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Kobus M, Friedrich T, Zorn E, Burmeister N, Maison W. Medicinal Chemistry of Drugs with N-Oxide Functionalities. J Med Chem 2024; 67:5168-5184. [PMID: 38549449 PMCID: PMC11017254 DOI: 10.1021/acs.jmedchem.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/08/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
Abstract
Molecules with N-oxide functionalities are omnipresent in nature and play an important role in Medicinal Chemistry. They are synthetic or biosynthetic intermediates, prodrugs, drugs, or polymers for applications in drug development and surface engineering. Typically, the N-oxide group is critical for biomedical applications of these molecules. It may provide water solubility or decrease membrane permeability or immunogenicity. In other cases, the N-oxide has a special redox reactivity which is important for drug targeting and/or cytotoxicity. Many of the underlying mechanisms have only recently been discovered, and the number of applications of N-oxides in the healthcare field is rapidly growing. This Perspective article gives a short summary of the properties of N-oxides and their synthesis. It also provides a discussion of current applications of N-oxides in the biomedical field and explains the basic molecular mechanisms responsible for their biological activity.
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Affiliation(s)
- Michelle Kobus
- Universität Hamburg, Department of Chemistry, Bundesstrasse 45, 20146 Hamburg, Germany
| | - Timo Friedrich
- Universität Hamburg, Department of Chemistry, Bundesstrasse 45, 20146 Hamburg, Germany
| | - Eilika Zorn
- Universität Hamburg, Department of Chemistry, Bundesstrasse 45, 20146 Hamburg, Germany
| | - Nils Burmeister
- Universität Hamburg, Department of Chemistry, Bundesstrasse 45, 20146 Hamburg, Germany
| | - Wolfgang Maison
- Universität Hamburg, Department of Chemistry, Bundesstrasse 45, 20146 Hamburg, Germany
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2
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Posey AE, Ross KA, Bagheri M, Lanum EN, Khan MA, Jennings CE, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes. Protein Sci 2023; 32:e4787. [PMID: 37743569 PMCID: PMC10578129 DOI: 10.1002/pro.4787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" important for regulation. For the mitochondrial fission dynamin, dynamin-related protein 1, a regulatory role for the variable domain (VD) is demonstrated by gain- and loss-of-function mutations, yet the basis for this is unclear. Here, the isolated VD is shown to be intrinsically disordered and undergo a cooperative transition in the stabilizing osmolyte trimethylamine N-oxide. However, the osmolyte-induced state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, which appears to promote phase separation. Since dynamin-related protein 1 is found assembled into discrete punctate structures on the mitochondrial surface, the inference from the present work is that these structures might arise from a condensed state involving the VD that may enable rapid tuning of mechanoenzyme assembly necessary for fission.
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Affiliation(s)
- Ammon E. Posey
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Present address:
Department of Biomedical EngineeringWashington UniversitySt. LouisMissouriUSA
| | - Kyle A. Ross
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Mehran Bagheri
- Department of PhysicsUniversity of OttawaOttawaOntarioUSA
| | - Elizabeth N. Lanum
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Misha A. Khan
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | - Megan C. Harwig
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Nolan W. Kennedy
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Vincent J. Hilser
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - R. Blake Hill
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
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Georgoulis I, Bock C, Lannig G, Pörtner HO, Sokolova IM, Feidantsis K, Giantsis IA, Michaelidis B. Heat hardening enhances metabolite-driven thermoprotection in the Mediterranean mussel Mytilus galloprovincialis. Front Physiol 2023; 14:1244314. [PMID: 37841313 PMCID: PMC10570847 DOI: 10.3389/fphys.2023.1244314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Temperature affects organisms' metabolism and ecological performance. Owing to climate change, sea warming constituting a severe source of environmental stress for marine organisms, since it increases at alarming rates. Rapid warming can exceed resilience of marine organisms leading to fitness loss and mortality. However, organisms can improve their thermal tolerance when briefly exposed to sublethal thermal stress (heat hardening), thus generating heat tolerant phenotypes. Methods: We investigated the "stress memory" effect caused by heat hardening on M. galloprovincialis metabolite profile of in order to identify the underlying biochemical mechanisms, which enhance mussels' thermal tolerance. Results: The heat hardening led to accumulation of amino acids (e.g., leucine, isoleucine and valine), including osmolytes and cytoprotective agents with antioxidant and anti-inflammatory properties that can contribute to thermal protection of the mussels. Moreover, proteolysis was inhibited and protein turnover regulated by the heat hardening. Heat stress alters the metabolic profile of heat stressed mussels, benefiting the heat-hardened individuals in increasing their heat tolerance compared to the non-heat-hardened ones. Discussion: These findings provide new insights in the metabolic mechanisms that may reinforce mussels' tolerance against thermal stress providing both natural protection and potential manipulative tools (e.g., in aquaculture) against the devastating climate change effects on marine organisms.
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Affiliation(s)
- Ioannis Georgoulis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Environmental Control and Research Laboratory, Region of Central Macedonia, Thessaloniki, Greece
| | - Christian Bock
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
| | - Gisela Lannig
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
| | - Hans O. Pörtner
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research, Integrative Ecophysiology, Bremerhaven, Germany
| | - Inna M. Sokolova
- Department of Marine Biology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Konstantinos Feidantsis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Environmental Control and Research Laboratory, Region of Central Macedonia, Thessaloniki, Greece
- Department of Fisheries and Aquaculture, University of Patras, Mesolonghi, Greece
| | - Ioannis A. Giantsis
- Environmental Control and Research Laboratory, Region of Central Macedonia, Thessaloniki, Greece
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Kozani, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Environmental Control and Research Laboratory, Region of Central Macedonia, Thessaloniki, Greece
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Posey AE, Bagheri M, Ross KA, Lanum EN, Khan MA, Jennings CM, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542732. [PMID: 37398258 PMCID: PMC10312466 DOI: 10.1101/2023.05.29.542732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory and stimulatory activity is unclear. Here, isolated VD is shown to be intrinsically disordered (ID) yet undergoes a cooperative transition in the stabilizing osmolyte TMAO. However, the TMAO stabilized state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, raising the possibility that phase separation may enable rapid tuning of Drp1 assembly necessary for fission.
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5
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Cheah KM, Jun JV, Wittrup KD, Raines RT. Host-Guest Complexation by β-Cyclodextrin Enhances the Solubility of an Esterified Protein. Mol Pharm 2022; 19:3869-3876. [PMID: 36036888 DOI: 10.1021/acs.molpharmaceut.2c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carboxyl groups of a protein can be esterified by reaction with a diazo compound, 2-diazo-2-(p-methylphenyl)-N,N-dimethylacetamide. This esterification enables the entry of the protein into the cytosol of a mammalian cell, where the nascent ester groups are hydrolyzed by endogenous esterases. The low aqueous solubility of the ensuing esterified protein is, however, a major practical challenge. Solubility screening revealed that β-cyclodextrin (β-CD) is an optimal solubilizing agent for esterified green fluorescent protein (est-GFP). Its addition can increase the recovery of est-GFP by 10-fold. α-CD, γ-CD, and cucurbit-7-uril are less effective excipients. 1H NMR titration experiments revealed that β-CD encapsulates the hydrophobic tolyl group of ester conjugates with Ka = 321 M-1. Combining l-arginine and sucrose with β-CD enables the nearly quantitative recovery of est-GFP. Thus, the insolubility of esterified proteins can be overcome with excipients.
