1
|
Zheng L, Lu H, Zan B, Li S, Liu H, Liu Z, Huang J, Liu Y, Jiang F, Liu Q, Feng Y, Hong L. Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity. Nucleic Acids Res 2022; 50:7529-7544. [PMID: 35766425 PMCID: PMC9303296 DOI: 10.1093/nar/gkac565] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) widely participate in hosts to defend against the invasion of nucleic acids. Compared with the CRISPR-Cas system, which requires a specific motif on the target and can only use RNA as guide, pAgos exhibit precise endonuclease activity on any arbitrary target sequence and can use both RNA and DNA as guide, thus rendering great potential for genome editing applications. Hitherto, most in-depth studies on the structure-function relationship of pAgos were conducted on thermophilic ones, functioning at ∼60 to 100°C, whose structures were, however, determined experimentally at much lower temperatures (20-33°C). It remains unclear whether these low-temperature structures can represent the true conformations of the thermophilic pAgos under their physiological conditions. The present work studied three pAgos, PfAgo, TtAgo and CbAgo, whose physiological temperatures differ significantly (95, 75 and 37°C). By conducting thorough experimental and simulation studies, we found that thermophilic pAgos (PfAgo and TtAgo) adopt a loosely-packed structure with a partially-melted surface at the physiological temperatures, largely different from the compact crystalline structures determined at moderate temperatures. In contrast, the mesophilic pAgo (CbAgo) assumes a compact crystalline structure at its optimal function temperature. Such a partially-disrupted structure endows thermophilic pAgos with great flexibility both globally and locally at the catalytic sites, which is crucial for them to achieve high DNA-cleavage activity. To further prove this, we incubated thermophilic pAgos with urea to purposely disrupt their structures, and the resulting cleavage activity was significantly enhanced below the physiological temperature, even at human body temperature. Further testing of many thermophilic Agos present in various thermophilic prokaryotes demonstrated that their structures are generally disrupted under physiological conditions. Therefore, our findings suggest that the highly dynamical structure with a partially-melted surface, distinct from the low-temperature crystalline structure, could be a general strategy assumed by thermophilic pAgos to achieve the high DNA-cleavage activity.
Collapse
Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Lu
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongjia Liu
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Liu
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
2
|
Zovo K, Pupart H, Van Wieren A, Gillilan RE, Huang Q, Majumdar S, Lukk T. Substitution of the Methionine Axial Ligand of the T1 Copper for the Fungal-like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations that Lead to Thermal Instability and Reduced Catalytic Efficiency of the Small Laccase from Streptomyces coelicolor A3(2). ACS OMEGA 2022; 7:6184-6194. [PMID: 35224382 PMCID: PMC8867573 DOI: 10.1021/acsomega.1c06668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Many industrial processes operate at elevated temperatures or within broad pH and salinity ranges. However, the utilization of enzymes to carry out biocatalysis in such processes is often impractical or even impossible. Laccases (EC 1.10.3.2), which constitute a large family of multicopper oxidases, have long been used in the industrial setting. Although fungal laccases are in many respects considered superior to their bacterial counterparts, the bacterial laccases have been receiving greater attention recently. Albeit lower in redox potential than fungal laccases, bacterial laccases are commonly thermally more stable, act within broader pH ranges, do not contain posttranslational modifications, and could therefore serve as a high potential scaffold for directed evolution for the production of enzymes with enhanced properties. Several examples focusing on the axial ligand mutations of the T1 copper site have been published in the past. However, structural evidence on the local and global changes induced by those mutations have thus far been of computational nature only. In this study, we set out to structurally and kinetically characterize a few of the most commonly reported axial ligand mutations of a bacterial small laccase (SLAC) from Streptomyces coelicolor. While one of the mutations (Met to Leu) equips the enzyme with better thermal stability, the other (Met to Phe) induces an opposite effect. These mutations cause local structural rearrangement of the T1 site as demonstrated by X-ray crystallography. Our analysis confirms past findings that for SLACs, single point mutations that change the identity of the axial ligand of the T1 copper are not enough to provide a substantial increase in the catalytic efficiency but can in some cases have a detrimental effect on the enzyme's thermal stability parameters instead.
