential. Amyloid 2017; 24:167-175. [PMID: 28699800 DOI: 10.1080/13506129.2017.1348347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ScFv-h3D6 is a single-chain variable fragment derived from the monoclonal antibody bapineuzumab that prevents Aβ-induced cytotoxicity by capturing Aβ oligomers. The benefits of scFv-h3D6 treatment in Alzheimer's disease are known at the behavioural, cellular and molecular levels in the 3xTg-AD mouse model. Antibody-based therapeutics are only stable in a limited temperature range, so their benefit in vivo depends on their capability for maintaining the proper fold. Here, we have stabilized the scFv-h3D6 folding by introducing the mutation VH-K64R and combining it with the previously described elongation of the VL domain (C3). The stabilities of the different scFv-h3D6 constructs were calculated from urea and thermal denaturation followed by Trp-fluorescence, CD and DSC and resulted in the order C3 > K64R/C3 > VH-K64R ≥ scFv-h3D6; showing that the combination of both mutations was not additive, instead they partially cancelled each other. The three mutants assayed showed a decreased aggregation tendency but maintained their capability to aggregate in the form of worm-like fibrils, basis of the protective effect of scFv-h3D6. Cytotoxicity assays showed that all the mutants recovered cell viability of Aβ-treated neuroblastoma cell cultures in a dose-dependent manner and with efficiencies that correlated with stability, therefore improving the therapeutic ability of this antibody.
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Affiliation(s)
- Laia Montoliu-Gaya
- a Protein Folding and Stability Group, Departament de Bioquímica i Biologia Molecular , Unitat de Biociències, Universitat Autònoma de Barcelona , Spain
| | - Javier Murciano-Calles
- b Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences , University of Granada, Campus Fuentenueva , Granada , Spain
| | - Jose C Martinez
- b Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences , University of Granada, Campus Fuentenueva , Granada , Spain
| | - Sandra Villegas
- a Protein Folding and Stability Group, Departament de Bioquímica i Biologia Molecular , Unitat de Biociències, Universitat Autònoma de Barcelona , Spain
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42
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Abstract
Deciphering the mechanism of activation of heterotrimeric G proteins by their cognate receptors continues to be an intriguing area of research. The recently solved crystal structure of the ternary complex captured the receptor-bound α-subunit in an open conformation, without bound nucleotide has improved our understanding of the activation process. Despite these advancements, the mechanism by which the receptor causes GDP release from the α-subunit remains elusive. To elucidate the mechanism of activation, we studied guanine nucleotide-induced structural stability of the α-subunit (in response to thermal/chaotrope-mediated stress). Inherent stabilities of the inactive (GDP-bound) and active (GTP-bound) forms contribute antagonistically to the difference in conformational stability whereas the GDP-bound protein is able to switch to a stable intermediate state, GTP-bound protein loses this ability. Partial perturbation of the protein fold reveals the underlying influence of the bound nucleotide providing an insight into the mechanism of activation. An extra stable, pretransition intermediate, 'empty pocket' state (conformationally active-state like) in the unfolding pathway of GDP-bound protein mimics a gating system - the activation process having to overcome this stable intermediate state. We demonstrate that a relatively more complex conformational fold of the GDP-bound protein is at the core of the gating system. We report capturing this threshold, 'metastable empty pocket' conformation (the gate) of α-subunit of G protein and hypothesize that the receptor activates the G protein by enabling it to achieve this structure through mild structural perturbation.
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Affiliation(s)
- Sai Krishna Andhirka
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Ravichandran Vignesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Gopala Krishna Aradhyam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
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43
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Jafarisani M, Bathaie SZ, Mousavi MF. Saffron carotenoids (crocin and crocetin) binding to human serum albumin as investigated by different spectroscopic methods and molecular docking. J Biomol Struct Dyn 2017; 36:1681-1690. [PMID: 28537197 DOI: 10.1080/07391102.2017.1331865] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Therapeutic effects of saffron ingredients were studied in some diseases. The pharmacokinetics and pharmacodynamics of these ingredients were also studied, but their transport mechanism is not clearly known. Serum albumin has been known as the most important transporter of many drugs in the body that affects their disposition, transportation, and bioavailability. Here, we investigated the interaction of crocin (Cro) with HSA, for the first time, and compared with the crocetin (Crt)-HSA interaction. UV and fluorescence spectroscopy, circular dichroism (CD), and molecular docking was applied to investigate the possibility and mechanism of binding of HSA with these natural carotenoids. The gradually addition of Cro increased HSA absorbency at 278 nm, while Crt decreased it. Both of these changes induced HSA unfolding that was confirmed by the decreased α-helix content, as determined by the CD. Both carotenoids quenched HSA fluorescence emission, but with different mechanisms. The Stern-Volmer plots indicated a dynamic quenching of intrinsic emission of HSA due to Cro addition, while Crt quenching followed both static and dynamic quenching mechanisms. Docking results indicated binding of Cro/Crt in sub-domain IIA, Sudlow site I of HSA, which accompanied with the hydrogen bonding of Cro/Crt with Tyr138. The interaction of these ligands (Cro/Crt) caused HSA unfolding and affects the hydrophobic environment of Trp241, which result in the quenching of Trp fluorescence. The UV spectroscopy and fluorescence quenching data indicated the differences in the mechanisms of interaction of Cro/Crt with HSA, which is due to the differences in the structure and hydrophobicity of these ligands.