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Mandalaparthy V, Noid WG. A simple theory for interfacial properties of dilute solutions. J Chem Phys 2022; 157:034703. [DOI: 10.1063/5.0098579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent studies suggest that cosolute mixtures may exert significant non-additive effects upon protein stability. The corresponding liquid–vapor interfaces may provide useful insight into these non-additive effects. Accordingly, in this work, we relate the interfacial properties of dilute multicomponent solutions to the interactions between solutes. We first derive a simple model for the surface excess of solutes in terms of thermodynamic observables. We then develop a lattice-based statistical mechanical perturbation theory to derive these observables from microscopic interactions. Rather than adopting a random mixing approximation, this dilute solution theory (DST) exactly treats solute–solute interactions to lowest order in perturbation theory. Although it cannot treat concentrated solutions, Monte Carlo (MC) simulations demonstrate that DST describes the interactions in dilute solutions with much greater accuracy than regular solution theory. Importantly, DST emphasizes a fundamental distinction between the “intrinsic” and “effective” preferences of solutes for interfaces. DST predicts that three classes of solutes can be distinguished by their intrinsic preference for interfaces. While the surface preference of strong depletants is relatively insensitive to interactions, the surface preference of strong surfactants can be modulated by interactions at the interface. Moreover, DST predicts that the surface preference of weak depletants and weak surfactants can be qualitatively inverted by interactions in the bulk. We also demonstrate that DST can be extended to treat surface polarization effects and to model experimental data. MC simulations validate the accuracy of DST predictions for lattice systems that correspond to molar concentrations.
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Affiliation(s)
- Varun Mandalaparthy
- Department of Chemistry, Penn State University, University Park, State College, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, Penn State University, University Park, State College, Pennsylvania 16802, USA
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Bhat MY, Mir IA, Ul Hussain M, Singh LR, Dar TA. Urea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction. J Biomol Struct Dyn 2022; 41:3659-3666. [PMID: 35315738 DOI: 10.1080/07391102.2022.2053744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Trimethylamine N-oxide (TMAO) is generally accumulated by organisms and cells to cope with denaturing effects of urea/hydrodynamic pressure on proteins and can even reverse misfolded or aggregated proteins so as to sustain proteostasis. However, most of the work regarding this urea-TMAO counteraction has been performed on folded proteins. Compelling evidence of aggregation of intrinsically disordered proteins (IDPs) like tau, α-synuclein, amyloid β etc., by TMAO and its potential to impact various protein processes in absence of stressing agents (such as urea) suggests that the contrary feature of interaction profiles of urea and TMAO maximizes their chances of offsetting the perturbing effects of each other. Recently, our lab observed that TMAO induces aggregation of α-casein, a model IDP. In this context, the present study, for the first time, evaluated urea for its potential to counteract the TMAO-induced aggregation of α-casein. It was observed that, at the biologically relevant ratios of 2:1 or 3:1 (urea:TMAO), urea was able to inhibit TMAO-induced aggregation of α-casein. However, urea did not reverse the effects of TMAO on α-casein. In addition to this, α-casein in presence of 1:1 and 2:1 urea:TMAO working ratios show aggregation-induced cytotoxic effect on HEK-293, Neuro2A and HCT-116 cell lines but not in presence of 3:1 working ratio, as there was no aggregation at all. The study infers that the accumulation of TMAO alone in the cells, in absence of stress (such as urea), might result in loss of conformational flexibility and aggregation of IDPs in TMAO accumulating organisms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Younus Bhat
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, India
| | - Irfan Ahmad Mir
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | | | | | - Tanveer Ali Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, India
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Eronina TB, Mikhaylova VV, Chebotareva NA, Kleymenov SY, Pivovarova AV, Kurganov BI. Combined action of chemical chaperones on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b. Int J Biol Macromol 2022; 203:406-416. [PMID: 35066023 DOI: 10.1016/j.ijbiomac.2022.01.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 01/19/2023]
Abstract
Chemical chaperones are a class of small molecules, which enhance protein stability, folding, inhibit protein aggregation, and are used for long-term storage of therapeutic proteins. The combined action of chemical chaperones trehalose, betaine and lysine on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b (Phb) has been studied. Dynamic light scattering data indicate that the affinity of trehalose to Phb increased in the presence of betaine or lysine at both stages (stage of nucleation and aggregate growth) of enzyme aggregation at 48 °C, in contrast, the affinity of betaine to the enzyme in the presence of lysine remained practically unchanged. According to differential scanning calorimetry and analytical ultracentrifugation data, the mixture of trehalose and betaine stabilized Phb stronger than either of them in total. Moreover, the destabilizing effect of lysine on the enzyme was almost completely compensated by trehalose and only partially by betaine. The main protective effect of the mixtures of osmolytes and lysine is associated with their influence on the dissociation/denaturation stage, which is the rate-limiting one of Phb aggregation. Thus, a pair of chaperones affects the stability, oligomeric state, and aggregation of Phb differently than individual chaperones.
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Affiliation(s)
- Tatiana B Eronina
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia.
| | - Valeriya V Mikhaylova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Natalia A Chebotareva
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Sergey Y Kleymenov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia; Koltsov's Institute of Developmental Biology, Russian Academy of Sciences, Vavilova 26, Moscow 119991, Russia
| | - Anastasia V Pivovarova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Boris I Kurganov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
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9
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Gut microbiota dependent trimethylamine N-oxide aggravates angiotensin II-induced hypertension. Redox Biol 2021; 46:102115. [PMID: 34474396 PMCID: PMC8408632 DOI: 10.1016/j.redox.2021.102115] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota produce Trimethylamine N-oxide (TMAO) by metabolizing dietary phosphatidylcholine, choline, l-carnitine and betaine. TMAO is implicated in the pathogenesis of chronic kidney disease (CKD), diabetes, obesity and atherosclerosis. We test, whether TMAO augments angiotensin II (Ang II)-induced vasoconstriction and hence promotes Ang II-induced hypertension. Plasma TMAO levels were indeed elevated in hypertensive patients, thus the potential pathways by which TMAO mediates these effects were explored. Ang II (400 ng/kg−1min−1) was chronically infused for 14 days via osmotic minipumps in C57Bl/6 mice. TMAO (1%) or antibiotics were given via drinking water. Vasoconstriction of renal afferent arterioles and mesenteric arteries were assessed by microperfusion and wire myograph, respectively. In Ang II-induced hypertensive mice, TMAO elevated systolic blood pressure and caused vasoconstriction, which was alleviated by antibiotics. TMAO enhanced the Ang II-induced acute pressor responses (12.2 ± 1.9 versus 20.6 ± 1.4 mmHg; P < 0.05) and vasoconstriction (32.3 ± 2.6 versus 55.9 ± 7.0%, P < 0.001). Ang II-induced intracellular Ca2+ release in afferent arterioles (147 ± 7 versus 234 ± 26%; P < 0.001) and mouse vascular smooth muscle cells (VSMC, 123 ± 3 versus 157 ± 9%; P < 0.001) increased by TMAO treatment. Preincubation of VSMC with TMAO activated the PERK/ROS/CaMKII/PLCβ3 pathway. Pharmacological inhibition of PERK, ROS, CaMKII and PLCβ3 impaired the effect of TMAO on Ca2+ release. Thus, TMAO facilitates Ang II-induced vasoconstriction, thereby promoting Ang II-induced hypertension, which involves the PERK/ROS/CaMKII/PLCβ3 axis. Orally administered TMAO aggravates Ang II-induced hypertension. Antibiotics alleviate Ang II-induced hypertension by reducing TMAO generation. High concentrations of TMAO constrict afferent arterioles and mesenteric arteries and increase blood pressure. Low concentrations of TMAO enhance Ang II-induced vasoconstriction and acute pressor response via activating PERK/ROS/CaMKII/PLCβ3/Ca2+ pathway.
