1
|
Florea CM, Rosu R, Moldovan R, Vlase L, Toma V, Decea N, Baldea I, Filip GA. The impact of chronic Trimethylamine N-oxide administration on liver oxidative stress, inflammation, and fibrosis. Food Chem Toxicol 2024; 184:114429. [PMID: 38176578 DOI: 10.1016/j.fct.2023.114429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
TMAO, a gut microbiota derived byproduct, has been associated with various cardiometabolic diseases by promoting oxidative stress and inflammation. The liver is the main organ for TMAO production and chronic exposure to high doses of TMAO could alter its function. In this study, we evaluated the effect of chronic exposure of high TMAO doses on liver oxidative stress, inflammation, and fibrosis. TMAO was administered daily via gastric gavage to laboratory rats for 3 months. Blood was drawn for the quantification of TMAO, and liver tissues were harvested for the assessment of oxidative stress (MDA, GSH, GSSG, GPx, CAT, and 8-oxo-dG) and inflammation by quantification of IL-1α, TNF-α, IL-10, TGF-β, NOS and COX-2 expression. The evaluation of fibrosis was made by Western blot analysis of α-SMA and Collagen-3 protein expression. Histological investigation and immunohistochemical staining of iNOS were performed in order to assess the liver damage. After 3 months of TMAO exposure, TMAO serum levels enhanced in parallel with increases in MDA and GSSG levels in liver tissue and lower values of GSH and GSH/GSSG ratio as well as a decrease in GPx and CAT activities. Inflammation was also highlighted, with enhanced iNOS, COX-2, and IL-10 expression, without structural changes and without induction of liver fibrosis.
Collapse
Affiliation(s)
- Cristian Marius Florea
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Rosu
- Fifth Department of Internal Medicine, Cardiology Clinic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Remus Moldovan
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Vlad Toma
- Department of Molecular Biology and Biotechnologies, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Department of Experimental Biology and Biochemistry, Institute of Biological Research, branch of NIRDBS, Cluj-Napoca, Romania; Center for Systems Biology, Biodiversity and Bioresources "3B", Babeș-Bolyai University, Cluj-Napoca, Romania.
| | - Nicoleta Decea
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Baldea
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Gabriela Adriana Filip
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| |
Collapse
|
2
|
Kanoh S, Noma T, Ito H, Tsureyama M, Funabara D. Myosin light chain of shark fast skeletal muscle exhibits intrinsic urea-resistibility. Sci Rep 2023; 13:4909. [PMID: 36966252 PMCID: PMC10039937 DOI: 10.1038/s41598-023-32228-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 03/24/2023] [Indexed: 03/27/2023] Open
Abstract
Marine elasmobranch fish contain urea, a protein denaturant, in their bodies. The urea-trimethylamine N-oxide (TMAO) counteraction mechanism contributes to urea-resistibility, where TMAO compensates for protein denaturation by urea. However, previous studies revealed that shark fast skeletal muscle myosin exhibits native activity at physiological urea concentrations in the absence of TMAO, suggesting that shark myosin has urea-resistibility. In this study, we compared the urea-resistibility of myosin alkali light chains (A1-LC and A2-LC) from banded houndshark and carp by examining the α-helical content at various urea concentrations. The α-helical content of carp myosin A1-LC and A2-LC gradually decreased as urea concentrations increased to 2 M. In contrast, the α-helical content of banded houndshark A1-LC increased between 0 and 0.5 M urea, and the α-helical content of A2-LC remained constant until 0.5 M urea. We determined the full-length sequences of the banded houndshark myosin light chains (A1-LC, A2-LC and DTNB-LC). Hydrophilicity analysis revealed that the N-terminal region (residues 28-34) of A1-LC from banded houndshark is more hydrophilic than the corresponding region of A1-LC from carp. These findings support the notion that shark myosin exhibits urea-resistibility independent of the urea-TMAO counteraction mechanism.
