51
|
Meyer RM, Berger L, Nerkamp J, Scheler S, Nehring S, Friess W. Identification of monoclonal antibody variants involved in aggregate formation - Part 2: Hydrophobicity variants. Eur J Pharm Biopharm 2021; 160:134-142. [PMID: 33524536 DOI: 10.1016/j.ejpb.2021.01.006] [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: 10/26/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
Monoclonal antibodies (mAbs) are valuable tools both in therapy and in diagnostic. Their tendency to aggregate is a serious concern. Since a mAb drug substance (DS) is composed of different variants, it is important for manufacturers to know the behavior and stability not only of the mAb as a whole, but also of the variants contained in the product. We present a method to separate hydrophobicity variants of a mAb and subsequently analyzed these variants for stability and aggregation propensity. We identified a potentially aggregation prone hydrophilic variant which is interrelated with another previously identified aggregation prone acidic charge variant. Additionally, we assessed the risk posed by the aggregation prone variant to the DS by spiking hydrophobicity variants into DS and did not observe an enhanced aggregation propensity. Thus we present an approach to separate, characterize and analyze the criticality of aggregation prone variants in protein DS which is a step forward to further assure drug safety.
Collapse
Affiliation(s)
- Robina M Meyer
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, University of Munich, Butenandtstr. 5, 81377 Munich, Germany
| | - Lukas Berger
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Joerg Nerkamp
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Stefan Scheler
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Sebastian Nehring
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Wolfgang Friess
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, University of Munich, Butenandtstr. 5, 81377 Munich, Germany.
| |
Collapse
|
52
|
Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alvarado LHA, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, de la Campa MOA, Paredes I, Wheeler B, Rupert A, Sam A, See K, Zapata SS, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33299989 DOI: 10.1101/2020.12.01.406637] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
Collapse
|
53
|
Garajová K, Sedláková D, Berta M, Gazova Z, Sedlák E. Destabilization effect of imidazolium cation-Hofmeister anion salts on cytochrome c. Int J Biol Macromol 2020; 164:3808-3813. [DOI: 10.1016/j.ijbiomac.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 01/15/2023]
|
54
|
Tamoliu Nas K, Galamba N. Protein Denaturation, Zero Entropy Temperature, and the Structure of Water around Hydrophobic and Amphiphilic Solutes. J Phys Chem B 2020; 124:10994-11006. [PMID: 33201713 DOI: 10.1021/acs.jpcb.0c08055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The hydrophobic effect plays a key role in many chemical and biological processes, including protein folding. Nonetheless, a comprehensive picture of the effect of temperature on hydrophobic hydration and protein denaturation remains elusive. Here, we study the effect of temperature on the hydration of model hydrophobic and amphiphilic solutes, through molecular dynamics, aiming at getting insight on the singular behavior of water, concerning the zero-entropy temperature, TS, and entropy convergence, TS*, also observed for some proteins, upon denaturation. We show that, similar to hydrocarbons, polar amphiphilic solutes exhibit a TS, although strongly dependent on solute-water interactions, opposite to hydrocarbons. Further, the temperature dependence of the hydration entropy, normalized by the solvent accessible surface area, is shown to be nearly solute size independent for hydrophobic but not for amphiphilic solutes, for similar reasons. These results are further discussed in the light of information theory (IT) and the structure of water around hydrophobic groups. The latter shows that the tetrahedral enhancement of some water molecules around hydrophobic groups, associated with the reduction of water defects, leads to the strengthening of the weakest hydrogen bonds, relative to bulk water. In addition, a larger tetrahedrality is found in low density water populations, demonstrating that pure water has encoded structural information, similar to that associated with hydrophobic hydration. The reversal of the hydration entropy dependence on the solute size, above TS*, is also analyzed and shown to be associated with a greater loss of water molecules exhibiting enhanced orientational order, in the coordination sphere of large solutes. Finally, the source of the differences between Kauzmann's "hydrocarbon model" on protein denaturation and hydrophobic hydration is discussed, with relatively large amphiphilic hydrocarbons seemingly displaying a more similar behavior to some globular proteins than aliphatic hydrocarbons.
Collapse
Affiliation(s)
- Kazimieras Tamoliu Nas
- Centre of Chemistry and Biochemistry and Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- Centre of Chemistry and Biochemistry and Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| |
Collapse
|
55
|
Ostermeier L, de Oliveira GAP, Dzwolak W, Silva JL, Winter R. Exploring the polymorphism, conformational dynamics and function of amyloidogenic peptides and proteins by temperature and pressure modulation. Biophys Chem 2020; 268:106506. [PMID: 33221697 DOI: 10.1016/j.bpc.2020.106506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/15/2022]
Abstract
Our understanding of amyloid structures and the mechanisms by which disease-associated peptides and proteins self-assemble into these fibrillar aggregates, has advanced considerably in recent years. It is also established that amyloid fibrils are generally polymorphic. The molecular structures of the aggregation intermediates and the causes of molecular and structural polymorphism are less understood, however. Such information is mandatory to explain the pathological diversity of amyloid diseases. What is also clear is that not only protein mutations, but also the physiological milieu, i.e. pH, cosolutes, crowding and surface interactions, have an impact on fibril formation. In this minireview, we focus on the effect of the less explored physical parameters temperature and pressure on the fibrillization propensity of proteins and how these variables can be used to reveal additional mechanistic information about intermediate states of fibril formation and molecular and structural polymorphism. Generally, amyloids are very stable and can resist harsh environmental conditions, such as extreme pH, high temperature and high pressure, and can hence serve as valuable functional amyloid. As an example, we discuss the effect of temperature and pressure on the catalytic activity of peptide amyloid fibrils that exhibit enzymatic activity.
Collapse
Affiliation(s)
- Lena Ostermeier
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 Str., 02-093 Warsaw, Poland.