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10
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Assessing the role of osmolytes on the conformational harmony of islet amyloid polypeptide. Int J Biol Macromol 2020; 164:2569-2582. [DOI: 10.1016/j.ijbiomac.2020.08.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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Ganguly P, Polák J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea–TMAO Solutions. J Phys Chem B 2020; 124:6181-6197. [DOI: 10.1021/acs.jpcb.0c04357] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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12
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Bockus AB, LaBreck CJ, Camberg JL, Collie JS, Seibel BA. Thermal Range and Physiological Tolerance Mechanisms in Two Shark Species from the Northwest Atlantic. THE BIOLOGICAL BULLETIN 2020; 238:131-144. [PMID: 32412839 DOI: 10.1086/708718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Spiny dogfish (Squalus acanthias) and smoothhound (Mustelus canis) sharks in the northwest Atlantic undergo seasonal migrations driven by changes in water temperature. However, the recognized thermal habitats of these regional populations are poorly described. Here, we report the thermal range, catch frequency with bottom temperature, and catch frequency with time of year for both shark species in Narragansett Bay, Rhode Island. Additionally, we describe levels of two thermal stress response indicators, heat-shock protein 70 and trimethylamine N-oxide, with an experimental increase in water temperature from 15 °C to 21 °C. Our results show that S. acanthias can be found in this region year-round and co-occurs with M. canis from June to November. Further, adult S. acanthias routinely inhabits colder waters than M. canis (highest catch frequencies at bottom temperatures of 10 °C and 21 °C, respectively), but both exhibit similar upper thermal ranges in this region (bottom temperatures of 22-23 °C). Additionally, acute exposure to a 6 °C increase in water temperature for 72 hours leads to a nearly threefold increase in heat-shock protein 70 levels in S. acanthias but not M. canis. Therefore, these species display differences in their thermal tolerance and stress response with experimental exposure to 21 °C, a common summer temperature in Narragansett Bay. Further, in temperature-stressed S. acanthias there is no accumulation of trimethylamine N-oxide. At the whole-organism level, elasmobranchs' trimethylamine N-oxide regulatory capacity may be limited by other factors. Alternatively, elasmobranchs may not rely on trimethylamine N-oxide as a primary thermal protective mechanism under the conditions tested. Findings from this study are in contrast with previous research conducted with elasmobranch cells in vitro that showed accumulation of trimethylamine N-oxide after thermal stress and subsequent suppression of the heat-shock protein 70 response.
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13
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Gupta P, Khan FI, Ambreen D, Lai D, Alajmi MF, Hussain A, Islam A, Ahmad F, Hassan MI. Investigation of guanidinium chloride-induced unfolding pathway of sphingosine kinase 1. Int J Biol Macromol 2020; 147:177-186. [PMID: 31917989 DOI: 10.1016/j.ijbiomac.2020.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 01/11/2023]
Abstract
Sphingosine kinase 1 (SphK1) is a lipid kinase which plays vital role in the regulation of varieties of biological processes including, cell growth, apoptosis and mitogenesis. In the present study, we investigated the guanidinium chloride (GdmCl)-induced denaturation of SphK1 at pH 8.0 and 25 °C using two different spectroscopic probes, i.e., mean residue ellipticity at 222 nm ([θ]222) and fluorescence emission maxima (λmax). A significant overlap between the transition curves obtained from both the spectral properties indicate that GdmCl-induced unfolding of SphK1 follows two-state process i.e., Native (N) ⇌ Denatured (D) state. Interestingly, a visible protein aggregation was observed at low concentrations of GdmCl ([GdmCl] ≤ 1.5 M). The analysis of transition curves was done to estimate the thermodynamic parameters associated with the stability of SphK1. To complement our experimental findings, 100 ns molecular dynamics (MD) simulations were performed. Spectroscopic studies together with MD simulations provided mechanistic insights of unfolding pathway of SphK1 along with its stability parameters.
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Affiliation(s)
- Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Dilkash Ambreen
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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14
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Wang QJ, Shen YE, Wang X, Fu S, Zhang X, Zhang YN, Wang RT. Concomitant memantine and Lactobacillus plantarum treatment attenuates cognitive impairments in APP/PS1 mice. Aging (Albany NY) 2020; 12:628-649. [PMID: 31907339 PMCID: PMC6977692 DOI: 10.18632/aging.102645] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
Trimethylamine-N-oxide (TMAO) is a gut microbial metabolite that promotes Alzheimer's disease (AD) progression. Given that probiotics can alleviate AD symptoms by inhibiting the synthesis of TMAO, here we investigated the correlation between TMAO and cognitive deterioration by measuring TMAO levels in the plasma of choline-treated APP/PS1 mice (an AD mouse model) with and without probiotic treatments. We found that declines in L. plantarum in the gut were associated with cognitive impairment. Moreover, 12-weeks of treatment with memantine plus L. plantarum ameliorated cognitive deterioration, decreased Αβ levels in the hippocampus, and protected neuronal integrity and plasticity. These effects were accompanied by reductions in TMAO synthesis and neuroinflammation. These experiments demonstrate that L. plantarum augments the beneficial therapeutic effects of memantine treatment in APP/PS1 mice by remodeling the intestinal microbiota, inhibiting the synthesis of TMAO, and reducing clusterin levels. Our results thus highlight intestinal microbiota as a potential therapeutic target to decrease the risk of AD.
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Affiliation(s)
- Qiu-Jun Wang
- General Practice Department, The Second Affiliated Hospital, Harbin Medical University, Harbin 150086, China
| | - Yue-E Shen
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xin Wang
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin 150081, China
| | - Shuang Fu
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin 150081, China
| | - Xin Zhang
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin 150081, China
| | - Yi-Na Zhang
- Department of Geriatrics, The Second Affiliated Hospital, Harbin Medical University, Harbin 150086, China
| | - Rui-Tao Wang
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin 150081, China
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15
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Sahle CJ, Schroer MA, Niskanen J, Elbers M, Jeffries CM, Sternemann C. Hydration in aqueous osmolyte solutions: the case of TMAO and urea. Phys Chem Chem Phys 2020; 22:11614-11624. [DOI: 10.1039/c9cp06785j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray Raman scattering spectroscopy and first principles simulations reveal details of the hydration and hydrogen-bond topology of trimethylamine N-oxide (TMAO) and urea in aqueous solutions.