Collapse
Affiliation(s)
- Satoshi Kanoh
- Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Takayuki Noma
- Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
- Kogakkan High School, Ise, Mie, 516-8577, Japan
| | - Hirotaka Ito
- Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
- ASGEN Pharmaceutical Co., Ltd., Mizunami, Gifu, 509-6104, Japan
| | - Masatomo Tsureyama
- Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
- Kracie Foods, Ltd., Minato, Tokyo, 108-8080, Japan
| | - Daisuke Funabara
- Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
| |
Collapse
|
3
|
TMAO to the rescue of pathogenic protein variants. Biochim Biophys Acta Gen Subj 2022; 1866:130214. [PMID: 35902028 DOI: 10.1016/j.bbagen.2022.130214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a chemical chaperone found in various organisms including humans. Various studies unveiled that it is an excellent protein-stabilizing agent, and induces folding of unstructured proteins. It is also well established that it can counteract the deleterious effects of urea, salt, and hydrostatic pressure on macromolecular integrity. There is also existence of large body of data regarding its ability to restore functional deficiency of various mutant proteins or pathogenic variants by correcting misfolding defects and inhibiting the formation of high-order toxic protein oligomers. Since an important class of human disease called "protein conformational disorders" is due to protein misfolding and/or formation of high-order oligomers, TMAO stands as a promising molecule for the therapeutic intervention of such diseases. The present review has been designed to gather a comprehensive knowledge of the TMAO's effect on the functional restoration of various mutants, identify its shortcomings and explore its potentiality as a lead molecule. Future prospects have also been suitably incorporated.
Collapse
|
4
|
Loo RL, Chan Q, Nicholson JK, Holmes E. Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine- N-oxide. J Proteome Res 2022; 21:560-589. [PMID: 35142516 DOI: 10.1021/acs.jproteome.1c00851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA-TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.
Collapse
Affiliation(s)
- Ruey Leng Loo
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Jeremy K Nicholson
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, United Kingdom
| | - Elaine Holmes
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Nutrition Research, Department of Metabolism, Nutrition and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| |
Collapse
|
5
|
Kumari K, Warepam M, Bansal AK, Dar TA, Uversky VN, Singh LR. The gut metabolite, trimethylamine N-oxide inhibits protein folding by affecting cis-trans isomerization and induces cell cycle arrest. Cell Mol Life Sci 2021; 79:12. [PMID: 34953141 PMCID: PMC11072907 DOI: 10.1007/s00018-021-04087-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022]
Abstract
Trimethylamine N-Oxide (TMAO) is an important metabolite, which is derived from choline, betaine, and carnitine in various organisms. In humans, it is synthesized through gut microbiota and is abundantly found in serum and cerebrospinal fluid (CSF). Although TMAO is a stress protectant especially in urea-rich organisms, it is an atherogenic agent in humans and is associated with various diseases. Studies have also unveiled its exceptional role in protein folding and restoration of mutant protein functions. However, most of these data were obtained from studies carried on fast-folding proteins. In the present study, we have investigated the effect of TMAO on the folding behavior of a well-characterized protein with slow folding kinetics, carbonic anhydrase (CA). We discovered that TMAO inhibits the folding of this protein via its effect on proline cis-trans isomerization. Furthermore, TMAO is capable of inducing cell cycle arrest. This study highlights the potential role of TMAO in developing proteopathies and associated diseases.
Collapse
Affiliation(s)
- Kritika Kumari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Marina Warepam
- Department of Biotechnology, Manipur University, Manipur, 795003, India
| | - Aniket Kumar Bansal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Tanveer Ali Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
- Institute for Biomedical Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Moscow, Russia
| | | |
Collapse
|
6
|
Gut Metabolite Trimethylamine N-Oxide Protects INS-1 β-Cell and Rat Islet Function under Diabetic Glucolipotoxic Conditions. Biomolecules 2021; 11:biom11121892. [PMID: 34944536 PMCID: PMC8699500 DOI: 10.3390/biom11121892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
Serum accumulation of the gut microbial metabolite trimethylamine N-oxide (TMAO) is associated with high caloric intake and type 2 diabetes (T2D). Impaired pancreatic β-cell function is a hallmark of diet-induced T2D, which is linked to hyperglycemia and hyperlipidemia. While TMAO production via the gut microbiome-liver axis is well defined, its molecular effects on metabolic tissues are unclear, since studies in various tissues show deleterious and beneficial TMAO effects. We investigated the molecular effects of TMAO on functional β-cell mass. We hypothesized that TMAO may damage functional β-cell mass by inhibiting β-cell viability, survival, proliferation, or function to promote T2D pathogenesis. We treated INS-1 832/13 β-cells and primary rat islets with physiological TMAO concentrations and compared functional β-cell mass under healthy standard cell culture (SCC) and T2D-like glucolipotoxic (GLT) conditions. GLT significantly impeded β-cell mass and function by inducing oxidative and endoplasmic reticulum (ER) stress. TMAO normalized GLT-mediated damage in β-cells and primary islet function. Acute 40µM TMAO recovered insulin production, insulin granule formation, and insulin secretion by upregulating the IRE1α unfolded protein response to GLT-induced ER and oxidative stress. These novel results demonstrate that TMAO protects β-cell function and suggest that TMAO may play a beneficial molecular role in diet-induced T2D conditions.