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| |
Collapse
|
56
|
Zhou L, Wang J, Liu G, Lu Q, Dong R, Tian G, Yang J, Peng L. Probing antiviral drugs against SARS-CoV-2 through virus-drug association prediction based on the KATZ method. Genomics 2020; 112:4427-4434. [PMID: 32745502 PMCID: PMC7832256 DOI: 10.1016/j.ygeno.2020.07.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/04/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022]
Abstract
It is urgent to find an effective antiviral drug against SARS-CoV-2. In this study, 96 virus-drug associations (VDAs) from 12 viruses including SARS-CoV-2 and similar viruses and 78 small molecules are selected. Complete genomic sequence similarity of viruses and chemical structure similarity of drugs are then computed. A KATZ-based VDA prediction method (VDA-KATZ) is developed to infer possible drugs associated with SARS-CoV-2. VDA-KATZ obtained the best AUCs of 0.8803 when the walking length is 2. The predicted top 3 antiviral drugs against SARS-CoV-2 are remdesivir, oseltamivir, and zanamivir. Molecular docking is conducted between the predicted top 10 drugs and the virus spike protein/human ACE2. The results showed that the above 3 chemical agents have higher molecular binding energies with ACE2. For the first time, we found that zidovudine may be effective clues of treatment of COVID-19. We hope that our predicted drugs could help to prevent the spreading of COVID.
Collapse
Affiliation(s)
- Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou 412007, China
| | - Juanjuan Wang
- School of Computer Science, Hunan University of Technology, Zhuzhou 412007, China
| | - Guangyi Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou 412007, China
| | - Qingqing Lu
- Geneis (Beijing) Co. Ltd., Beijing 100102, China
| | - Ruyi Dong
- Geneis (Beijing) Co. Ltd., Beijing 100102, China
| | - Geng Tian
- Geneis (Beijing) Co. Ltd., Beijing 100102, China
| | | | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou 412007, China.
| |
Collapse
|
57
|
|
58
|
Saotome T, Mezaki T, Brindha S, Unzai S, Martinez JC, Kidokoro SI, Kuroda Y. Thermodynamic Analysis of Point Mutations Inhibiting High-Temperature Reversible Oligomerization of PDZ3. Biophys J 2020; 119:1391-1401. [PMID: 32961107 DOI: 10.1016/j.bpj.2020.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022] Open
Abstract
Differential scanning calorimetry (DSC) indicated that PDZ3 undergoes a peculiar thermal denaturation, exhibiting two endothermic peaks because of the formation of reversible oligomers at high temperature (N↔I6↔D). This contrasts sharply with the standard two-state denaturation model observed for small, globular proteins. We performed an alanine scanning analysis by individually mutating three hydrophobic residues at the crystallographic oligomeric interface (Phe340, Leu342, and Ile389) and one away from the interface (Leu349, as a control). DSC analysis indicated that PDZ3-F340A and PDZ3-L342A exhibited a single endothermic peak. Furthermore, PDZ3-L342A underwent a perfect two-state denaturation, as evidenced by the single endothermic peak and confirmed by detailed DSC analysis, including global fitting of data measured at different protein concentrations. Reversible oligomerization (RO) at high temperatures by small globular proteins is a rare event. Furthermore, our present study showing that a point mutation, L342A, designed based on the crystal structure inhibited RO is surprising because RO occurs at a high-temperature. Future studies will determine how and why mutations designed using crystal structures determined at ambient temperatures influence the formation of RO at high temperatures, and whether high-temperature ROs are related to the propensity of proteins to aggregate or precipitate at lower temperatures, which would provide a novel and unique way of controlling protein solubility and aggregation.
Collapse
Affiliation(s)
- Tomonori Saotome
- Department of Biotechnology and Life Science; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Taichi Mezaki
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | | | - Satoru Unzai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan
| | - Jose C Martinez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | | |
Collapse
|
59
|
Stenzoski NE, Zou J, Piserchio A, Ghose R, Holehouse AS, Raleigh DP. The Cold-Unfolded State Is Expanded but Contains Long- and Medium-Range Contacts and Is Poorly Described by Homopolymer Models. Biochemistry 2020; 59:3290-3299. [PMID: 32786415 DOI: 10.1021/acs.biochem.0c00469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cold unfolding of proteins is predicted by the Gibbs-Helmholtz equation and is thought to be driven by a strongly temperature-dependent interaction of protein nonpolar groups with water. Studies of the cold-unfolded state provide insight into protein energetics, partially structured states, and folding cooperativity and are of practical interest in biotechnology. However, structural characterization of the cold-unfolded state is much less extensive than studies of thermally or chemically denatured unfolded states, in large part because the midpoint of the cold unfolding transition is usually below freezing. We exploit a rationally designed point mutation (I98A) in the hydrophobic core of the C-terminal domain of the ribosomal protein L9 that allows the cold denatured state ensemble to be observed above 0 °C at near neutral pH and ambient pressure in the absence of added denaturants. A combined approach consisting of paramagnetic relaxation enhancement measurements, analysis of small-angle X-ray scattering data, all-atom simulations, and polymer theory provides a detailed description of the cold-unfolded state. Despite a globally expanded ensemble, as determined by small-angle X-ray scattering, sequence-specific medium- and long-range interactions in the cold-unfolded state give rise to deviations from homopolymer-like behavior. Our results reveal that the cold-denatured state is heterogeneous with local and long-range intramolecular interactions that may prime the folded state and also demonstrate that significant long-range interactions are compatible with expanded unfolded ensembles. The work also highlights the limitations of homopolymer-based descriptions of unfolded states of proteins.
Collapse
Affiliation(s)
- Natalie E Stenzoski
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States.,Graduate Programs in Biochemistry, Chemistry and Physics, The Graduate Center of CUNY, New York, New York 10016, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.,Center for Science and Engineering of Living Systems, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel P Raleigh
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| |
Collapse
|
60
|
Ashbaugh HS, Bukannan H. Temperature, Pressure, and Concentration Derivatives of Nonpolar Gas Hydration: Impact on the Heat Capacity, Temperature of Maximum Density, and Speed of Sound of Aqueous Mixtures. J Phys Chem B 2020; 124:6924-6942. [PMID: 32692557 DOI: 10.1021/acs.jpcb.0c04035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrophobic effect is an umbrella term encompassing a number of solvation phenomena associated with solutions of nonpolar species in water, including the following: a meager solubility opposed by entropy at room temperature; large positive hydration heat capacities; positive shifts in the temperature of maximum density of aqueous mixtures; increases in the speed of sound of dilute aqueous mixtures; and negative volumes of association between interacting solutes. Here we present a molecular simulation study of nonpolar gas hydration over the temperature range 273.15-373.15 K and a pressure range -500 to 1000 bar to investigate the interrelationships between distinct hydrophobic phenomena. We develop a new free energy correlation for the solute chemical potentials founded on the Tait equation description of the equation-of-state of liquid water. This analytical correlation is shown to provide a quantitatively accurate description of nonpolar gas hydration over the entire range of thermodynamic state points simulated, with an error of ∼0.02 kBT or lower in the fitted chemical potentials. Our simulations and the correlation accurately reproduce many of the available experimental results for the hydration of the solutes examined here. Moreover, the correlation reproduces the characteristic entropies of hydration, temperature dependence of the hydration heat capacity, perturbations in the temperature of maximum density, and changes in the speed of sound. While negative volumes of association result from pairwise interactions in solution, beyond the limits of our simulations performed at infinite dilution, we discuss how our correlation could be supplemented with second virial coefficient information to expand to finite concentrations. In total, this work demonstrates that many distinct phenomena associated with the hydrophobic effect can be captured within a single thermodynamically consistent correlation for solute hydration free energies.