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Affiliation(s)
| | - Martin A. Schroer
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- Hamburg 22607
- Germany
| | - Johannes Niskanen
- Department of Physics and Astronomy
- University of Turku
- FI-20014 Turun Yliopisto
- Finland
| | - Mirko Elbers
- Fakultät Physik/DELTA
- Technische Universität Dortmund
- 44221 Dortmund
- Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- Hamburg 22607
- Germany
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16
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Bruce EE, van der Vegt NFA. Molecular Scale Solvation in Complex Solutions. J Am Chem Soc 2019; 141:12948-12956. [DOI: 10.1021/jacs.9b03469] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ellen E. Bruce
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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17
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Unfoldness of the denatured state of proteins determines urea: Methylamine counteraction in terms of Gibbs free energy of stabilization. Int J Biol Macromol 2019; 132:666-676. [PMID: 30946906 DOI: 10.1016/j.ijbiomac.2019.03.236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/30/2019] [Accepted: 03/31/2019] [Indexed: 11/22/2022]
Abstract
In many tissues and organisms, large amount of urea gets accumulated to maintain osmotic balance. To evade the threatening impact of urea, living organisms accumulate methylamines, a class of osmolytes, in proportion of 2:1 (urea:methylamine). To understand underlying cause(s) for protein-specific counteraction behavior, thermodynamic stability (ΔGDo) of three disulfide free proteins (myoglobin, bovine cytochrome c and barstar) in the mixture of urea and methylamine has been estimated from guanidinium chloride-(GdmCl) driven denaturation curves. Using the experimentally measured values of ΔGDo obtained in the presence of individual methylamines and urea, we predicted the molar ratio of urea and a methylamine required for perfect compensation for each of the proteins. Interestingly, for all proteins studied, a similar ratio has been observed for perfect compensation. The predicted ratio for perfect compensation in terms of thermodynamic parameters was about 2:1 M ratio of urea to methylamine. Furthermore, a partial counteraction was observed in the myoglobin and barstar. However, for bovine cytochrome c, perfect compensation was observed in both GdmCl- and heat-driven denaturations. Our observations clearly suggest that the counteraction phenomenon depends on the extent of the unfolding of the denatured states of proteins.
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18
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Walker EJ, Bettinger JQ, Welle KA, Hryhorenko JR, Ghaemmaghami S. Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome. Proc Natl Acad Sci U S A 2019; 116:6081-6090. [PMID: 30846556 PMCID: PMC6442572 DOI: 10.1073/pnas.1819851116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The stability of proteins influences their tendency to aggregate, undergo degradation, or become modified in cells. Despite their significance to understanding protein folding and function, quantitative analyses of thermodynamic stabilities have been mostly limited to soluble proteins in purified systems. We have used a highly multiplexed proteomics approach, based on analyses of methionine oxidation rates, to quantify stabilities of ∼10,000 unique regions within ∼3,000 proteins in human cell extracts. The data identify lysosomal and extracellular proteins as the most stable ontological subsets of the proteome. We show that the stability of proteins impacts their tendency to become oxidized and is globally altered by the osmolyte trimethylamine N-oxide (TMAO). We also show that most proteins designated as intrinsically disordered retain their unfolded structure in the complex environment of the cell. Together, the data provide a census of the stability of the human proteome and validate a methodology for global quantitation of folding thermodynamics.
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Affiliation(s)
- Ethan J Walker
- Department of Biology, University of Rochester, NY 14627
- Department of Biochemistry, University of Rochester Medical Center, NY 14627
| | | | - Kevin A Welle
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, NY 14627
| | - Jennifer R Hryhorenko
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, NY 14627
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, NY 14627;
- Mass Spectrometry Resource Laboratory, University of Rochester Medical Center, NY 14627
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19
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Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction of denaturant-induced protein unfolding is a general property of stabilizing agents. Phys Chem Chem Phys 2018; 20:29389-29398. [PMID: 30451257 DOI: 10.1039/c8cp04421j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DSC measurements on RNase A at neutral pH show that five stabilizing agents, namely trimethylamine N-oxide, glucose, sucrose, betaine and sodium sulfate, can counteract the destabilizing action of urea, sodium perchlorate, guanidinium chloride and guanidinium thiocyanate. This is an important finding inferring that counteraction has a common physical origin, regardless of the chemical differences among the stabilizing agents and among the destabilizing ones. A rationalization is provided grounded on the following line of reasoning: (a) the decrease in solvent-excluded volume effect is the main stabilizing contribution of the native state; (b) its magnitude increases on increasing the density of the aqueous solution; (c) the density increases significantly in the ternary solutions containing water, a stabilizing agent and a destabilizing one, as indicated by the present experimental data.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia - 80126 Napoli, Italy.
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20
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Li J, Hilser VJ. Assessing Allostery in Intrinsically Disordered Proteins With Ensemble Allosteric Model. Methods Enzymol 2018; 611:531-557. [PMID: 30471699 DOI: 10.1016/bs.mie.2018.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intrinsically disordered (ID) proteins have been shown to play a major role in signaling in a broad range of proteins, using a process known as allostery, wherein the protein can integrate one or a number of inputs to regulate its function. The disorder-mediated allostery can be understood energetically with ensemble allosteric model (EAM). In this model, the molecule without effectors is considered as an ensemble of preexisting conformations, and effector binding is treated as an energetic perturbation of the ensemble to redistribute the microstates that are favorable or unfavorable to the second binding partner. As it only considers the intrinsic energetics of the system and does not depend on a crystallographic structure, it can be applied to both structured proteins, ID proteins, and mixed proteins with both structured and ID domains. Simulation with EAM on the basis of experimental data can help quantitatively explain experimental observations, as well as to make predictions to direct future research. This has recently been illustrated with the case of human glucocorticoid receptor, a multidomain transcription factor that contains both structured and disordered regions. In this chapter, we describe the assays for measuring the transcriptional activity, binding affinity to cognate DNA, conformational stability, either on single domain or tandem coupled domains in the GR two-domain isoforms. We then explain how these data are utilized as input parameters or constraints in the EAM for quantitative estimates of stabilities and coupling energies for each domain through global minimization method.
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Affiliation(s)
- Jing Li
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Vincent J Hilser
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Department of Biology, Johns Hopkins University, Baltimore, MD, United States.
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21
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Moosa MM, Ferreon JC, Ferreon ACM. Ligand interactions and the protein order-disorder energetic continuum. Semin Cell Dev Biol 2018; 99:78-85. [PMID: 29753880 DOI: 10.1016/j.semcdb.2018.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 04/05/2018] [Accepted: 05/04/2018] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins as computationally predicted account for ∼1/3 of eukaryotic proteomes, are involved in a plethora of biological functions, and have been linked to several human diseases as a result of their dysfunctions. Here, we present a picture wherein an energetic continuum describes protein structural and conformational propensities, ranging from the hyperstable folded proteins on one end to the hyperdestabilized and sometimes functionally disordered proteins on the other. We distinguish between proteins that are folding-competent but disordered because of marginal stability and those that are disordered due mainly to the absence of folding code-completing structure-determining interactions, and postulate that disordered proteins that are unstructured by way of partial population of protein denatured states represent a sizable proportion of the proteome.