Collapse
|
7
|
Krueger ES, Lloyd TS, Tessem JS. The Accumulation and Molecular Effects of Trimethylamine N-Oxide on Metabolic Tissues: It's Not All Bad. Nutrients 2021; 13:nu13082873. [PMID: 34445033 PMCID: PMC8400152 DOI: 10.3390/nu13082873] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Since elevated serum levels of trimethylamine N-oxide (TMAO) were first associated with increased risk of cardiovascular disease (CVD), TMAO research among chronic diseases has grown exponentially. We now know that serum TMAO accumulation begins with dietary choline metabolism across the microbiome-liver-kidney axis, which is typically dysregulated during pathogenesis. While CVD research links TMAO to atherosclerotic mechanisms in vascular tissue, its molecular effects on metabolic tissues are unclear. Here we report the current standing of TMAO research in metabolic disease contexts across relevant tissues including the liver, kidney, brain, adipose, and muscle. Since poor blood glucose management is a hallmark of metabolic diseases, we also explore the variable TMAO effects on insulin resistance and insulin production. Among metabolic tissues, hepatic TMAO research is the most common, whereas its effects on other tissues including the insulin producing pancreatic β-cells are largely unexplored. Studies on diseases including obesity, diabetes, liver diseases, chronic kidney disease, and cognitive diseases reveal that TMAO effects are unique under pathologic conditions compared to healthy controls. We conclude that molecular TMAO effects are highly context-dependent and call for further research to clarify the deleterious and beneficial molecular effects observed in metabolic disease research.
Collapse
Affiliation(s)
- Emily S. Krueger
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA; (E.S.K.); (T.S.L.)
| | - Trevor S. Lloyd
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA; (E.S.K.); (T.S.L.)
- Medical Education Program, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Jeffery S. Tessem
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA; (E.S.K.); (T.S.L.)
- Correspondence: ; Tel.: +1-801-422-9082
| |
Collapse
|
8
|
Costa Dos Santos G, Renovato-Martins M, de Brito NM. The remodel of the "central dogma": a metabolomics interaction perspective. Metabolomics 2021; 17:48. [PMID: 33969452 PMCID: PMC8106972 DOI: 10.1007/s11306-021-01800-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND In 1957, Francis Crick drew a linear diagram on a blackboard. This diagram is often called the "central dogma." Subsequently, the relationships between different steps of the "central dogma" have been shown to be considerably complex, mostly because of the emerging world of small molecules. It is noteworthy that metabolites can be generated from the diet through gut microbiome metabolism, serve as substrates for epigenetic modifications, destabilize DNA quadruplexes, and follow Lamarckian inheritance. Small molecules were once considered the missing link in the "central dogma"; however, recently they have acquired a central role, and their general perception as downstream products has become reductionist. Metabolomics is a large-scale analysis of metabolites, and this emerging field has been shown to be the closest omics associated with the phenotype and concomitantly, the basis for all omics. AIM OF REVIEW Herein, we propose a broad updated perspective for the flux of information diagram centered in metabolomics, including the influence of other factors, such as epigenomics, diet, nutrition, and the gut- microbiome. KEY SCIENTIFIC CONCEPTS OF REVIEW Metabolites are the beginning and the end of the flux of information.