Collapse
Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Hussain Bukannan
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| |
Collapse
|
61
|
Rezaeian Marjani L, Imani M, Zarei Jaliani H. Enhancement of Pharmaceutical Urate Oxidase Thermostability by Rational Design of De Novo Disulfide Bridge. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2662. [PMID: 33850949 PMCID: PMC8035418 DOI: 10.30498/ijb.2020.2662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background and Purpose As a therapeutic enzyme, urate oxidase is utilized in the reduction of uric acid in various conditions such as gout or tumor syndrome lysis. However, even bearing kinetical advantage over other counterparts, it suffers from structural instability most likely due to its subcellular and fungal origin. Objectives In this research, by using rational design and introduction of de novo disulfide bridge in urate oxidase structure, we designed and created a thermostable urate oxidase for the first time. Materials and Methods Utilizing site-directed mutagenesis and only with one point mutation we constructed two separate mutants: Ala6Cys and Ser282Cys which covalently linked subunits of enzyme each other. Single mutation to cysteine created three inter-chain disulfide bridges and one hydrogen bond in Ala6Cys and two disulfide bridges in Ser282Cys. Results Both mutants showed 10 °C increase in optimum activity compared to wild-type enzyme while the Km values for both increased by 50% and their specific activity compromised. The thermal stability of Ser282Cys increased remarkably by comparing Ala6Cys and wild-type enzymes. Estimation of half life for wild-type enzyme demonstrated 38.5 min, while for Ala6Cys and Ser282Cys were 138 and 115 min, respectively. Interestingly, the optimal pH of both mutants was broaden from 7 to 10, which could make them candidates for industrial applications. Conclusion It seemed that introducing disulfide bridges resulted in local and overall rigidity by bringing two adjacent sites of enzyme together and decreasing the conformational entropy of unfolding state is responsible for the enhancement of thermostability.
Collapse
Affiliation(s)
- Leila Rezaeian Marjani
- Department of Cellular and Molecular Biotechnology, Institute of Biotechnology, Urmia University, Urmia, Iran
| | - Mehdi Imani
- Department of Cellular and Molecular Biotechnology, Institute of Biotechnology, Urmia University, Urmia, Iran.,Department of Basic Sciences, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Hossein Zarei Jaliani
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| |
Collapse
|
62
|
Forces maintaining the DNA double helix. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:315-321. [PMID: 32462263 PMCID: PMC7351851 DOI: 10.1007/s00249-020-01437-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/22/2020] [Accepted: 05/10/2020] [Indexed: 10/28/2022]
Abstract
Despite the common acceptance that the enthalpy of DNA duplex unfolding does not depend on temperature and is greater for the CG base pair held by three hydrogen bonds than for the AT base pair held by only two, direct calorimetric measurements have shown that the enthalpic and entropic contributions of both base pairs are temperature dependent and at all temperatures are greater for the AT than the CG pair. The temperature dependence results from hydration of the apolar surfaces of bases that become exposed upon duplex dissociation. The larger enthalpic and entropic contributions of the AT pair are caused by water fixed by this pair in the minor groove of DNA and released on duplex dissociation. Analysis of the experimental thermodynamic characteristics of unfolding/refolding DNA duplexes of various compositions shows that the enthalpy of base pairing is negligibly small, while the entropic contribution is considerable. Thus, DNA base pairing is entropy driven and is coupled to the enthalpy driven van der Waals base pair stacking. Each of these two processes is responsible for about half the Gibbs energy of duplex stabilization, but all the enthalpy, i.e., the total heat of melting, results from dissociation of the stacked base pairs. Both these processes tightly cooperate: while the pairing of conjugate bases is critical for recognition of complementary strands, stacking of the flat apolar surfaces of the base pairs reinforces the DNA duplex formed.
Collapse
|
63
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
64
|
Sawada M, Yamaguchi K, Hirano M, Noji M, So M, Otzen D, Kawata Y, Goto Y. Amyloid Formation of α-Synuclein Based on the Solubility- and Supersaturation-Dependent Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4671-4681. [PMID: 32271585 DOI: 10.1021/acs.langmuir.0c00426] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amyloid fibrils are formed by denatured proteins when the supersaturation of denatured proteins is broken by agitation, such as ultrasonication, or by seeding, although the detailed mechanism of how solubility and supersaturation regulate amyloid formation remains unclear. To further understand the mechanism of amyloid formation, we examined α-synuclein (α-syn) amyloid formation at varying concentrations of SDS, LPA, heparin, or NaCl at pH 7.5. Amyloid fibrils were formed below or around the critical micelle concentrations (CMCs) of SDS (2.75 mM) and LPA (0.24 mM), although no fibrils were formed above the CMCs. On the other hand, amyloid fibrils were formed with 0.01-2.5 mg/mL of heparin and 0.5-1.0 M NaCl, and amyloid formation was gradually suppressed at higher concentrations of heparin and NaCl. To reproduce these concentration-dependent effects of additives, we constructed two models: (i) the ligand-binding-dependent solubility-modulation model and (ii) the cosolute-dependent direct solubility-modulation model, both of which were used by Tanford and colleagues to analyze the additive-dependent conformational transitions of proteins. The solubility of α-syn was assumed to vary depending on the concentration of additives either by the decreased solubility of the additive-α-syn complex (model i) or by the direct regulation of α-syn solubility (model ii). Both models well reproduced additive-dependent bell-shaped profiles of acceleration and inhibition observed for SDS and LPA. As for heparin and NaCl, participation of amorphous aggregates at high concentrations of additives was suggested. The models confirmed that solubility and supersaturation play major roles in driving amyloid formation in vitro, furthering our understanding of the pathogenesis of amyloidosis in vivo.