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Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
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22
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Roles of osmolytes in protein folding and aggregation in cells and their biotechnological applications. Int J Biol Macromol 2018; 109:483-491. [DOI: 10.1016/j.ijbiomac.2017.12.100] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022]
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23
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Dar MA, Wahiduzzaman, Islam A, Hassan MI, Ahmad F. Counteraction of the deleterious effects of urea on structure and stability of mammalian kidney proteins by osmolytes. Int J Biol Macromol 2018; 107:1659-1667. [DOI: 10.1016/j.ijbiomac.2017.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/26/2017] [Accepted: 10/05/2017] [Indexed: 11/29/2022]
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24
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Rani A, Venkatesu P. Changing relations between proteins and osmolytes: a choice of nature. Phys Chem Chem Phys 2018; 20:20315-20333. [DOI: 10.1039/c8cp02949k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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25
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Ganguly P, Boserman P, van der Vegt NFA, Shea JE. Trimethylamine N-oxide Counteracts Urea Denaturation by Inhibiting Protein–Urea Preferential Interaction. J Am Chem Soc 2017; 140:483-492. [DOI: 10.1021/jacs.7b11695] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pritam Ganguly
- Department
of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Pablo Boserman
- Department
of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut
für Anorganische und Physikalische Chemie, Center of Smart
Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße
10, Darmstadt 64287, Germany
| | - Joan-Emma Shea
- Department
of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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26
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Phromsiri P, Gerling RR, Blose JM. The effects of a neutral cosolute on the B to Z transition for DNA duplexes incorporating both CG and CA steps. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:690-703. [PMID: 29185909 DOI: 10.1080/15257770.2017.1388395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the cell, nearly 40% of the volume is occupied by macromolecular crowding agents and smaller osmolytes accumulate in response to environmental stresses. Of particular interest is the influence of osmolytes on the transition of the right-handed B-DNA to the left-handed Z-DNA. Due to the correlation between Z-DNA formation potential and regions of active transcription, Z-DNA is believed to serve a vital role in the transcription process, and changes in osmolyte concentration may influence transcription as a part of the stress response. We utilized circular dichroism spectroscopy to monitor changes in conformation of DNA duplexes containing a full-turn of Z-DNA in the presence and absence of PEG 200. We used PEG 200 as a model neutral cosolute. Sodium ion titrations revealed that PEG 200 influenced the folding of Z-DNA compared to dilute solution conditions by decreasing the free energy of folding, increasing folding cooperativity, and decreasing the in vitro [Na+] and Δn required for folding for all sequences tested, even those that included 40% CA steps instead of the classic CG repeats. Moreover, the presence of 40% PEG 200 induced the Z-form conformation in sequences that would not fully adopt the Z-form structure even in 5 M NaCl. These results suggest that osmolytes may play a significant role in supporting the transient formation of Z-DNA in vivo, and that sequences containing a significant amounts of CA instead of CG repeats may more favorably adopt the Z-conformation as a part of binding and regulatory processes than had been previously considered.
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Affiliation(s)
- Pakinee Phromsiri
- a The College at Brockport , State University of New York, Department of Chemistry and Biochemistry , Brockport , NY
| | - Rebecca R Gerling
- a The College at Brockport , State University of New York, Department of Chemistry and Biochemistry , Brockport , NY
| | - Joshua M Blose
- a The College at Brockport , State University of New York, Department of Chemistry and Biochemistry , Brockport , NY
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27
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Rabbani G. WITHDRAWN: Role of osmolytes in protein folding and aggregation in cells and its applications in biotechnology. Int J Biol Macromol 2017:S0141-8130(17)32827-1. [PMID: 29137994 DOI: 10.1016/j.ijbiomac.2017.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Gulam Rabbani
- Department of Medical Biotechnology, YeungNam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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28
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van der Vegt NFA, Nayar D. The Hydrophobic Effect and the Role of Cosolvents. J Phys Chem B 2017; 121:9986-9998. [DOI: 10.1021/acs.jpcb.7b06453] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nico F. A. van der Vegt
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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29
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Rani A, Taha M, Venkatesu P, Lee MJ. Coherent Experimental and Simulation Approach To Explore the Underlying Mechanism of Denaturation of Stem Bromelain in Osmolytes. J Phys Chem B 2017; 121:6456-6470. [DOI: 10.1021/acs.jpcb.7b01776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjeeta Rani
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Mohamed Taha
- Department
of Chemistry, College of Science, Sultan Qaboos University, PO Box 36, PC 123 Muscat, Oman
| | | | - Ming- Jer Lee
- Department of Chemical Engineering, National Taiwan University of Science & Technology, Taipei 10607, Taiwan
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30
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Hong J, Xiong S. TMAO-Protein Preferential Interaction Profile Determines TMAO's Conditional In Vivo Compatibility. Biophys J 2017; 111:1866-1875. [PMID: 27806268 DOI: 10.1016/j.bpj.2016.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/16/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) exemplifies how Nature uses the solute effect as a simple chemical strategy to cope with hydrodynamic pressure or urea stress to maintain proteostasis. It is a gut-microbe-generated metabolite that strongly promotes the development of atherosclerosis. It remains unclear how TMAO exerts its effects. In this study, we experimentally characterized the profile of the preferential interaction potential of TMAO with proteins, a thermodynamic key to understanding the effects of TMAO on protein processes and the distinction of TMAO among osmolytes. TMAO is thus found to be highly preferentially excluded from most types of protein surface, which explains why TMAO is a strong globular protein stabilizer and identifies the dominant stabilizing factor as the unfavorable interaction of TMAO with the hydrophobic surface exposed upon unfolding. We dissected the mechanism of the counteracting effects of TMAO and urea: the contrary feature of the interaction profiles of the two solutes maximizes the possibility for them to offset each other's perturbing effect on protein processes. The interaction profile also predicts that TMAO promotes aggregation of amyloidogenic intrinsically disordered peptide, as demonstrated here in Aβ42, and that TMAO has a strong potential to impact protein processes in the absence of stressors. Our data suggest that although TMAO is an evolutionally selected chemical chaperone for some organisms or organs, its compatibility in vivo is conditional and determined by its interaction profile with biopolymers and the nature of the essential biopolymer processes. Our thermodynamic framework plus the TMAO-protein interaction profile provides a basis for exploring the broad biological significance of TMAO, including its pathological impact in the absence of stressors. We argue for the general importance of controlling in vivo background solutes and the pathological significance of a control failure.
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Affiliation(s)
- Jiang Hong
- School of Life Sciences, Shanghai University, Shanghai, China; Experimental Center for Life Sciences, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Shangqin Xiong
- School of Life Sciences, Shanghai University, Shanghai, China
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31
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Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates. Biophys J 2016; 110:1280-90. [PMID: 27028638 DOI: 10.1016/j.bpj.2015.12.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/08/2015] [Accepted: 12/31/2015] [Indexed: 12/19/2022] Open
Abstract
Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments.