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Affiliation(s)
- Moslem Jafarisani
- a Faculty of Medical Sciences, Department of Clinical Biochemistry , Tarbiat Modares University , Tehran , Iran
| | - S Zahra Bathaie
- a Faculty of Medical Sciences, Department of Clinical Biochemistry , Tarbiat Modares University , Tehran , Iran
| | - Mir F Mousavi
- b Department of Chemistry , Tarbiat Modares University , Tehran 14115-175 , Iran
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44
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Abstract
A simple theory of the unfolding kinetics of a semi-flexible polymer chain is presented in terms of a Kramers type picture for the energy of elongation. The hydrodynamic interactions are discussed in terms of slender body theory. It turns out that the elongation of the chain is basically linear in time and independent of the viscosity. The former prediction agrees with experiments on the stretching dynamics of DNA under planar elongational flow. Nevertheless, the theory overestimates the experimental rate by a significant amount for reasons that are unclear.
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Affiliation(s)
- Theo Odijk
- Lorentz Institute for Theoretical Physics, Leiden University, 2333 CA Leiden, The Netherlands.
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45
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Dobson J, Kumar A, Willis LF, Tuma R, Higazi DR, Turner R, Lowe DC, Ashcroft AE, Radford SE, Kapur N, Brockwell DJ. Inducing protein aggregation by extensional flow. Proc Natl Acad Sci U S A 2017; 114:4673-8. [PMID: 28416674 DOI: 10.1073/pnas.1702724114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Relative to other extrinsic factors, the effects of hydrodynamic flow fields on protein stability and conformation remain poorly understood. Flow-induced protein remodeling and/or aggregation is observed both in Nature and during the large-scale industrial manufacture of proteins. Despite its ubiquity, the relationships between the type and magnitude of hydrodynamic flow, a protein's structure and stability, and the resultant aggregation propensity are unclear. Here, we assess the effects of a defined and quantified flow field dominated by extensional flow on the aggregation of BSA, β2-microglobulin (β2m), granulocyte colony stimulating factor (G-CSF), and three monoclonal antibodies (mAbs). We show that the device induces protein aggregation after exposure to an extensional flow field for 0.36-1.8 ms, at concentrations as low as 0.5 mg mL-1 In addition, we reveal that the extent of aggregation depends on the applied strain rate and the concentration, structural scaffold, and sequence of the protein. Finally we demonstrate the in situ labeling of a buried cysteine residue in BSA during extensional stress. Together, these data indicate that an extensional flow readily unfolds thermodynamically and kinetically stable proteins, exposing previously sequestered sequences whose aggregation propensity determines the probability and extent of aggregation.
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46
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Ripstein ZA, Huang R, Augustyniak R, Kay LE, Rubinstein JL. Structure of a AAA+ unfoldase in the process of unfolding substrate. eLife 2017; 6. [PMID: 28390173 PMCID: PMC5423775 DOI: 10.7554/elife.25754] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/06/2017] [Indexed: 12/19/2022] Open
Abstract
AAA+ unfoldases are thought to unfold substrate through the central pore of their hexameric structures, but how this process occurs is not known. VAT, the Thermoplasma acidophilum homologue of eukaryotic CDC48/p97, works in conjunction with the proteasome to degrade misfolded or damaged proteins. We show that in the presence of ATP, VAT with its regulatory N-terminal domains removed unfolds other VAT complexes as substrate. We captured images of this transient process by electron cryomicroscopy (cryo-EM) to reveal the structure of the substrate-bound intermediate. Substrate binding breaks the six-fold symmetry of the complex, allowing five of the six VAT subunits to constrict into a tight helix that grips an ~80 Å stretch of unfolded protein. The structure suggests a processive hand-over-hand unfolding mechanism, where each VAT subunit releases the substrate in turn before re-engaging further along the target protein, thereby unfolding it.