Collapse
Affiliation(s)
- Maya Sawada
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keiichi Yamaguchi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Miki Hirano
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Noji
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama Minami, Tottori 680-8552, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
65
|
Seal S, Chowdhury N, Biswas R, Chakraborty T, Sinha D, Bagchi A, Sau S. Removal of an atypical region from a staphylococcal cyclophilin affects its structure, function, stability, and shape. Int J Biol Macromol 2020; 151:1287-1298. [DOI: 10.1016/j.ijbiomac.2019.10.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
|
66
|
Shahabadi N, Zendehcheshm S. Evaluation of ct-DNA and HSA binding propensity of antibacterial drug chloroxine: Multi-spectroscopic analysis, atomic force microscopy and docking simulation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118042. [PMID: 31972466 DOI: 10.1016/j.saa.2020.118042] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/03/2020] [Accepted: 01/05/2020] [Indexed: 06/10/2023]
Abstract
In the present study, the binding interactions of chloroxine, an antibacterial drug and antibiotic agent with calf thymus-deoxyribonucleic acid (ct-DNA) and human serum albumin (HSA) have been deliberated under simulative physiological conditions (pH = 7.40) employing multiple biophysical, atomic force microscopy and molecular modeling approaches. The ct-DNA binding properties of chloroxine exhibit that it binds to ct-DNA through a groove binding mode, and the binding constant values were computed employing the absorption and emission spectral data. The fluorescence study shows the presence of the static quenching mechanism in the ct-DNA- chloroxine interaction. These results are further supported by UV-vis spectra. Large complexes contain the ct-DNA chains with an average size of 225.45 nm were observed by employing AFM for chloroxine -ct-DNA. The results revealed that the fluorescence quenching of albumin by chloroxine was a static quenching process as a result of albumin-chloroxine (1:1) complex. The distance between chloroxine and albumin was obtained based on the Förster's theory of non-radiative energy transfer. The results of AFM, synchronous and three-dimensional fluorescence spectra all revealed that chloroxine induced the conformational changes of albumin. Molecular docking technology represents the binding of chloroxine to the major groove of ct-DNA and site I (subdomain II A) of albumin.
Collapse
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Saba Zendehcheshm
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| |
Collapse
|
67
|
Bao Y, Luo Z, Cui S. Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials. Chem Soc Rev 2020; 49:2799-2827. [PMID: 32236171 DOI: 10.1039/c9cs00855a] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.
Collapse
Affiliation(s)
- Yu Bao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China.
| | | | | |
Collapse
|
68
|
Timr S, Madern D, Sterpone F. Protein thermal stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:239-272. [PMID: 32145947 DOI: 10.1016/bs.pmbts.2019.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins, in general, fold to a well-organized three-dimensional structure in order to function. The stability of this functional shape can be perturbed by external environmental conditions, such as temperature. Understanding the molecular factors underlying the resistance of proteins to the thermal stress has important consequences. First of all, it can aid the design of thermostable enzymes able to perform efficient catalysis in the high-temperature regime. Second, it is an essential brick of knowledge required to decipher the evolutionary pathways of life adaptation on Earth. Thanks to the development of atomistic simulations and ad hoc enhanced sampling techniques, it is now possible to investigate this problem in silico, and therefore provide support to experiments. After having described the methodological aspects, the chapter proposes an extended discussion on two problems. First, we focus on thermophilic proteins, a perfect model to address the issue of thermal stability and molecular evolution. Second, we discuss the issue of how protein thermal stability is affected by crowded in vivo-like conditions.
Collapse
Affiliation(s)
- Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | | | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
| |
Collapse
|
69
|
Rodrigues RM, Claro B, Bastos M, Pereira RN, Vicente AA, Petersen SB. Multi-step thermally induced transitions of β-lactoglobulin – An in situ spectroscopy approach. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2019.104562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
70
|
L. Mpye K, Gildenhuys S, Mosebi S. The effects of temperature on streptavidin-biotin binding using affinity isothermal titration calorimetry. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
|
71
|
Deng GH, Shen Y, Chen H, Chen Y, Jiang B, Wu G, Yang X, Yuan K, Zheng J. Ordered-to-Disordered Transformation of Enhanced Water Structure on Hydrophobic Surfaces in Concentrated Alcohol-Water Solutions. J Phys Chem Lett 2019; 10:7922-7928. [PMID: 31794227 DOI: 10.1021/acs.jpclett.9b03429] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The effects of hydrophobic solutes on the structure of the surrounding water have been a topic of debate for almost 70 years. However, a consistent description of the physical insight into the causes of the anomalous thermodynamic properties of alcohol-water mixtures is lacking. Here we report experimental results that combined temperature-dependent linear and femtosecond infrared spectroscopy measurements to explore the water structural transformation in concentrated alcohol-water solutions. Experiments show that the enhancement of water structure arises around microhydrophobic interfaces at room temperature in the solutions. As temperature increases, this ordered water structure disappears and a surface topography-dependent new disordered water structure arises at concentrated solutions of large alcohols. The water structural transformation is dependent on not only the length of the alkyl chain but also the clustering of the alcohols. A more-ordered-than-water structure can transform into a less-ordered-than-water structure.
Collapse
Affiliation(s)
- Gang-Hua Deng
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Yuneng Shen
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hailong Chen
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics , Institute of Physics, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yajing Chen
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Bo Jiang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Kaijun Yuan
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Junrong Zheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences , Peking University , Beijing 100871 , China
| |
Collapse
|
72
|
Li-Blatter X, Seelig J. Thermal and Chemical Unfolding of Lysozyme. Multistate Zimm-Bragg Theory Versus Two-State Model. J Phys Chem B 2019; 123:10181-10191. [PMID: 31686511 DOI: 10.1021/acs.jpcb.9b08816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Thermal and chemical unfolding of lysozyme in the presence of the guanidine HCl denaturant is a model system to compare the conventional two-state model of protein unfolding with the multistate Zimm-Bragg theory. The two-state model is shown to be the noncooperative limit of the Zimm-Bragg theory. In particular, the Zimm-Bragg theory provides a molecular interpretation of the empirical linear extrapolation method (LEM) of the two-state model. Differential scanning calorimetry (DSC) experiments reported in the literature are analyzed with both methods. Lysozyme unfolding is associated with a large endothermic enthalpy that decreases significantly upon addition of guanidine HCl. In contrast, the Gibbs free energy of unfolding is small, negative, and independent of the guanidine HCl concentration, contradicting, in part, the conclusions of the LEM. The unfolding enthalpy is compensated by an even larger entropy term. The multistate Zimm-Bragg theory predicts a larger conformational enthalpy and a smaller Gibbs free energy than the two-state model. The Zimm-Bragg theory provides the protein cooperativity parameter, the average length of independently folding protein domains, and the Gibbs free energy of unfolding of individual amino acid residues. Guanidine HCl binding to lysozyme is exothermic and counteracts the endothermic unfolding enthalpy. The number of bound denaturant molecules is determined from the decrease in enthalpy and is extrapolated to the guanidine HCl-to-amino acid stoichiometry at complete lysozyme unfolding. Chemical unfolding isotherms measured with circular dichroism (CD) spectroscopy are analyzed with both models. The chemical Zimm-Bragg theory is a cooperative molecular model, yielding the guanidine HCl binding constant and the protein cooperativity parameter. It allows a quantitative comparison between thermal and chemical protein unfolding. The two reactions have almost identical changes in Gibbs free energy. However, thermal unfolding is significantly more cooperative than chemical unfolding. Finally, distinct differences are observed in thermal unfolding between DSC and CD spectroscopy.