Collapse
Affiliation(s)
- Kairit Zovo
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Hegne Pupart
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Arie Van Wieren
- Department
of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, United States
| | - Richard E. Gillilan
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United
States
| | - Qingqiu Huang
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United
States
| | - Sudipta Majumdar
- Department
of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, United States
| | - Tiit Lukk
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| |
Collapse
|
3
|
Schroer MA, Schewa S, Gruzinov AY, Rönnau C, Lahey-Rudolph JM, Blanchet CE, Zickmantel T, Song YH, Svergun DI, Roessle M. Probing the existence of non-thermal Terahertz radiation induced changes of the protein solution structure. Sci Rep 2021; 11:22311. [PMID: 34785744 PMCID: PMC8595702 DOI: 10.1038/s41598-021-01774-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/26/2021] [Indexed: 01/14/2023] Open
Abstract
During the last decades discussions were taking place on the existence of global, non-thermal structural changes in biological macromolecules induced by Terahertz (THz) radiation. Despite numerous studies, a clear experimental proof of this effect for biological particles in solution is still missing. We developed a setup combining THz-irradiation with small angle X-ray scattering (SAXS), which is a sensitive method for detecting the expected structural changes. We investigated in detail protein systems with different shape morphologies (bovine serum albumin, microtubules), which have been proposed to be susceptible to THz-radiation, under variable parameters (THz wavelength, THz power densities up to 6.8 mW/cm2, protein concentrations). None of the studied systems and conditions revealed structural changes detectable by SAXS suggesting that the expected non-thermal THz-induced effects do not lead to alterations of the overall structures, which are revealed by scattering from dissolved macromolecules. This leaves us with the conclusion that, if such effects are present, these are either local or outside of the spectrum and power range covered by the present study.
Collapse
Affiliation(s)
- Martin A. Schroer
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany ,grid.5718.b0000 0001 2187 5445Present Address: Nanoparticle Process Technology, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
| | - Siawosch Schewa
- University of Applied Sciences Luebeck, Moenkhofer Weg 239, 23562 Luebeck, Germany
| | - Andrey Yu. Gruzinov
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Rönnau
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | | | - Clement E. Blanchet
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Till Zickmantel
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Young-Hwa Song
- grid.4562.50000 0001 0057 2672Institute of Physics, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Dmitri I. Svergun
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory (EMBL), Hamburg Outstation C/O DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Manfred Roessle
- University of Applied Sciences Luebeck, Moenkhofer Weg 239, 23562 Luebeck, Germany
| |
Collapse
|
4
|
Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
Collapse
Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
5
|
Levengood JD, Peterson J, Tolbert BS, Roche J. Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 2021; 89:781-791. [PMID: 33550645 DOI: 10.1002/prot.26058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/21/2020] [Accepted: 01/31/2021] [Indexed: 11/09/2022]
Abstract
We have investigated the pressure- and temperature-induced conformational changes associated with the low complexity domain of hnRNP A1, an RNA-binding protein able to phase separate in response to cellular stress. Solution NMR spectra of the hnRNP A1 low-complexity domain fused with protein-G B1 domain were collected from 1 to 2500 bar and from 268 to 290 K. While the GB1 domain shows the typical pressure-induced and cold temperature-induced unfolding expected for small globular domains, the low-complexity domain of hnRNP A1 exhibits unusual pressure and temperature dependences. We observed that the low-complexity domain is pressure sensitive, undergoing a major conformational transition within the prescribed pressure range. Remarkably, this transition has the inverse temperature dependence of a typical folding-unfolding transition. Our results suggest the presence of a low-lying extended and fully solvated state(s) of the low-complexity domain that may play a role in phase separation. This study highlights the exquisite sensitivity of solution NMR spectroscopy to observe subtle conformational changes and illustrates how pressure perturbation can be used to determine the properties of metastable conformational ensembles.
Collapse
Affiliation(s)
- Jeffrey D Levengood
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jake Peterson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| |
Collapse
|
6
|
Cohen NR, Kayatekin C, Zitzewitz JA, Bilsel O, Matthews CR. Friction-Limited Folding of Disulfide-Reduced Monomeric SOD1. Biophys J 2020; 118:1992-2000. [PMID: 32191862 DOI: 10.1016/j.bpj.2020.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/04/2020] [Accepted: 02/28/2020] [Indexed: 11/16/2022] Open
Abstract
The folding reaction of a stable monomeric variant of Cu/Zn superoxide dismutase (mSOD1), an enzyme responsible for the conversion of superoxide free radicals into hydrogen peroxide and oxygen, is known to be among the slowest folding processes that adhere to two-state behavior. The long lifetime, ∼10 s, of the unfolded state presents ample opportunities for the polypeptide chain to transiently sample nonnative structures before the formation of the productive folding transition state. We recently observed the formation of a nonnative structure in a peptide model of the C-terminus of SOD1, a sequence that might serve as a potential source of internal chain friction-limited folding. To test for friction-limited folding, we performed a comprehensive thermodynamic and kinetic analysis of the folding mechanism of mSOD1 in the presence of the viscogens glycerol and glucose. Using a, to our knowledge, novel analysis of the folding reactions, we found the disulfide-reduced form of the protein that exposes the C-terminal sequence, but not its disulfide-oxidized counterpart that protects it, experiences internal chain friction during folding. The sensitivity of the internal friction to the disulfide bond status suggests that one or both of the cross-linked regions play a critical role in driving the friction-limited folding. We speculate that the molecular mechanisms giving rise to the internal friction of disulfide-reduced mSOD1 might play a role in the amyotrophic lateral sclerosis-linked aggregation of SOD1.