Collapse
Affiliation(s)
- Gilson Costa Dos Santos
- Laboratory of NMR Metabolomics, IBRAG, Department of Genetics, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
| | - Mariana Renovato-Martins
- Department of Cellular and Molecular Biology, IB, Federal Fluminense University, Niterói, 24210-200, Brazil
| | - Natália Mesquita de Brito
- Laboratory of Cellular and Molecular Pharmacology, IBRAG, Department of Cell Biology, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
| |
Collapse
|
9
|
Sharma GS, Krishna S, Khan S, Dar TA, Khan KA, Singh LR. Protecting thermodynamic stability of protein: The basic paradigm against stress and unfolded protein response by osmolytes. Int J Biol Macromol 2021; 177:229-240. [PMID: 33607142 DOI: 10.1016/j.ijbiomac.2021.02.102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 01/10/2023]
Abstract
Organic osmolytes are known to play important role in stress protection by stabilizing macromolecules and suppressing harmful effects on functional activity. There is existence of several reports in the literature regarding their effects on structural, functional and thermodynamic aspects of many enzymes and the interaction parameters with proteins have been explored. Osmolytes are compatible with enzyme function and therefore, can be accumulated up to several millimolar concentrations. From the thermodynamic point of view, osmolyte raises mid-point of thermal denaturation (Tm) of proteins while having no significant effect on ΔGD° (free energy change at physiological condition). Unfavorable interaction with the peptide backbone due to preferential hydration is the major driving force for folding of unfolded polypeptide in presence of osmolyte. However, the thermodynamic basis of stress protection and origin of compatibility paradigm has been a debatable issue. In the present manuscript, we attempt to elaborate the origin of stress protection and compatibility paradigm of osmolytes based on the effect on thermodynamic stability of proteins. We also infer that protective effects of osmolytes on ΔGD° (of proteins) could also indicate its potential involvement in unfolded protein response and overall stress biology on macromolecular level.
Collapse
Affiliation(s)
- Gurumayum Suraj Sharma
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, India
| | - Snigdha Krishna
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Sheeza Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Tanveer A Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, J&K, India
| | - Khurshid A Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | | |
Collapse
|
10
|
VanDelinder V, Sickafoose I, Imam ZI, Ko R, Bachand GD. The effects of osmolytes on in vitro kinesin-microtubule motility assays. RSC Adv 2020; 10:42810-42815. [PMID: 35514903 PMCID: PMC9057942 DOI: 10.1039/d0ra08148e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023] Open
Abstract
The gliding motility of microtubule filaments has been used to study the biophysical properties of kinesin motors, as well as being used in a variety of nanotechnological applications. While microtubules are generally stabilized in vitro with paclitaxel (Taxol®), osmolytes such as polyethylene glycol (PEG) and trimethylamine N-oxide (TMAO) are also able to inhibit depolymerization over extended periods of time. High concentrations of TMAO have also been reported to reversibly inhibit kinesin motility of paclitaxel-stabilized microtubules. Here, we examined the effects of the osmolytes PEG, TMAO, and glycerol on stabilizing microtubules during gliding motility on kinesin-coated substrates. As previously observed, microtubule depolymerization was inhibited in a concentration dependent manner by the addition of the different osmolytes. Kinesin-driven motility also exhibited concentration dependent effects with the addition of the osmolytes, specifically reducing the velocity, increasing rates of pinning, and altering trajectories of the microtubules. These data suggest that there is a delicate balance between the ability of osmolytes to stabilize microtubules without inhibiting motility. Overall, these findings provide a more comprehensive understanding of how osmolytes affect the dynamics of microtubules and kinesin motors, and their interactions in crowded environments.
Collapse
Affiliation(s)
- Virginia VanDelinder
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque NM USA
| | - Ian Sickafoose
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque NM USA
| | - Zachary I Imam
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque NM USA
| | - Randy Ko
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque NM USA
| | - George D Bachand
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque NM USA
| |
Collapse
|
11
|
The roles and applications of chaotropes and kosmotropes in industrial fermentation processes. World J Microbiol Biotechnol 2020; 36:89. [PMID: 32507915 DOI: 10.1007/s11274-020-02865-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
Chaotropicity has long been recognised as a property of some compounds. Chaotropes tend to disrupt non-covalent interactions in biological macromolecules (e.g. proteins and nucleic acids) and supramolecular assemblies (e.g. phospholipid membranes). This results in the destabilisation and unfolding of these macromolecules and assemblies. Unsurprisingly, these compounds are typically harmful to living cells since they act against multiple targets, comprising cellular integrity and function. Kosmotropes are the opposite of chaotropes and these compounds promote the ordering and rigidification of biological macromolecules and assemblies. Since many biological macromolecules have optimum levels of flexibility, kosmotropes can also inhibit their activity and can be harmful to cells. Some products of industrial fermentations, most notably alcohols, are chaotropic. This property can be a limiting factor on rates of production and yields. It has been hypothesised that the addition of kosmotropes may mitigate the chaotropicity of some fermentation products. Some microbes naturally adapt to chaotropic environments by producing kosmotropic compatible solutes. Exploitation of this in industrial fermentations has been hampered by scientific and economic issues. The cost of the kosmotropes and their removal during purification needs to be considered. We lack a complete understanding of the chemistry of chaotropicity and a robust, quantitative framework for estimating overall chaotropicities of mixtures. This makes it difficult to predict the amount of kosmotrope required to neutralise the chaotropicity. This review considers examples of industrial fermentations where chaotropicity is an issue and suggests possible mitigations.