Collapse
Affiliation(s)
- Xiaochun Li-Blatter
- Biozentrum , University of Basel , Klingelbergstrasse 50/70 , CH-4056 Basel , Switzerland
| | - Joachim Seelig
- Biozentrum , University of Basel , Klingelbergstrasse 50/70 , CH-4056 Basel , Switzerland
| |
Collapse
|
73
|
Ikeda A, Capellan A, Welch JT. The secondary structure of a heptapeptide containing trifluoromethyl-λ 6-tetrafluorosulfanyl substituted amino acids. Org Biomol Chem 2019; 17:8079-8082. [PMID: 31454017 DOI: 10.1039/c9ob01797f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Site specific introduction of the polar hydrophobic trifluoromethyl-λ6-tetrafluorosulfanyl (CF3SF4) group can effectively control the secondary structure of a heptapeptide, the minimum repeat unit of an α-helix. The structural influence of CF3SF4-containing amino acid on the heptapeptide was established using NMR methods.
Collapse
Affiliation(s)
- Akari Ikeda
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Aimée Capellan
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - John T Welch
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| |
Collapse
|
74
|
Cinar H, Fetahaj Z, Cinar S, Vernon RM, Chan HS, Winter RHA. Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications. Chemistry 2019; 25:13049-13069. [PMID: 31237369 DOI: 10.1002/chem.201902210] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/23/2019] [Indexed: 01/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.
Collapse
Affiliation(s)
- Hasan Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Zamira Fetahaj
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Süleyman Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Robert M Vernon
- Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Hue Sun Chan
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada
| | - Roland H A Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| |
Collapse
|
75
|
Abstract
A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.
Collapse
Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
76
|
Yasin MZ, Rashid MH. Purification and extreme thermostabilization of glucoamylase by zinc produce of novel fungus Gymnoascella citrina. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
77
|
Judy E, Kishore N. A look back at the molten globule state of proteins: thermodynamic aspects. Biophys Rev 2019; 11:365-375. [PMID: 31055760 PMCID: PMC6557940 DOI: 10.1007/s12551-019-00527-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/22/2019] [Indexed: 12/23/2022] Open
Abstract
Interest in protein folding intermediates lies in their significance to protein folding pathways. The molten globule (MG) state is one such intermediate lying on the kinetic (and sometimes thermodynamic) pathway between native and unfolded states. Development of our qualitative and quantitative understanding of the MG state can provide deeper insight into the folding pathways and hence potentially facilitate solution of the protein folding problem. An extensive look at literature suggests that most studies into protein MG states have been largely qualitative. Attempts to obtain quantitative insights into MG states have involved application of high-sensitivity calorimetry (differential scanning calorimetry and isothermal titration calorimetry). This review addresses the progress made in this direction by discussing the knowledge gained to date, along with the future promise of calorimetry, in providing quantitative information on the structural features of MG states. Particular attention is paid to the question of whether such states share common structural features or not. The difference in the nature of the transition from the MG state to the unfolded state, in terms of cooperativity, has also been addressed and discussed.
Collapse
Affiliation(s)
- Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076 India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076 India
| |
Collapse
|
78
|
Mandelman D, Ballut L, Wolff DA, Feller G, Gerday C, Haser R, Aghajari N. Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase. Extremophiles 2019; 23:495-506. [DOI: 10.1007/s00792-019-01102-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/21/2019] [Indexed: 11/30/2022]
|
79
|
Winzor DJ, Wills PR. Quantitative interpretation of isopiestic measurements on aqueous solutions: Urea revisited. Biophys Chem 2019; 251:106175. [PMID: 31128561 DOI: 10.1016/j.bpc.2019.106175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 10/27/2022]
Abstract
This investigation amends the analysis of isopiestic measurements of solvent thermodynamic activity by taking into account the fact that the solvent activity, traditionally expressed in mole-fraction terms, is a molal parameter because of the constraints (constant temperature and pressure) under which the measurements are made. Application of the revised procedure to published isopiestic measurements on aqueous urea solutions at 25 °C yields a dimerization constant of 0.066 molal-1, which is two-fold larger than an earlier published estimate based on an incorrect definition of the solute activity coefficient. Despite amendments to the quantitative detail, the present study confirms the existence of a large negative entropic contribution that largely counters its enthalpic counterpart arising from the hydrogen bonding responsible for dimer formation. This evidence of enthalpy-entropy compensation is entirely consistent with quantum-mechanical predictions of the adverse effect of water on urea dimerization. Changes in water structure thus contribute significantly to the energetics of urea dimerization in aqueous solution.
Collapse
Affiliation(s)
- Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter R Wills
- Department of Physics, University of Auckland, PB 92019, Auckland 1142, New Zealand.
| |
Collapse
|
80
|
Molecular design, synthesis and biomedical applications of stimuli-responsive shape memory hydrogels. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
81
|
Ghindes-Azaria L, Melamed O, Nadav-Tsubery M, Levy E, Keinan-Adamsky K, Goobes G. Dynamics in hydrophilic and hydrophobic molecular chains tethered to MCM41-type mesoporous silica upon wetting and dehydration processes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 98:24-35. [PMID: 30738232 DOI: 10.1016/j.ssnmr.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Surface modified mesoporous silica materials are important materials for heterogeneous catalysis and are attracting attention as potential drug carriers. The functionality of these materials relies on the physical and chemical properties of the tethers attached to MCM41 silica surface. These chemically linked tails act as molecular brushes, that can capture pollutant molecules, anchor points for catalysts and can host drug molecules. To utilize the full potential of the tailored silica surfaces, one should infer their properties at different levels of solvation. Here, 1H MAS NMR spectroscopy is used to monitor the dynamic properties of two modified MCM41 materials, an aminopropyl tethered MCM41 and an octyl tethered MCM41, through the process of controlled hydration. The surface site resolved measurements demonstrate how the chemical nature of the two tethers governs the way water molecules are directed to the different sites in the porous materials.