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Affiliation(s)
- Zev A Ripstein
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Rui Huang
- Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - Rafal Augustyniak
- Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - Lewis E Kay
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - John L Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
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Polley S, Seal S, Mahapa A, Jana B, Biswas A, Mandal S, Sinha D, Sau K, Sau S. Identification and characterization of a cyclosporin binding cyclophilin from Staphylococcus aureus Newman. Bioinformation 2017; 13:78-85. [PMID: 28584448 PMCID: PMC5450249 DOI: 10.6026/97320630013078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/04/2017] [Indexed: 01/24/2023] Open
Abstract
Cyclophilins, a class of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes, are inhibited by cyclosporin A (CsA), an
immunosuppressive drug. Staphylococcus aureus Newman, a pathogenic bacterium, carries a gene for encoding a putative cyclophilin
(SaCyp). SaCyp shows significant homology with other cyclophilins at the sequence level. A three-dimensional model structure of
SaCyp harbors a binding site for CsA. To verify whether SaCyp possesses both the PPIase activity and the CsA binding ability, we
have purified and investigated a recombinant SaCyp (rCyp) using various in vitro tools. Our RNase T1 refolding assay indicates that
rCyp has a substantial extent of PPIase activity. rCyp that exists as a monomer in the aqueous solution is truly a cyclophilin as its
catalytic activity specifically shows sensitivity to CsA. rCyp appears to bind CsA with a reasonably high affinity. Additional
investigations reveal that binding of CsA to rCyp alters its structure and shape to some extent. Both rCyp and rCyp-CsA are unfolded
via the formation of at least one intermediate in the presence of guanidine hydrochloride. Unfolding study also indicates that there is
substantial extent of thermodynamic stabilization of rCyp in the presence of CsA as well. The data suggest that rCyp may be exploited
to screen the new antimicrobial agents in the future.
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Affiliation(s)
- Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Biswanath Jana
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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48
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Yoneda JS, Miles AJ, Araujo APU, Wallace BA. Differential dehydration effects on globular proteins and intrinsically disordered proteins during film formation. Protein Sci 2017; 26:718-726. [PMID: 28097742 PMCID: PMC5368061 DOI: 10.1002/pro.3118] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/22/2022]
Abstract
Globular proteins composed of different secondary structures and fold types were examined by synchrotron radiation circular dichroism spectroscopy to determine the effects of dehydration on their secondary structures. They exhibited only minor changes upon removal of bulk water during film formation, contrary to previously reported studies of proteins dehydrated by lyophilization (where substantial loss of helical structure and gain in sheet structure was detected). This near lack of conformational change observed for globular proteins contrasts with intrinsically disordered proteins (IDPs) dried in the same manner: the IDPs, which have almost completely unordered structures in solution, exhibited increased amounts of regular (mostly helical) secondary structures when dehydrated, suggesting formation of new intra-protein hydrogen bonds replacing solvent-protein hydrogen bonds, in a process which may mimic interactions that occur when IDPs bind to partner molecules. This study has thus shown that the secondary structures of globular and intrinsically disordered proteins behave very differently upon dehydration, and that films are a potentially useful format for examining dehydrated soluble proteins and assessing IDPs structures.
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Affiliation(s)
- Juliana Sakamoto Yoneda
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.,Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Andew J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | | | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
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49
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Abstract
Although person-fit analysis has a long-standing tradition within item response theory, it has been applied in combination with dominance response models almost exclusively. In this article, a popular log likelihood-based parametric person-fit statistic under the framework of the generalized graded unfolding model is used. Results from a simulation study indicate that the person-fit statistic performed relatively well in detecting midpoint response style patterns and not so well in detecting extreme response style patterns.
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50
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Abstract
Judging goodness of fit in multidimensional scaling requires a comprehensive set of diagnostic tools instead of relying on stress rules of thumb. This article elaborates on corresponding strategies and gives practical guidelines for researchers to obtain a clear picture of the goodness of fit of a solution. Special emphasis will be placed on the use of permutation tests. The second part of the article focuses on goodness-of-fit assessment of an important variant of multidimensional scaling called unfolding, which can be applied to a broad range of psychological data settings. Two real-life data sets are presented in order to walk the reader through the entire set of diagnostic measures, tests, and plots. R code is provided as supplementary information that makes the whole goodness-of-fit assessment workflow, as presented in this article, fully reproducible.
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