Collapse
Affiliation(s)
- Noah R Cohen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Can Kayatekin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts; Rare and Neurological Therapeutic Area, Sanofi, Framingham, Massachusetts
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - C R Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
| |
Collapse
|
7
|
Coroaba A, Chiriac AE, Sacarescu L, Pinteala T, Minea B, Ibanescu SA, Pertea M, Moraru A, Esanu I, Maier SS, Chiriac A, Pinteala M. New insights into human hair: SAXS, SEM, TEM and EDX for Alopecia Areata investigations. PeerJ 2020; 8:e8376. [PMID: 31976181 PMCID: PMC6968496 DOI: 10.7717/peerj.8376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Background Alopecia areata (AA) is a T-cell-mediated autoimmune disease and affects up to 2% of the population. There is a need for a more profound and rigorous understanding of the structure and composition of human hair affected by AA in order to manage this disease. The aim of this article is to understand the effects of AA on the structure and composition of human hair. Methods Several physico-chemical investigation methods, such as Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Energy-Dispersive X-ray Spectroscopy (EDX), and microbeam Small Angle X-ray Scattering (SAXS), were used to analyze human hair samples obtained from healthy donors and patients with AA. Results SEM revealed more severe hair surface defects for the white regrown hair (W-AA) samples. TEM showed the presence of air-like vesicles located in the endocuticle of regrown hair. Analysis of ultrathin sections of W-AA showed the existence of empty vesicles and smaller melanin granules compared to control samples. SAXS demonstrated that unaffected hair of patients with AA (B-AA) and W-AA melanin aggregates are different in their sizes and shapes compared to the control samples. EDX data showed that W-AA elemental composition was significantly different from the other sample groups. Our study showcases promising non-invasive techniques for a better and more accurate understanding of changes in the internal structure and composition of hair affected by AA.
Collapse
Affiliation(s)
- Adina Coroaba
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Iasi, Romania
| | - Anca E Chiriac
- Department of Epidemiology, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Iasi, Romania
| | - Liviu Sacarescu
- Department of Inorganic Polymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Iasi, Romania
| | - Tudor Pinteala
- Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Iasi, Romania
| | - Bogdan Minea
- Department of Surgery, Faculty of Dental Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Iasi, Romania
| | - Sorin-Alexandru Ibanescu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Iasi, Romania
| | - Mihaela Pertea
- Department of Surgery I, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Iasi, Romania.,Clinic of Plastic and Reconstructive Microsurgery, "Sf. Spiridon" Emergency Hospital, Iasi, Iasi, Romania
| | - Aurelian Moraru
- Romanian Academy, Bucharest, Bucharest, Romania.,"Dr. Iacob Czihac" Military Emergency Clinical Hospital, Iasi, Iasi, Romania
| | - Irina Esanu
- Department of Internal Medicine I, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Iasi, Romania
| | - Stelian S Maier
- Faculty of Textiles, Leather and Industrial Management, "Gheorghe Asachi" Technical University of Iasi, Iasi, Iasi, Romania
| | - Anca Chiriac
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Iasi, Romania.,Department of Dermatophysiology, "Apollonia" University, Iasi, Iasi, Romania.,Department of Dermatology, Nicolina Medical Center, Iasi, Iasi, Romania
| | - Mariana Pinteala
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Iasi, Romania
| |
Collapse
|
8
|
Sung HL, Nesbitt DJ. DNA Hairpin Hybridization under Extreme Pressures: A Single-Molecule FRET Study. J Phys Chem B 2019; 124:110-120. [PMID: 31840514 DOI: 10.1021/acs.jpcb.9b10131] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Organisms have evolved to live in a variety of complex environments, which clearly has required cellular biology to accommodate to extreme conditions of hydraulic pressure and elevated temperature. In this work, we exploit single-molecule Forster resonance energy transfer (FRET) spectroscopy to probe structural changes in DNA hairpins as a function of pressure and temperature, which allows us to extract detailed thermodynamic information on changes in free energy (ΔG°), free volume (ΔV°), enthalpy (ΔH°), and entropy (ΔS°) associated with DNA loop formation and sequence-dependent stem hybridization. Specifically, time-correlated single-photon counting experiments on freely diffusing 40A DNA hairpin FRET constructs are performed in a 50 μm × 50 μm square quartz capillary cell pressurized from ambient pressure up to 3 kbar. By pressure-dependent van't Hoff analysis of the equilibrium constants, ΔV° for hybridization of the DNA hairpin can be determined as a function of stem length (nstem = 7-10) with single base-pair resolution, which further motivates a simple linear deconstruction into additive stem (ΔV°stem = ΔV°bp x nstem) and loop (ΔV°loop) contributions. We find that increasing pressure destabilizes the DNA hairpin stem region [ΔV°bp = +1.98(16) cm3/(mol bp)], with additional positive free volume changes [ΔV°loop = +7.0(14) cm3/mol] we ascribe to bending and base stacking disruption of the 40-dA loop. From a van't Hoff temperature-dependent analysis of the DNA 40A hairpin equilibria, the data support a similar additive loop/stem deconstruction of enthalpic (ΔH° = ΔH°loop + ΔH°stem) and entropic (ΔS° = ΔS°loop + ΔS°stem) contributions, which permits insightful comparison with predictions from nearest-neighbor thermodynamic models for DNA duplex formation. In particular, the stem thermodynamics is consistent with exothermically favored (ΔH°stem < 0) and entropically penalized (ΔS°stem < 0) hydrogen bonding but with additional enthalpic (ΔH°loop > 0) and entropic (ΔS°loop > 0) contributions due to loop bending effects consistent with distortion of dA base stacking in the 40-dA linker.
Collapse
Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| |
Collapse
|
9
|
Oprzeska-Zingrebe EA, Smiatek J. Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior? J Phys Chem B 2019; 123:4415-4424. [PMID: 31046272 DOI: 10.1021/acs.jpcb.9b02598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.
Collapse
Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics , University of Stuttgart , D-70569 Stuttgart , Germany.,Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12) , Forschungszentrum Jülich GmbH , D-48149 Münster , Germany
| |
Collapse
|
10
|
Roche J, Royer CA. Lessons from pressure denaturation of proteins. J R Soc Interface 2018; 15:rsif.2018.0244. [PMID: 30282759 DOI: 10.1098/rsif.2018.0244] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022] Open
Abstract
Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.
Collapse
Affiliation(s)
- Julien Roche
- Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| |
Collapse
|
11
|
Lehofer B, Golub M, Kornmueller K, Kriechbaum M, Martinez N, Nagy G, Kohlbrecher J, Amenitsch H, Peters J, Prassl R. High Hydrostatic Pressure Induces a Lipid Phase Transition and Molecular Rearrangements in Low-Density Lipoprotein Nanoparticles. PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION : MEASUREMENT AND DESCRIPTION OF PARTICLE PROPERTIES AND BEHAVIOR IN POWDERS AND OTHER DISPERSE SYSTEMS 2018; 35:1800149. [PMID: 30283212 PMCID: PMC6166783 DOI: 10.1002/ppsc.201800149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Low-density lipoproteins (LDL) are natural lipid transporter in human plasma whose chemically modified forms contribute to the progression of atherosclerosis and cardiovascular diseases accounting for a vast majority of deaths in westernized civilizations. For the development of new treatment strategies, it is important to have a detailed picture of LDL nanoparticles on a molecular basis. Through the combination of X-ray and neutron small-angle scattering (SAS) techniques with high hydrostatic pressure (HHP) this study describes structural features of normolipidemic, triglyceride-rich and oxidized forms of LDL. Due to the different scattering contrasts for X-rays and neutrons, information on the effects of HHP on the internal structure determined by lipid rearrangements and changes in particle shape becomes accessible. Independent pressure and temperature variations provoke a phase transition in the lipid core domain. With increasing pressure an inter-related anisotropic deformation and flattening of the particle are induced. All LDL nanoparticles maintain their structural integrity even at 3000 bar and show a reversible response toward pressure variations. The present work depicts the complementarity of pressure and temperature as independent thermodynamic parameters and introduces HHP as a tool to study molecular assembling and interaction processes in distinct lipoprotein particles in a nondestructive manner.