Collapse
Affiliation(s)
- Lee Ghindes-Azaria
- Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Ofer Melamed
- The Center for Academic Studies, Or Yehuda, 6021816, Israel
| | | | - Esthy Levy
- Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
| | | | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel.
| |
Collapse
|
82
|
Mondal A, Das M, Mazumdar S. Substitution of iron with cobalt in the prosthetic group of bacterial cytochrome P450: Effects on the stability and structure of the protein. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.12.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
83
|
Biswas A, Ghosh S, Sinha D, Dutta A, Seal S, Bagchi A, Sau S. Dimerization ability, denaturation mechanism, and the stability of a staphylococcal phage repressor and its two domains. Int J Biol Macromol 2019; 124:903-914. [DOI: 10.1016/j.ijbiomac.2018.11.263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
|
84
|
Corkrey R, Macdonald C, McMeekin T. The Biokinetic Spectrum for Temperature and optimal Darwinian fitness. J Theor Biol 2019; 462:171-183. [PMID: 30385312 DOI: 10.1016/j.jtbi.2018.10.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
Abstract
Darwinian fitness is maximised at a temperature below Topt, but what this temperature is remains unclear. By linking our previous work on the Biokinetic Spectrum for Temperature with a model for temperature-dependent biological growth rate we obtain a plausible value for such a temperature. We find this approach reveals considerable commonalities in how life responds to temperature with implications that follow in evolution, physiology and ecology. We described a data set consisting of 17,021 observations of temperature-dependent population growth rates from 2411 bacterial, archaeal and eukaryal strains. We fitted a thermodynamic model to describe the strains' temperature-dependent growth rate curves that assumed growth was limited by a single rate-limiting enzyme. We defined Umes as an empirical measure of the temperature at which strains grew as fast and also as efficiently as possible. We propose that Darwinian fitness is optimised at Umes by trading-off growth rate and physiological efficiency. Using the full data set we calculated the Biokinetic Spectrum for Temperature (BKST): the distribution of temperature-dependent growth rates for each temperature. We used quantile regression to fit alternative models to the BKST to obtain quantile curves. A quantile is a value that contains a particular proportion of the data. The quantile curves suggested commonalities in temperature-dependencies spanning taxa and ecotype, consistent with the single rate-limiting enzyme concept. We showed that on the log scale, the slopes of the quantile curves were the same as the slopes of the thermodynamic model growth curves at Umes. This was true for Bacteria, Archaea, and Eukarya, and across other conditions (pH, water activity, metabolic type and trophic type). We showed that the quantile curves were the loci of the temperatures and growth rates that optimised Darwinian fitness for each strain at a given temperature-dependence and independently of other conditions. The quantile curves for Archaea and Bacteria shared a number of similarities attributable to the influence of the properties of water on protein folding. Other implications have impact on evolutionary biology, ecology, and physiology. The model predicts the existence of eurythermic strains that grow with about equal efficiency over a broad temperature range. These strains will have higher evolutionary rates with lower mutational costs that are independent of environmental conditions, a factor likely to have been significant during the Precambrian if the early Earth was warmer than today. The model predicts that random mutations are likely to result in shifts along the quantile curves and not across them. It predicts that some psychrophiles will be capable of performing well under climate change, and that selection will favour faster growth rates as the temperature increases. Last, it predicts trade-offs between growth rate and soma production, so that temperature-dependence, and possibly Darwinian fitness, remain constant over a broad temperature range and growth rates.
Collapse
Affiliation(s)
- Ross Corkrey
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia.
| | - Cameron Macdonald
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom McMeekin
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| |
Collapse
|
85
|
Klamt A, Nagarathinam K, Tanabe M, Kumar A, Balbach J. Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy. J Phys Chem B 2019; 123:792-801. [PMID: 30608169 DOI: 10.1021/acs.jpcb.8b11019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For a comprehensive understanding of the thermodynamic state functions describing the stability of a protein, the influence of the intensive properties of temperature and pressure has to be known. With the zinc-finger-containing Kti11, we found a suitable protein for this purpose because folding and unfolding transitions occur at an experimentally accessible temperature (280-330 °K) and pressure (0.1-240 MPa) range. We solved the crystal structure of the apo form of Kti11 to reveal two disulfide bonds at the metal-binding site, which seals off a cavity in the β-barrel part of the protein. From a generally applicable proton NMR approach, we could determine the populations of folded and unfolded chains under all conditions, leading to a hyperbolic pressure-temperature phase diagram rarely observed for proteins. A global fit of a two-state model to all derived populations disclosed reliable values for the change in Gibbs free energy, volume, entropy, heat capacity, compressibility, and thermal expansion upon unfolding. The unfolded state of apoKti11 has a lower compressibility compared to the native state and a smaller volume at ambient pressure. Therefore, a pressure increase up to 200 MPa reduces the population of the native state, and above this value, the native population increases again. Pressure-induced chemical-shift changes in two-dimensional 1H-15N NMR spectra could be employed for a molecular interpretation of the thermodynamic properties of apoKti11.
Collapse
Affiliation(s)
- Andi Klamt
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany
| | - Kumar Nagarathinam
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Straße 1 , D-30625 Hannover , Germany
| | - Mikio Tanabe
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Structural Biology Research Center, Institute of Materials Structure Science , KEK/High Energy Accelerator Research Organization , 1-1 Oho , Tsukuba , Ibaraki , 305-0801 , Japan
| | - Amit Kumar
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,Department of Diabetes, Faculty of Lifesciences and Medicine , King's College London , Great Maze Pond , London SE1 1UL , U.K
| | - Jochen Balbach
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany
| |
Collapse
|
86
|
Deng Y, Ma Q, Yuan H, Lum GC, Shum HC. Development of dual-component protein microparticles in all-aqueous systems for biomedical applications. J Mater Chem B 2019. [DOI: 10.1039/c8tb03074j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein microparticles assisted by an emulsion droplet template have shown great promise in drug/cell delivery and tissue engineering, as well as diagnosis and treatment of diseases.