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32
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Ganguly P, van der Vegt NFA, Shea JE. Hydrophobic Association in Mixed Urea-TMAO Solutions. J Phys Chem Lett 2016; 7:3052-9. [PMID: 27440555 DOI: 10.1021/acs.jpclett.6b01344] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The formation of a hydrophobic core is key to the folding and resulting function of most proteins in the cell. In several organisms, as well as in many in vitro experiments, protein folding is modulated by the presence of osmolytes, but the mechanism by which hydrophobic association occurs is not well understood. We present a study of the solvation thermodynamics of hydrophobic self-association in mixed-osmolyte urea-TMAO solutions, with neopentane as a model hydrophobic molecule. Using molecular dynamics simulations and the Kirkwood-Buff theory of solutions, we show that a sensitive balance between the TMAO-water and the TMAO-urea interactions governs the osmolyte-induced changes in hydrophobic association in mixed urea-TMAO solutions. This balance must be correctly incorporated in force-field parametrization because hydrophobic association can be either enhanced or prevented all together by slightly increasing or decreasing the osmolyte-water affinity and osmolyte-osmolyte self-affinity of TMAO molecules.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara , Santa Barbara, California 93106, United States
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33
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Fonin AV, Uversky VN, Kuznetsova IM, Turoverov KK. Protein folding and stability in the presence of osmolytes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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34
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Mikles DC, Bhat V, Schuchardt BJ, McDonald CB, Farooq A. Effect of osmolytes on the binding of EGR1 transcription factor to DNA. Biopolymers 2016; 103:74-87. [PMID: 25269753 DOI: 10.1002/bip.22556] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 08/16/2014] [Accepted: 08/19/2014] [Indexed: 11/11/2022]
Abstract
Osmolytes play a key role in maintaining protein stability and mediating macromolecular interactions within the intracellular environment of the cell. Herein, we show that osmolytes such as glycerol, sucrose, and polyethylene glycol 400 (PEG400) mitigate the binding of early growth response (protein) 1 (EGR1) transcription factor to DNA in a differential manner. Thus, while physiological concentrations of glycerol only moderately reduce the binding affinity, addition of sucrose and PEG400 is concomitant with a loss in the binding affinity by an order of magnitude. This salient observation suggests that EGR1 is most likely subject to conformational equilibrium and that the osmolytes exert their effect via favorable interactions with the unliganded conformation. Consistent with this notion, our analysis reveals that while EGR1 displays rather high structural stability in complex with DNA, the unliganded conformation becomes significantly destabilized in solution. In particular, while liganded EGR1 adopts a well-defined arc-like architecture, the unliganded protein samples a comparatively large conformational space between two distinct states that periodically interconvert between an elongated rod-like shape and an arc-like conformation on a submicrosecond time scale. Consequently, the ability of osmolytes to favorably interact with the unliganded conformation so as to stabilize it could account for the negative effect of osmotic stress on EGR1-DNA interaction observed here. Taken together, our study sheds new light on the role of osmolytes in modulating a key protein-DNA interaction.
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Affiliation(s)
- David C Mikles
- Department of Biochemistry and Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL, 33136
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35
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Comez L, Paolantoni M, Corezzi S, Lupi L, Sassi P, Morresi A, Fioretto D. Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide. Phys Chem Chem Phys 2016; 18:8881-9. [PMID: 26958663 DOI: 10.1039/c5cp04357c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy. and Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - M Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - S Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - L Lupi
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - P Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - A Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - D Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota. mBio 2016; 7:e02210-15. [PMID: 27048804 PMCID: PMC4817264 DOI: 10.1128/mbio.02210-15] [Citation(s) in RCA: 481] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The gut microbiota is found to be strongly associated with atherosclerosis (AS). Resveratrol (RSV) is a natural phytoalexin with anti-AS effects; however, its mechanisms of action remain unclear. Therefore, we sought to determine whether the anti-AS effects of RSV were related to changes in the gut microbiota. We found that RSV attenuated trimethylamine-N-oxide (TMAO)-induced AS in ApoE−/− mice. Meanwhile, RSV decreased TMAO levels by inhibiting commensal microbial trimethylamine (TMA) production via gut microbiota remodeling in mice. Moreover, RSV increased levels of the genera Lactobacillus and Bifidobacterium, which increased the bile salt hydrolase activity, thereby enhancing bile acid (BA) deconjugation and fecal excretion in C57BL/6J and ApoE−/− mice. This was associated with a decrease in ileal BA content, repression of the enterohepatic farnesoid X receptor (FXR)-fibroblast growth factor 15 (FGF15) axis, and increased cholesterol 7a-hydroxylase (CYP7A1) expression and hepatic BA neosynthesis. An FXR antagonist had the same effect on FGF15 and CYP7A1 expression as RSV, while an FXR agonist abolished RSV-induced alterations in FGF15 and CYP7A1 expression. In mice treated with antibiotics, RSV neither decreased TMAO levels nor increased hepatic BA synthesis. Additionally, RSV-induced inhibition of TMAO-caused AS was also markedly abolished by antibiotics. In conclusion, RSV attenuated TMAO-induced AS by decreasing TMAO levels and increasing hepatic BA neosynthesis via gut microbiota remodeling, and the BA neosynthesis was partially mediated through the enterohepatic FXR-FGF15 axis. Recently, trimethylamine-N-oxide (TMAO) has been identified as a novel and independent risk factor for promoting atherosclerosis (AS) partially through inhibiting hepatic bile acid (BA) synthesis. The gut microbiota plays a key role in the pathophysiology of TMAO-induced AS. Resveratrol (RSV) is a natural phytoalexin with prebiotic benefits. A growing body of evidence supports the hypothesis that phenolic phytochemicals with poor bioavailability are possibly acting primarily through remodeling of the gut microbiota. The current study showed that RSV attenuated TMAO-induced AS by decreasing TMAO levels and increasing hepatic BA neosynthesis via gut microbiota remodeling. And RSV-induced hepatic BA neosynthesis was partially mediated through downregulating the enterohepatic farnesoid X receptor-fibroblast growth factor 15 axis. These results offer new insights into the mechanisms responsible for RSV’s anti-AS effects and indicate that the gut microbiota may become an interesting target for pharmacological or dietary interventions to decrease the risk of developing cardiovascular diseases.
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37
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Tang C, Lew S, He D. Using a second-order differential model to fit data without baselines in protein isothermal chemical denaturation. Protein Sci 2016; 25:898-904. [PMID: 26757366 DOI: 10.1002/pro.2878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/06/2022]
Abstract
In vitro protein stability studies are commonly conducted via thermal or chemical denaturation/renaturation of protein. Conventional data analyses on the protein unfolding/(re)folding require well-defined pre- and post-transition baselines to evaluate Gibbs free-energy change associated with the protein unfolding/(re)folding. This evaluation becomes problematic when there is insufficient data for determining the pre- or post-transition baselines. In this study, fitting on such partial data obtained in protein chemical denaturation is established by introducing second-order differential (SOD) analysis to overcome the limitations that the conventional fitting method has. By reducing numbers of the baseline-related fitting parameters, the SOD analysis can successfully fit incomplete chemical denaturation data sets with high agreement to the conventional evaluation on the equivalent completed data, where the conventional fitting fails in analyzing them. This SOD fitting for the abbreviated isothermal chemical denaturation further fulfills data analysis methods on the insufficient data sets conducted in the two prevalent protein stability studies.
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Affiliation(s)
- Chuanning Tang
- Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, Beijing Normal University, Beijing, 100875, China
| | - Scott Lew
- Neotein Therapeutics, New York, New York, 10706, USA
| | - Dacheng He
- Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, Beijing Normal University, Beijing, 100875, China
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Yang Y, Mu Y, Li W. Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Phys Chem Chem Phys 2016; 18:22081-8. [DOI: 10.1039/c6cp01205a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins with a higher hydrophobic content are better protected by TMAO against the deleterious effect of urea.