Collapse
Affiliation(s)
- Bernhard Lehofer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/IV, 8010 Graz, Austria
| | - Maksym Golub
- Institut Laue-Langevin, 71 avenue des Martyrs, 38044 Grenoble, France; Univ. Grenoble Alpes, CNRS + CEA, IBS, 38000 Grenoble, France
| | - Karin Kornmueller
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/IV, 8010 Graz, Austria
| | - Manfred Kriechbaum
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Nicolas Martinez
- Institut Laue-Langevin, 71 avenue des Martyrs, 38044 Grenoble, France; Univ. Grenoble Alpes, CNRS + CEA, IBS, 38000 Grenoble, France
| | - Gergely Nagy
- Paul Scherrer Institut, 5232 Villigen, Switzerland; Wigner Research Centre for Physics, 1121 Budapest, Hungary; European Spallation Source ERIC, 22363 Lund, Sweden
| | | | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Judith Peters
- Institut Laue-Langevin, 71 avenue des Martyrs, 38044 Grenoble, France; Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
| | - Ruth Prassl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging Biophysics, Medical University of Graz, Neue Stiftingtalstraße 6/IV, 8010 Graz, Austria
| |
Collapse
|
12
|
Cinar H, Cinar S, Chan HS, Winter R. Pressure-Induced Dissolution and Reentrant Formation of Condensed, Liquid-Liquid Phase-Separated Elastomeric α-Elastin. Chemistry 2018; 24:8286-8291. [PMID: 29738068 DOI: 10.1002/chem.201801643] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/07/2018] [Indexed: 02/05/2023]
Abstract
We investigated the combined effects of temperature and pressure on liquid-liquid phase separation (LLPS) phenomena of α-elastin up to the multi-kbar regime. FT-IR spectroscopy, CD, UV/Vis absorption, phase-contrast light and fluorescence microscopy techniques were employed to reveal structural changes and mesoscopic phase states of the system. A novel pressure-induced reentrant LLPS was observed in the intermediate temperature range. A molecular-level picture, in particular on the role of hydrophobic interactions, hydration, and void volume in controlling LLPS phenomena is presented. The potential role of the LLPS phenomena in the development of early cellular compartmentalization is discussed, which might have started in the deep sea, where pressures up to the kbar level are encountered.
Collapse
Affiliation(s)
- Hasan Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Süleyman Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| |
Collapse
|
13
|
Recent developments in small-angle X-ray scattering and hybrid method approaches for biomacromolecular solutions. Emerg Top Life Sci 2018; 2:69-79. [PMID: 33525782 DOI: 10.1042/etls20170138] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 01/05/2023]
Abstract
Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.
Collapse
|
14
|
Schneider S, Paulsen H, Reiter KC, Hinze E, Schiene-Fischer C, Hübner CG. Single molecule FRET investigation of pressure-driven unfolding of cold shock protein A. J Chem Phys 2018; 148:123336. [DOI: 10.1063/1.5009662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sven Schneider
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Hauke Paulsen
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Kim Colin Reiter
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Erik Hinze
- Max Planck Research Unit for Enzymology of Protein Folding Halle, Halle/Saale D-06120, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale D-06120, Germany
| | | |
Collapse
|
15
|
Roche J, Royer CA, Roumestand C. Monitoring protein folding through high pressure NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:15-31. [PMID: 29157491 DOI: 10.1016/j.pnmrs.2017.05.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding.
Collapse
Affiliation(s)
- Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christian Roumestand
- Centre de Biochimie Structural INSERM U1054, CNRS UMMR 5058, Université de Montpellier, Montpellier 34090, France.
| |
Collapse
|
16
|
Pica A, Graziano G. Hydrostatic pressure effect on PNIPAM cononsolvency in water-methanol solutions. Biophys Chem 2017; 231:34-38. [PMID: 28081859 DOI: 10.1016/j.bpc.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 12/31/2016] [Accepted: 01/02/2017] [Indexed: 10/20/2022]
Abstract
When methanol is added to water at room temperature and 1atm, poly (N-isopropylacrylamide), PNIPAM, undergoes a coil-to-globule collapse transition. This intriguing phenomenon is called cononsolvency. Spectroscopic measurements have shown that application of high hydrostatic pressure destroys PNIPAM cononsolvency in water-methanol solutions. We have developed a theoretical approach that identifies the decrease in solvent-excluded volume effect as the driving force of PNIPAM collapse on increasing the temperature. The same approach indicates that cononsolvency, at room temperature and P=1atm, is caused by the inability of PNIPAM to make all the attractive energetic interactions that it could be engaged in, due to competition between water and methanol molecules. The present analysis suggests that high hydrostatic pressure destroys cononsolvency because the coil state becomes more compact, and the quantity measuring PNIPAM-solvent attractions increases in magnitude due to the solution density increase, and the ability of small water molecules to substitute methanol molecules on PNIPAM surface.