Collapse
Affiliation(s)
- Yi Deng
- School of Chemical Engineering
- Sichuan University
- Chengdu 610065
- China
- Department of Mechanical Engineering
| | - Qingming Ma
- Department of Pharmaceutics
- School of Pharmacy
- Qingdao University
- Qingdao 266021
- China
| | - Hao Yuan
- Department of Mechanical Engineering
- University of Hong Kong
- Hong Kong SAR
- China
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI)
| | - Galen Chit Lum
- Department of Mechanical and Industrial Engineering
- University of Toronto
- Toronto
- Canada
| | - Ho Cheung Shum
- Department of Mechanical Engineering
- University of Hong Kong
- Hong Kong SAR
- China
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI)
| |
Collapse
|
87
|
Roche J, Royer CA, Roumestand C. Exploring Protein Conformational Landscapes Using High-Pressure NMR. Methods Enzymol 2019; 614:293-320. [DOI: 10.1016/bs.mie.2018.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
88
|
Cai Y, Zhao H. Protein-Induced Dissociation of Biomolecular Assemblies. ACS APPLIED BIO MATERIALS 2018; 2:470-479. [DOI: 10.1021/acsabm.8b00672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yaqian Cai
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Hanying Zhao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| |
Collapse
|
89
|
Torktaz I, Karkhane AA, Hemmat J. Rational engineering of Cel5E from Clostridium thermocellum to improve its thermal stability and catalytic activity. Appl Microbiol Biotechnol 2018; 102:8389-8402. [DOI: 10.1007/s00253-018-9204-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 10/28/2022]
|
90
|
Carlsson ACC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry 2018; 57:4135-4147. [PMID: 29921126 PMCID: PMC6052408 DOI: 10.1021/acs.biochem.8b00603] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The construction of more stable proteins
is important in biomolecular
engineering, particularly in the design of biologics-based therapeutics.
We show here that replacing the tyrosine at position 18 (Y18) of T4
lysozyme with the unnatural amino acid m-chlorotyrosine
(mClY) increases both the thermal stability
(increasing the melting temperature by ∼1 °C and the melting
enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures
(15% higher than that of the parent enzyme at 40 °C) of this
classic enzyme. The chlorine of mClY forms
a halogen bond (XB) to the carbonyl oxygen of the peptide bond at
glycine 28 (G28) in a tight loop near the active site. In this case,
the XB potential of the typically weak XB donor Cl is shown from quantum
chemical calculations to be significantly enhanced by polarization
via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl
substituent of the tyrosyl side chain, resulting in a distinctive
synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger
halogens (bromine and iodine) are not well accommodated within this
same loop and, consequently, do not exhibit the effects on protein
stability or function associated with the HeX-B interaction. Thus,
we have for the first time demonstrated that an XB can be engineered
to stabilize and increase the activity of an enzyme, with the increased
stabilizing potential of the HeX-B further extending the application
of halogenated amino acids in the design of more stable protein therapeutics.
Collapse
Affiliation(s)
- Anna-Carin C Carlsson
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Matthew R Scholfield
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Rhianon K Rowe
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Austin T Alexander
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - Ryan A Mehl
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| |
Collapse
|
91
|
Privalov PL, Crane-Robinson C. Forces maintaining the DNA double helix and its complexes with transcription factors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 135:30-48. [DOI: 10.1016/j.pbiomolbio.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
|
92
|
Kinetic analysis of the multistep aggregation pathway of human transthyretin. Proc Natl Acad Sci U S A 2018; 115:E6201-E6208. [PMID: 29915031 DOI: 10.1073/pnas.1807024115] [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] [Indexed: 01/24/2023] Open
Abstract
Aggregation of transthyretin (TTR) is the causative agent for TTR cardiomyopathy and polyneuropathy amyloidoses. Aggregation is initiated by dissociation of the TTR tetramer into a monomeric intermediate, which self-assembles into amyloid. The coupled multiple-step equilibria and low-concentration, aggregation-prone intermediates are challenging to probe using conventional assays. We report a 19F-NMR assay that leverages a highly sensitive trifluoroacetyl probe at a strategic site that gives distinct 19F chemical shifts for the TTR tetramer and monomeric intermediate and enables direct quantification of their populations during the aggregation process. Integration of real-time 19F-NMR and turbidity measurements as a function of temperature allows kinetic and mechanistic dissection of the aggregation pathway of both wild-type and mutant TTR. At physiological temperature, the monomeric intermediate formed by wild-type TTR under mildly acidic conditions rapidly aggregates into species that are invisible to NMR, leading to loss of the NMR signal at the same rate as the turbidity increase. Lower temperature accelerates tetramer dissociation and decelerates monomer tetramerization and oligomerization via reduced hydrophobic interactions associated with packing of a phenylalanine (F87) into a neighboring protomer. As a result, the intermediate accumulates to a higher level, and formation of higher-order aggregates is delayed. Application of this assay to pathogenic (V30M, L55P, and V122I) and protective (T119M) mutants revealed significant differences in behavior. A monomeric intermediate was observed only for V122I: aggregation of V30M and L55P proceeds without an observable monomeric intermediate, whereas the protective mutant T119M remains resistant to tetramer dissociation and aggregation.