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Affiliation(s)
- Yanmei Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
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Collins HL, Drazul-Schrader D, Sulpizio AC, Koster PD, Williamson Y, Adelman SJ, Owen K, Sanli T, Bellamine A. L-Carnitine intake and high trimethylamine N-oxide plasma levels correlate with low aortic lesions in ApoE(-/-) transgenic mice expressing CETP. Atherosclerosis 2015; 244:29-37. [PMID: 26584136 DOI: 10.1016/j.atherosclerosis.2015.10.108] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Dietary l-carnitine can be metabolized by intestinal microbiota to trimethylamine, which is absorbed by the gut and further oxidized to trimethylamine N-oxide (TMAO) in the liver. TMAO plasma levels have been associated with atherosclerosis development in ApoE(-/-) mice. To better understand the mechanisms behind this association, we conducted in vitro and in vivo studies looking at the effect of TMAO on different steps of atherosclerotic disease progression. METHODS J774 mouse macrophage cells were used to evaluate the effect of TMAO on foam cell formation. Male ApoE(-/-) mice transfected with human cholesteryl ester transfer protein (hCETP) were fed l-carnitine and/or methimazole, a flavin monooxygenase 3 (FMO3) inhibitor that prevents the formation of TMAO. Following 12 week treatment, l-carnitine and TMAO plasma levels, aortic lesion development, and lipid profiles were determined. RESULTS TMAO at concentrations up to 10-fold the Cmax reported in humans did not affect in vitro foam cell formation. In ApoE(-/-)mice expressing hCETP, high doses of l-carnitine resulted in a significant increase in plasma TMAO levels. Surprisingly, and independently from treatment group, TMAO levels inversely correlated with aortic lesion size in both aortic root and thoracic aorta. High TMAO levels were found to significantly correlate with smaller aortic lesion area. Plasma lipid and lipoprotein levels did not change with treatment nor with TMAO levels, suggesting that the observed effects on lesion area were independent from lipid changes. CONCLUSION These findings suggest that TMAO slows aortic lesion formation in this mouse model and may have a protective effect against atherosclerosis development in humans.
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40
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Eschmann NA, Do TD, LaPointe NE, Shea JE, Feinstein SC, Bowers MT, Han S. Tau Aggregation Propensity Engrained in Its Solution State. J Phys Chem B 2015; 119:14421-32. [PMID: 26484390 PMCID: PMC4645975 DOI: 10.1021/acs.jpcb.5b08092] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
A peptide fragment of the human tau
protein which stacks to form
neat cross β-sheet fibrils, resembling that found in pathological
aggregation, 273GKVQIINKKLDL284 (here
“R2/WT”), was modified with a spin-label at the N-terminus.
With the resulting peptide, R2/G273C-SL, we probed events at time
scales spanning seconds to hours after aggregation is initiated using
transmission electron microscopy (TEM), thioflavin T (THT) fluorescence,
ion mobility mass spectrometry (IMMS), electron paramagnetic resonance
(EPR), and Overhauser dynamic nuclear polarization (ODNP) to determine
if deliberate changes to its conformational states and population
in solution influence downstream propensity to form fibrillar aggregates.
We find varying solution conditions by adding the osmolyte urea or
TMAO, or simply using different buffers (acetate buffer, phosphate
buffer, or water), produces significant differences in early monomer/dimer
populations and conformations. Crucially, these characteristics of
the peptide in solution state before aggregation
is initiated dictate the fibril formation propensity after aggregation. We conclude the driving forces that accelerate aggregation,
when heparin is added, do not override the subtle intra- or interprotein
interactions induced by the initial solvent conditions. In other words,
the balance of protein–protein vs protein–solvent interactions
present in the initial solution conditions is a critical driving force
for fibril formation.
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Affiliation(s)
- Neil A Eschmann
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Thanh D Do
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Nichole E LaPointe
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Stuart C Feinstein
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
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41
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Rahman S, Warepam M, Singh LR, Dar TA. A current perspective on the compensatory effects of urea and methylamine on protein stability and function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:129-36. [PMID: 26095775 DOI: 10.1016/j.pbiomolbio.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/16/2022]
Abstract
Urea is a strong denaturant and inhibits many enzymes but is accumulated intracellularly at very high concentrations (up to 3-4 M) in mammalian kidney and in many marine fishes. It is known that the harmful effects of urea on the macromolecular structure and function is offset by the accumulation of an osmolytic agent called methylamine. Intracellular concentration of urea to methylamines falls in the ratio of 2:1 to 3:2 (molar ratio). At this ratio, the thermodynamic effects of urea and methylamines on protein stability and function are believed to be algebraically additive. The mechanism of urea-methylamine counteraction has been widely investigated on various approaches including, thermodynamic, structural and functional aspects. Recent advances have also revealed atomic level insights of counteraction and various molecular dynamic simulation studies have yielded significant molecular level informations on the interaction between urea and methylamines with proteins. It is worthwhile that urea-methylamine system not only plays pivotal role for the survival and functioning of the renal medullary cells but also is a key osmoregulatory component of the marine elasmobranchs, holocephalans and coelacanths. Therefore, it is important to combine all discoveries and discuss the developments in context to physiology of the mammalian kidney and adaptation of the marine organisms. In this article we have for the first time reviewed all major developments on urea-counteraction systems to date. We have also discussed about other additional urea-counteraction systems discovered so far including urea-NaCl, urea-myoinsoitol and urea-molecular chaperone systems. Insights for the possible future research have also been highlighted.
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Affiliation(s)
- Safikur Rahman
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Marina Warepam
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Laishram R Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Tanveer Ali Dar
- Clinical Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir 190006, India.
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42
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Warepam M, Singh LR. Osmolyte mixtures have different effects than individual osmolytes on protein folding and functional activity. Arch Biochem Biophys 2015; 573:77-83. [PMID: 25817170 DOI: 10.1016/j.abb.2015.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 03/11/2015] [Accepted: 03/20/2015] [Indexed: 10/23/2022]
Abstract
Osmolytes are small organic molecules accumulated by organisms under stress conditions to protect macromolecular structure and function. In the present study, we have investigated the effect of several binary osmolyte mixtures on the protein folding/stability and function of RNase-A. For this, we have measured ΔGD(o) (Gibbs free energy change at 25°C) and specific activity of RNase-A mediated hydrolysis of cytidine 2'-3' cyclic monophosphate in the presence and absence of individual and osmolyte mixtures. It was found that the osmolyte mixtures have different effect on protein stability and function than that of individual osmolytes. Refolding studies of RNase-A in the presence of osmolyte mixtures and individual osmolytes also revealed that osmolyte mixtures have a poor refolding efficiency relative to the individual osmolytes.
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Affiliation(s)
- Marina Warepam
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
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43
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Ganguly P, Hajari T, Shea JE, van der Vegt NFA. Mutual Exclusion of Urea and Trimethylamine N-Oxide from Amino Acids in Mixed Solvent Environment. J Phys Chem Lett 2015; 6:581-5. [PMID: 26262470 DOI: 10.1021/jz502634k] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We study the solvation of amino acids in pure-osmolyte and mixed-osmolyte urea and trimethylamine N-oxide (TMAO) solutions using molecular dynamics simulations. Analysis of Kirkwood-Buff integrals between the solution components provides evidence that in the mixed osmolytic solution, both urea and TMAO are mutually excluded from the amino acid surface, accompanied by an increase in osmolyte-osmolyte aggregation. Similar observations are made in simulations of a model protein backbone, represented by triglycine, and suggest that TMAO stabilizes proteins under urea denaturation conditions by effectively removing urea from the protein surface. The effects of the mixed osmolytes on the solvation of the amino acids and the backbone are found to be highly nonlinear in terms of the effects of the individual osmolytes and independent of differences in the strength of the TMAO-water interactions, as observed with different TMAO force fields.