Collapse
Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126 Napoli, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.
| |
Collapse
|
17
|
Son I, Chalikian TV. Volumetrically Derived Thermodynamic Profile of Interactions of Urea with a Native Protein. Biochemistry 2016; 55:6475-6483. [PMID: 27933780 DOI: 10.1021/acs.biochem.6b00805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ikbae Son
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| |
Collapse
|
18
|
Schroer MA, Westermeier F, Lehmkühler F, Conrad H, Schavkan A, Zozulya AV, Fischer B, Roseker W, Sprung M, Gutt C, Grübel G. Colloidal crystallite suspensions studied by high pressure small angle x-ray scattering. J Chem Phys 2016; 144:084903. [PMID: 26931722 DOI: 10.1063/1.4941563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on high pressure small angle x-ray scattering on suspensions of colloidal crystallites in water. The crystallites made out of charge-stabilized poly-acrylate particles exhibit a complex pressure dependence which is based on the specific pressure properties of the suspending medium water. The dominant effect is a compression of the crystallites caused by the compression of the water. In addition, we find indications that also the electrostatic properties of the system, i.e. the particle charge and the dissociation of ions, might play a role for the pressure dependence of the samples. The data further suggest that crystallites in a metastable state induced by shear-induced melting can relax to a similar structural state upon the application of pressure and dilution with water. X-ray cross correlation analysis of the two-dimensional scattering patterns indicates a pressure-dependent increase of the orientational order of the crystallites correlated with growth of these in the suspension. This study underlines the potential of pressure as a very relevant parameter to understand colloidal crystallite systems in aqueous suspension.
Collapse
Affiliation(s)
- M A Schroer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - F Westermeier
- Max-Planck-Institut für Struktur und Dynamik der Materie, CFEL, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - F Lehmkühler
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - H Conrad
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A Schavkan
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A V Zozulya
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - B Fischer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - W Roseker
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - M Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - C Gutt
- Department of Physics, University of Siegen, Walter-Flex-Str. 3, 57072 Siegen, Germany
| | - G Grübel
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| |
Collapse
|
19
|
Micciulla S, Michalowsky J, Schroer MA, Holm C, von Klitzing R, Smiatek J. Concentration dependent effects of urea binding to poly(N-isopropylacrylamide) brushes: a combined experimental and numerical study. Phys Chem Chem Phys 2016; 18:5324-35. [DOI: 10.1039/c5cp07544k] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The concentration-dependent binding of urea to PNIPAM influences the chain conformation as a result of the subtle interplay between hydration properties and urea repartition around the polymer surface.
Collapse
Affiliation(s)
- Samantha Micciulla
- Stranski-Laboratorium
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Julian Michalowsky
- Institut für Computerphysik
- Universität Stuttgart
- D-70569 Stuttgart
- Germany
| | - Martin A. Schroer
- Deutsches Elektronen-Synchrotron DESY
- D-22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging (CUI)
- D-22761 Hamburg
| | - Christian Holm
- Institut für Computerphysik
- Universität Stuttgart
- D-70569 Stuttgart
- Germany
| | - Regine von Klitzing
- Stranski-Laboratorium
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Jens Smiatek
- Institut für Computerphysik
- Universität Stuttgart
- D-70569 Stuttgart
- Germany
| |
Collapse
|
20
|
Schroer MA, Michalowsky J, Fischer B, Smiatek J, Grübel G. Stabilizing effect of TMAO on globular PNIPAM states: preferential attraction induces preferential hydration. Phys Chem Chem Phys 2016; 18:31459-31470. [DOI: 10.1039/c6cp05991k] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We study the effect of the organic co-solute trimethylamine N-oxide (TMAO) on the volume phase transition of microgel particles made from poly(N-isopropylacrylamide) (PNIPAM) using dynamic light scattering (DLS) and all-atom molecular dynamics (MD) simulations.