Collapse
|
93
|
Maggi F, M. Tang FH, Riley WJ. The Thermodynamic Links between Substrate, Enzyme, and Microbial Dynamics in Michaelis-Menten-Monod Kinetics. INT J CHEM KINET 2018. [DOI: 10.1002/kin.21163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Federico Maggi
- School of Civil Engineering; The University of Sydney; Sydney 2006 NSW Australia
| | - Fiona H. M. Tang
- School of Civil Engineering; The University of Sydney; Sydney 2006 NSW Australia
| | - William J. Riley
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720
| |
Collapse
|
94
|
Ikeda A, Zhong L, Savoie PR, von Hahmann CN, Zheng W, Welch JT. Synthesis of Trifluoromethyl Tetrafluoro‐λ
6
‐sulfanyl‐Substituted Alkenes, Ketones, and Acids: Polar Hydrophobic Building Blocks. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Akari Ikeda
- Department of Chemistry University at Albany, SUNY 1400 Washington Ave 12222 Albany NY USA
| | - Linbin Zhong
- Department of Chemistry University at Albany, SUNY 1400 Washington Ave 12222 Albany NY USA
| | - Paul R. Savoie
- Department of Chemistry University at Albany, SUNY 1400 Washington Ave 12222 Albany NY USA
| | - Cortney N. von Hahmann
- Department of Chemistry University at Albany, SUNY 1400 Washington Ave 12222 Albany NY USA
| | - Wei Zheng
- Department of Chemistry University at Albany, SUNY 1400 Washington Ave 12222 Albany NY USA
| | - John T. Welch
- Department of Chemistry University at Albany, SUNY 1400 Washington Ave 12222 Albany NY USA
| |
Collapse
|
95
|
Potekhin SA. High-Pressure Scanning Microcalorimetry – A New Method for Studying Conformational and Phase Transitions. BIOCHEMISTRY (MOSCOW) 2018; 83:S134-S145. [DOI: 10.1134/s0006297918140110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
96
|
Global versus local mechanisms of temperature sensing in ion channels. Pflugers Arch 2018; 470:733-744. [PMID: 29340775 DOI: 10.1007/s00424-017-2102-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Ion channels turn diverse types of inputs, ranging from neurotransmitters to physical forces, into electrical signals. Channel responses to ligands generally rely on binding to discrete sensor domains that are coupled to the portion of the channel responsible for ion permeation. By contrast, sensing physical cues such as voltage, pressure, and temperature arises from more varied mechanisms. Voltage is commonly sensed by a local, domain-based strategy, whereas the predominant paradigm for pressure sensing employs a global response in channel structure to membrane tension changes. Temperature sensing has been the most challenging response to understand and whether discrete sensor domains exist for pressure and temperature has been the subject of much investigation and debate. Recent exciting advances have uncovered discrete sensor modules for pressure and temperature in force-sensitive and thermal-sensitive ion channels, respectively. In particular, characterization of bacterial voltage-gated sodium channel (BacNaV) thermal responses has identified a coiled-coil thermosensor that controls channel function through a temperature-dependent unfolding event. This coiled-coil thermosensor blueprint recurs in other temperature sensitive ion channels and thermosensitive proteins. Together with the identification of ion channel pressure sensing domains, these examples demonstrate that "local" domain-based solutions for sensing force and temperature exist and highlight the diversity of both global and local strategies that channels use to sense physical inputs. The modular nature of these newly discovered physical signal sensors provides opportunities to engineer novel pressure-sensitive and thermosensitive proteins and raises new questions about how such modular sensors may have evolved and empowered ion channel pores with new sensibilities.
Collapse
|
97
|
Suárez IP, Gauto DF, Hails G, Mascali FC, Crespo R, Zhao L, Wang J, Rasia RM. Conformational sampling of the intrinsically disordered dsRBD-1 domain from Arabidopsis thaliana DCL1. Phys Chem Chem Phys 2018; 20:11237-11246. [DOI: 10.1039/c7cp07908g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Partial folding and stability of DCL1-dsRBD1.
Collapse
Affiliation(s)
- Irina P. Suárez
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Diego F. Gauto
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Guillermo Hails
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Florencia C. Mascali
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Roberta Crespo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Lingzi Zhao
- College of Physics
- Jilin University
- Jilin
- China
| | - Jin Wang
- State University of New York at Stony Brook
- USA
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
- Área Biofísica
- Facultad de Ciencias Bioquímicas y Farmacéuticas
| |
Collapse
|
98
|
Hong T, Iwashita K, Shiraki K. Viscosity Control of Protein Solution by Small Solutes: A Review. Curr Protein Pept Sci 2018; 19:746-758. [PMID: 29237380 PMCID: PMC6182935 DOI: 10.2174/1389203719666171213114919] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/22/2022]
Abstract
Viscosity of protein solution is one of the most troublesome issues for the high-concentration formulation of protein drugs. In this review, we summarize the practical methods that suppress the viscosity of protein solution using small molecular additives. The small amount of salts decreases the viscosity that results from electrostatic repulsion and attraction. The chaotrope suppresses the hydrophobic attraction and cluster formation, which can lower the solution viscosity. Arginine hydrochloride (ArgHCl) also suppresses the solution viscosity due to the hydrophobic and aromatic interactions between protein molecules. The small molecular additives are the simplest resolution of the high viscosity of protein solution as well as understanding of the primary cause in complex phenomena of protein interactions.
Collapse
Affiliation(s)
- Taehun Hong
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| | - Kazuki Iwashita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| |
Collapse
|
99
|
The flotation and adsorption of mixed collectors on oxide and silicate minerals. Adv Colloid Interface Sci 2017; 250:1-14. [PMID: 29150015 DOI: 10.1016/j.cis.2017.11.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 11/24/2022]
Abstract
The analysis of flotation and adsorption of mixed collectors on oxide and silicate minerals is of great importance for both industrial applications and theoretical research. Over the past years, significant progress has been achieved in understanding the adsorption of single collectors in micelles as well as at interfaces. By contrast, the self-assembly of mixed collectors at liquid/air and solid/liquid interfaces remains a developing area as a result of the complexity of the mixed systems involved and the limited availability of suitable analytical techniques. In this work, we systematically review the processes involved in the adsorption of mixed collectors onto micelles and at interface by examining four specific points, namely, theoretical background, factors that affect adsorption, analytical techniques, and self-assembly of mixed surfactants at the mineral/liquid interface. In the first part, the theoretical background of collector mixtures is introduced, together with several core solution theories, which are classified according to their application in the analysis of physicochemical properties of mixed collector systems. In the second part, we discuss the factors that can influence adsorption, including factors related to the structure of collectors and environmental conditions. We summarize their influence on the adsorption of mixed systems, with the objective to provide guidance on the progress achieved in this field to date. Advances in measurement techniques can greatly promote our understanding of adsorption processes. In the third part, therefore, modern techniques such as optical reflectometry, neutron scattering, neutron reflectometry, thermogravimetric analysis, fluorescence spectroscopy, ultrafiltration, atomic force microscopy, analytical ultracentrifugation, X-ray photoelectron spectroscopy, Vibrational Sum Frequency Generation Spectroscopy and molecular dynamics simulations are introduced in virtue of their application. Finally, focusing on oxide and silicate minerals, we review and summarize the flotation and adsorption of three most widely used mixed surfactant systems (anionic-cationic, anionic-nonionic, and cationic-nonionic) at the liquid/mineral interface in order to fully understand the self-assembly progress. In the end, the paper gives a brief future outlook of the possible development in the mixed surfactants.
Collapse
|
100
|
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
|