Collapse
|
12
|
Knierbein M, Held C, Hölzl C, Horinek D, Paulus M, Sadowski G, Sternemann C, Nase J. Density variations of TMAO solutions in the kilobar range: Experiments, PC-SAFT predictions, and molecular dynamics simulations. Biophys Chem 2019; 253:106222. [PMID: 31421516 DOI: 10.1016/j.bpc.2019.106222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/12/2023]
Abstract
We present measurements, molecular dynamics (MD) simulations, and predictions using Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) of the density of aqueous solutions in a pressure range from 1 bar to 5000 bar, a pressure regime that is highly relevant for both biochemical applications and the fundamental understanding of solvation. The accurate determination of density data of pressurized solutions remains challenging. We determined relative density changes from the variations in X-ray absorption through the sample and developed a new water parameter set for PC-SAFT modeling that is appropriate for high pressure conditions in the kilobar regime. As a showcase, we studied trimethylamine N-oxide (TMAO) solutions and demonstrated that their compressibility decreases with the TMAO content. This result is linked to the stabilizing effect of TMAO on the local H-bond network of water. Experiments and calculations, which represent two independent methods, are in very good agreement and are in accordance with results of force field molecular dynamics simulations of the same systems.
Collapse
Affiliation(s)
- Michael Knierbein
- Technische Universität Dortmund, Laboratory of Thermodynamics, D-44221 Dortmund, Germany
| | - Christoph Held
- Technische Universität Dortmund, Laboratory of Thermodynamics, D-44221 Dortmund, Germany
| | - Christoph Hölzl
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Michael Paulus
- Technische Universität Dortmund, Fakultät Physik/DELTA, D-44221 Dortmund, Germany
| | - Gabriele Sadowski
- Technische Universität Dortmund, Laboratory of Thermodynamics, D-44221 Dortmund, Germany
| | - Christian Sternemann
- Technische Universität Dortmund, Fakultät Physik/DELTA, D-44221 Dortmund, Germany
| | - Julia Nase
- Technische Universität Dortmund, Fakultät Physik/DELTA, D-44221 Dortmund, Germany.
| |
Collapse
|
13
|
Al-Ayoubi SR, Schummel PH, Cisse A, Seydel T, Peters J, Winter R. Osmolytes modify protein dynamics and function of tetrameric lactate dehydrogenase upon pressurization. Phys Chem Chem Phys 2019; 21:12806-12817. [PMID: 31165827 DOI: 10.1039/c9cp02310k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present a study of the combined effects of natural cosolvents (TMAO, glycine, urea) and pressure on the activity of the tetrameric enzyme lactate dehydrogenase (LDH). To this end, high-pressure stopped-flow methodology in concert with fast UV/Vis spectroscopic detection of product formation was applied. To reveal possible pressure effects on the stability and dynamics of the enzyme, FTIR spectroscopic and neutron scattering measurements were carried out. In neat buffer solution, the catalytic turnover number of the enzyme, kcat, increases up to 1000 bar, the pressure range where dissociation of the tetrameric species to dimers sets in. Accordingly, we obtain a negative activation volume, ΔV# = -45.3 mL mol-1. Further, the enzyme substrate complex has a larger volume compared to the enzyme and substrate in the unbound state. The neutron scattering data show that changes in the fast internal dynamics of the enzyme are not responsible for the increase of kcat upon compression. Whereas the magnitude of kcat is similar in the presence of the osmolytes, the pressure of deactivation is modulated by the addition of cosolvents. TMAO and glycine increase the pressure of deactivation, and in accordance with the observed stabilizing effect both cosolvents exhibit against denaturation and/or dissociation of proteins. While urea does not markedly affect the magnitude of the Michaelis constant, KM, both 1 M TMAO and 1 M glycine exhibit smaller KM values of about 0.07 mM and 0.05 mM below about 1 kbar. Such positive effect on the substrate affinity could be rationalized by the effect the two cosolutes impose on the thermodynamic activities of the reactants, which reflect changes in water-mediated intermolecular interactions. Our data show that the intracellular milieu, i.e., the solution conditions that have evolved, may be sufficient to maintain enzymatic activity under extreme environmental conditions, including the whole pressure range encountered on Earth.