Collapse
Affiliation(s)
- Martin A. Schroer
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging (CUI)
- 22761 Hamburg
| | | | - Birgit Fischer
- Institut für Physikalische Chemie
- Universität Hamburg
- 20146 Hamburg
- Germany
| | - Jens Smiatek
- Institut für Computerphysik
- Universität Stuttgart
- 70569 Stuttgart
- Germany
| | - Gerhard Grübel
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging (CUI)
- 22761 Hamburg
| |
Collapse
|
21
|
On the effect of hydrostatic pressure on the conformational stability of globular proteins. Biopolymers 2015; 103:711-8. [DOI: 10.1002/bip.22736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/20/2015] [Accepted: 08/17/2015] [Indexed: 11/07/2022]
|
22
|
A hypothesis to reconcile the physical and chemical unfolding of proteins. Proc Natl Acad Sci U S A 2015; 112:E2775-84. [PMID: 25964355 DOI: 10.1073/pnas.1500352112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
High pressure (HP) or urea is commonly used to disturb folding species. Pressure favors the reversible unfolding of proteins by causing changes in the volumetric properties of the protein-solvent system. However, no mechanistic model has fully elucidated the effects of urea on structure unfolding, even though protein-urea interactions are considered to be crucial. Here, we provide NMR spectroscopy and 3D reconstructions from X-ray scattering to develop the "push-and-pull" hypothesis, which helps to explain the initial mechanism of chemical unfolding in light of the physical events triggered by HP. In studying MpNep2 from Moniliophthora perniciosa, we tracked two cooperative units using HP-NMR as MpNep2 moved uphill in the energy landscape; this process contrasts with the overall structural unfolding that occurs upon reaching a threshold concentration of urea. At subdenaturing concentrations of urea, we were able to trap a state in which urea is preferentially bound to the protein (as determined by NMR intensities and chemical shifts); this state is still folded and not additionally exposed to solvent [fluorescence and small-angle X-ray scattering (SAXS)]. This state has a higher susceptibility to pressure denaturation (lower p1/2 and larger ΔVu); thus, urea and HP share concomitant effects of urea binding and pulling and water-inducing pushing, respectively. These observations explain the differences between the molecular mechanisms that control the physical and chemical unfolding of proteins, thus opening up new possibilities for the study of protein folding and providing an interpretation of the nature of cooperativity in the folding and unfolding processes.
Collapse
|
23
|
Bras W, Koizumi S, Terrill NJ. Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments. IUCRJ 2014; 1:478-91. [PMID: 25485128 PMCID: PMC4224466 DOI: 10.1107/s2052252514019198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 08/25/2014] [Indexed: 05/20/2023]
Abstract
Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.
Collapse
Affiliation(s)
- Wim Bras
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP 220, 6 Rue Jules Horowitz, Grenoble 38043, France
| | - Satoshi Koizumi
- College of Engineering, Ibaraki University, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Nicholas J Terrill
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| |
Collapse
|
24
|
Mori Y, Okumura H. Molecular dynamics of the structural changes of helical peptides induced by pressure. Proteins 2014; 82:2970-81. [DOI: 10.1002/prot.24654] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/24/2014] [Accepted: 07/15/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Yoshiharu Mori
- Department of Theoretical and Computational Molecular Science; Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
| | - Hisashi Okumura
- Department of Theoretical and Computational Molecular Science; Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
- Research Center for Computational Science; Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
- Department of Structural Molecular Science; The Graduate University for Advanced Studies; Okazaki Aichi 444-8585 Japan
| |
Collapse
|
25
|
Dias CL, Chan HS. Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J Phys Chem B 2014; 118:7488-7509. [DOI: 10.1021/jp501935f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cristiano L. Dias
- Department
of Physics, New Jersey Institute of Technology, University Heights, Tiernan Hall, Room 463, Newark, New Jersey 07102, United States
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| | - Hue Sun Chan
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| |
Collapse
|
26
|
Thermodynamic and functional characteristics of deep-sea enzymes revealed by pressure effects. Extremophiles 2014; 17:701-9. [PMID: 23798033 DOI: 10.1007/s00792-013-0556-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/13/2013] [Indexed: 01/14/2023]
Abstract
Hydrostatic pressure analysis is an ideal approach for studying protein dynamics and hydration. The development of full ocean depth submersibles and high pressure biological techniques allows us to investigate enzymes from deep-sea organisms at the molecular level. The aim of this review was to overview the thermodynamic and functional characteristics of deep-sea enzymes as revealed by pressure axis analysis after giving a brief introduction to the thermodynamic principles underlying the effects of pressure on the structural stability and function of enzymes.
Collapse
|
27
|
Somkuti J, Smeller L. High pressure effects on allergen food proteins. Biophys Chem 2013; 183:19-29. [DOI: 10.1016/j.bpc.2013.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
|
28
|
Graewert MA, Svergun DI. Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). Curr Opin Struct Biol 2013; 23:748-54. [PMID: 23835228 DOI: 10.1016/j.sbi.2013.06.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
The advances made in small and wide angle X-ray scattering over the past decades have had a large impact on structural biology. Many new insights into challenging biological probes including large and transient complexes, flexible macromolecules as well as other exciting objects of various sizes were gained with this low resolution technique. Here, we review the recent developments in the experimental setups and in software for data collection and analysis, specifically for hybrid approaches. These progresses have allowed scientists to address a number of intriguing questions which could not be answered with other structural methods alone.
Collapse
Affiliation(s)
- Melissa A Graewert
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestraße 85, Hamburg 22603, Germany
| | | |
Collapse
|
29
|
Milanesi L, Waltho JP, Hunter CA, Shaw DJ, Beddard GS, Reid GD, Dev S, Volk M. Measurement of energy landscape roughness of folded and unfolded proteins. Proc Natl Acad Sci U S A 2012; 109:19563-8. [PMID: 23150572 PMCID: PMC3511724 DOI: 10.1073/pnas.1211764109] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k(B)T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 k(B)T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues.