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Affiliation(s)
- Pritam Ganguly
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Timir Hajari
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | | | - Nico F A van der Vegt
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
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44
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Abstract
Virtually all taxa use osmolytes to protect cells against biochemical stress. Osmolytes often occur in mixtures, such as the classical combination of urea with TMAO (trimethylamine N-oxide) in cartilaginous fish or the cocktail of at least six different osmolytes in the kidney. The concentration patterns of osmolyte mixtures found in vivo make it likely that synergy between them plays an important role. Using statistical mechanical n-component Kirkwood-Buff theory, we show from first principles that synergy in protein-osmolyte systems can arise from two separable sources: (1) mutual alteration of protein surface solvation and (2) effects mediated through bulk osmolyte chemical activities. We illustrate both effects in a four-component system with the experimental example of the unfolding of a notch ankyrin domain in urea-TMAO mixtures, which make urea a less effective denaturant and TMAO a more effective stabilizer. Protein surface effects are primarily responsible for this synergy. The specific patterns of surface solvation point to denatured state expansion as the main factor, as opposed to direct competition.
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Affiliation(s)
- Jörg Rösgen
- Department of Biochemistry
and Molecular Biology, Penn State University
College of Medicine, Hershey, Pennsylvania 17033, United States
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45
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Bruździak P, Adamczak B, Kaczkowska E, Czub J, Stangret J. Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies. Phys Chem Chem Phys 2015; 17:23155-64. [DOI: 10.1039/c5cp03065j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Stabilizing osmolytes are not always preferentially excluded and can interact with the protein surface in two ways: indirectly or directly.
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Affiliation(s)
- P. Bruździak
- Department of Physical Chemistry
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - B. Adamczak
- Department of Physical Chemistry
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - E. Kaczkowska
- Department of Physical Chemistry
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - J. Czub
- Department of Physical Chemistry
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
| | - J. Stangret
- Department of Physical Chemistry
- Gdansk University of Technology
- 80-233 Gdansk
- Poland
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46
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Shen H, Cheng W, Zhang FS. Structural conservation of the short α-helix in modified higher and lower polarity water solutions. RSC Adv 2015. [DOI: 10.1039/c4ra14739a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Which conformation is preferred when the polarity of water molecules is scaled byEP=ELJ+S2EC?
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Affiliation(s)
- Hao Shen
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
| | - Wei Cheng
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
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47
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Hunger J, Ottosson N, Mazur K, Bonn M, Bakker HJ. Water-mediated interactions between trimethylamine-N-oxide and urea. Phys Chem Chem Phys 2015; 17:298-306. [DOI: 10.1039/c4cp02709d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The osmoprotectant trimethylamine-N-oxide (TMAO) interacts with the protein denaturant urea via the hydrogen-bonded water network.
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Affiliation(s)
| | | | - Kamila Mazur
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
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48
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Portillo A, Hashemi M, Zhang Y, Breydo L, Uversky VN, Lyubchenko YL. Role of monomer arrangement in the amyloid self-assembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:218-28. [PMID: 25542374 DOI: 10.1016/j.bbapap.2014.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/24/2014] [Accepted: 12/10/2014] [Indexed: 02/05/2023]
Abstract
Assembly of amyloid proteins into aggregates requires the ordering of the monomers in oligomers and especially in such highly organized structures as fibrils. This ordering is accompanied by structural transitions leading to the formation of ordered β-structural motifs in proteins and peptides lacking secondary structures. To characterize the effect of the monomer arrangements on the aggregation process at various stages, we performed comparative studies of the yeast prion protein Sup35 heptapeptide (GNNQQNY) along with its dimeric form CGNNQQNY-(d-Pro)-G-GNNQQNY. The (d-Pro)-G linker in this construct is capable of adopting a β-turn, facilitating the assembly of the dimer into the dimeric antiparallel hairpin structure (AP-hairpin). We applied Atomic Force Microscopy (AFM) techniques to follow peptide-peptide interactions at the single molecule level, to visualize the morphology of aggregates formed by both constructs, thioflavin T (ThT) fluorescence to follow the aggregation kinetics, and circular dichroism (CD) spectroscopy to characterize the secondary structure of the constructs. The ThT fluorescence data showed that the AP-hairpin aggregation kinetics is insensitive to the external environment such as ionic strength and pH contrary to the monomers the kinetics of which depends dramatically on the ionic strength and pH. The AFM topographic imaging revealed that AP-hairpins primarily assemble into globular aggregates, whereas linear fibrils are primary assemblies of the monomers suggesting that both constructs follow different aggregation pathways during the self-assembly. These morphological differences are in line with the AFM force spectroscopy experiments and CD spectroscopy measurements, suggesting that the AP-hairpin is structurally rigid regardless of changes of environmental factors.
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Affiliation(s)
- Alexander Portillo
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Leonid Breydo
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33647, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33647, USA; Department of Biological Science, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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49
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Moosa MM, Ferreon ACM, Deniz AA. Forced folding of a disordered protein accesses an alternative folding landscape. Chemphyschem 2014; 16:90-4. [PMID: 25345588 DOI: 10.1002/cphc.201402661] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Indexed: 11/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) are involved in diverse cellular functions. Many IDPs can interact with multiple binding partners, resulting in their folding into alternative ligand-specific functional structures. For such multi-structural IDPs, a key question is whether these multiple structures are fully encoded in the protein sequence, as is the case in many globular proteins. To answer this question, here we employed a combination of single-molecule and ensemble techniques to compare ligand-induced and osmolyte-forced folding of α-synuclein. Our results reveal context-dependent modulation of the protein's folding landscape, suggesting that the codes for the protein's native folds are partially encoded in its primary sequence, and are completed only upon interaction with binding partners. Our findings suggest a critical role for cellular interactions in expanding the repertoire of folds and functions available to disordered proteins.
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Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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Gasymov OK, Abduragimov AR, Glasgow BJ. Restoration of structural stability and ligand binding after removal of the conserved disulfide bond in tear lipocalin. Biochem Biophys Res Commun 2014; 452:1004-8. [PMID: 25223802 PMCID: PMC4219327 DOI: 10.1016/j.bbrc.2014.09.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 11/20/2022]
Abstract
Disulfide bonds play diverse structural and functional roles in proteins. In tear lipocalin (TL), the conserved sole disulfide bond regulates stability and ligand binding. Probing protein structure often involves thiol selective labeling for which removal of the disulfide bonds may be necessary. Loss of the disulfide bond may destabilize the protein so strategies to retain the native state are needed. Several approaches were tested to regain the native conformational state in the disulfide-less protein. These included the addition of trimethylamine N-oxide (TMAO) and the substitution of the Cys residues of disulfide bond with residues that can either form a potential salt bridge or others that can create a hydrophobic interaction. TMAO stabilized the protein relaxed by removal of the disulfide bond. In the disulfide-less mutants of TL, 1.0M TMAO increased the free energy change (ΔG(0)) significantly from 2.1 to 3.8kcal/mol. Moderate recovery was observed for the ligand binding tested with NBD-cholesterol. Because the disulfide bond of TL is solvent exposed, the substitution of the disulfide bond with a potential salt bridge or hydrophobic interaction did not stabilize the protein. This approach should work for buried disulfide bonds. However, for proteins with solvent exposed disulfide bonds, the use of TMAO may be an excellent strategy to restore the native conformational states in disulfide-less analogs of the proteins.
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Affiliation(s)
- Oktay K Gasymov
- Departments of Pathology and Ophthalmology and Jules Stein Eye Institute, University California at Los Angeles, CA 90095, United States.
| | - Adil R Abduragimov
- Departments of Pathology and Ophthalmology and Jules Stein Eye Institute, University California at Los Angeles, CA 90095, United States
| | - Ben J Glasgow
- Departments of Pathology and Ophthalmology and Jules Stein Eye Institute, University California at Los Angeles, CA 90095, United States.
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