Collapse
Affiliation(s)
- Lilia Milanesi
- Departments of Molecular Biology and Biotechnology and
- Chemistry, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jonathan P. Waltho
- Departments of Molecular Biology and Biotechnology and
- Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom
| | | | - Daniel J. Shaw
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Godfrey S. Beddard
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Gavin D. Reid
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Sagarika Dev
- Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Martin Volk
- Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| |
Collapse
|
30
|
Sarma R, Paul S. Effect of trimethylamine-N-oxide on pressure-induced dissolution of hydrophobic solute. J Chem Phys 2012; 137:114503. [DOI: 10.1063/1.4752104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
31
|
Somkuti J, Bublin M, Breiteneder H, Smeller L. Pressure–Temperature Stability, Ca2+ Binding, and Pressure–Temperature Phase Diagram of Cod Parvalbumin: Gad m 1. Biochemistry 2012; 51:5903-11. [DOI: 10.1021/bi300403h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Judit Somkuti
- Department of Biophysics and
Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Merima Bublin
- Department
of Pathophysiology
and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Heimo Breiteneder
- Department
of Pathophysiology
and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - László Smeller
- Department of Biophysics and
Radiation Biology, Semmelweis University, Budapest, Hungary
| |
Collapse
|
32
|
Revealing conformational substates of lipidated N-Ras protein by pressure modulation. Proc Natl Acad Sci U S A 2011; 109:460-5. [PMID: 22203965 DOI: 10.1073/pnas.1110553109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulation of protein function is often linked to a conformational switch triggered by chemical or physical signals. To evaluate such conformational changes and to elucidate the underlying molecular mechanisms of subsequent protein function, experimental identification of conformational substates and characterization of conformational equilibria are mandatory. We apply pressure modulation in combination with FTIR spectroscopy to reveal equilibria between spectroscopically resolved substates of the lipidated signaling protein N-Ras. Pressure has the advantage that its thermodynamic conjugate is volume, a parameter that is directly related to structure. The conformational dynamics of N-Ras in its different nucleotide binding states in the absence and presence of a model biomembrane was probed by pressure perturbation. We show that not only nucleotide binding but also the presence of the membrane has a drastic effect on the conformational dynamics and selection of conformational substates of the protein, and a new substate appearing upon membrane binding could be uncovered. Population of this new substate is accompanied by structural reorientations of the G domain, as also indicated by complementary ATR-FTIR and IRRAS measurements. These findings thus illustrate that the membrane controls signaling conformations by acting as an effective interaction partner, which has consequences for the G-domain orientation of membrane-associated N-Ras, which in turn is known to be critical for its effector and modulator interactions. Finally, these results provide insights into the influence of pressure on Ras-controlled signaling events in organisms living under extreme environmental conditions as they are encountered in the deep sea where pressures reach the kbar range.
Collapse
|
33
|
|
34
|
Hédoux A, Guinet Y, Paccou L. Analysis of the mechanism of lysozyme pressure denaturation from Raman spectroscopy investigations, and comparison with thermal denaturation. J Phys Chem B 2011; 115:6740-8. [PMID: 21542584 DOI: 10.1021/jp2014836] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pressure denaturation of lysozyme dissolved in H(2)O and D(2)O was analyzed using Raman investigations in a wide frequency range. The simultaneous analysis of regions corresponding to the molecular fingerprint of the protein (500-1800 cm(-1)), and the low- (50-450 cm(-1)) and high- (2600-3800 cm(-1)) frequency spectra, allow us to probe protein denaturation and the organization of water molecules. The pressure- and heat-induced transformations are compared. Both pressure- and heat-denatured states are obtained through an intermediate state characterized by intact secondary structure and enhanced water penetration in the tertiary structure. As a consequence of a weaker penetration upon pressurizing, it was found that the pressure-denatured state was partially unfolded compared with the heat-denatured state. The mechanism of pressure denaturation was related to the disruption of the hydrogen-bond network of water onto a set of clusters characterized by strengthened O - H interactions, inducing a hardening of protein dynamics. The mechanism is opposite to that observed upon heating, i.e., the softening of the hydrogen bond network of water inducing a softer protein dynamics. The analysis of the intramolecular O-H stretching reveals that pressurizing lysozyme aqueous solution favors the development of low-density water from the protein surface to the bulk, contrasting to the compression of pure water leading to crystallization of high-density ice-VI.
Collapse
|