Collapse
Affiliation(s)
- Samy R Al-Ayoubi
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
| | | | | | | | | | | |
Collapse
|
14
|
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.
Collapse
|
15
|
Childers CL, Storey KB. Purification and characterization of a urea sensitive lactate dehydrogenase from skeletal muscle of the African clawed frog, Xenopus laevis. J Comp Physiol B 2019; 189:271-281. [PMID: 30631901 DOI: 10.1007/s00360-018-1200-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/09/2018] [Accepted: 12/17/2018] [Indexed: 11/27/2022]
Abstract
The African clawed frog, Xenopus laevis endures whole body dehydration which can increase its reliance on anaerobic glycolysis for energy production. This makes the regulation of the terminal enzyme of glycolysis, lactate dehydrogenase (LDH), crucial to stress survival. We investigated the enzymatic properties and posttranslational modification state of purified LDH from the skeletal muscle of control and dehydrated (30% total body water loss) X. laevis. LDH from the muscle of dehydrated frogs showed a 93% reduction in phosphorylation on threonine residues and an 80% reduction of protein nitrosylation. LDH from dehydrated muscle also showed a 74% lower Vmax in the pyruvate oxidizing direction and a 78% decrease in Vmax in the lactate reducing direction along with a 33% lower Km for pyruvate and a 40% higher Km for lactate. In the presence of higher levels of urea and molecular crowding by polyethylene glycol, used to mimic conditions in the cells of dehydrated animals, the Km values of control and dehydrated LDH demonstrated opposite responses. In the pyruvate oxidizing direction, control muscle LDH was unaffected by these additives, whereas the affinity for pyruvate dropped further for LDH from dehydrated muscle. The opposite effect was more pronounced in the lactate reducing direction as control LDH showed an increased affinity for lactate, whereas LDH from dehydrated animals showed a further reduction in affinity. The physiological consequences of dehydration-induced LDH regulation appear to poise the enzyme towards lactate production when urea levels are high and lactate catabolism when urea levels are low, perhaps helping to maintain glycolysis under dehydrating conditions whilst providing for the ability to recycle lactate upon rehydration.
Collapse
Affiliation(s)
- Christine L Childers
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, Canada
| | - Kenneth B Storey
- Department of Biology and Chemistry, Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
| | | |
Collapse
|
17
|
Julius K, Al-Ayoubi SR, Paulus M, Tolan M, Winter R. The effects of osmolytes and crowding on the pressure-induced dissociation and inactivation of dimeric LADH. Phys Chem Chem Phys 2018; 20:7093-7104. [DOI: 10.1039/c7cp08242h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Compatible osmolytes are able to efficiently modulate the oligomeric state, stability and activity of enzymes at high pressures.
Collapse
Affiliation(s)
- Karin Julius
- Fakultät Physik/DELTA
- TU Dortmund University
- 44221 Dortmund
- Germany
| | - Samy R. Al-Ayoubi
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Michael Paulus
- Fakultät Physik/DELTA
- TU Dortmund University
- 44221 Dortmund
- Germany
| | - Metin Tolan
- Fakultät Physik/DELTA
- TU Dortmund University
- 44221 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| |
Collapse
|
18
|
Enhanced stability of kinesin-1 as a function of temperature. Biochem Biophys Res Commun 2017; 493:1318-1321. [PMID: 28986254 DOI: 10.1016/j.bbrc.2017.09.172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 09/30/2017] [Indexed: 11/21/2022]
Abstract
Kinesin-1 is a mechanochemical enzyme which mediates long distance intracellular cargo transport along microtubules in a wide variety of eukaryotic cells. Kinesin is also relatively easy to purify and shows robust function in vitro, leading to numerous proposals for using the kinesin-1/microtubule system for nanoscale transport in engineered devices. However, kinesin in vitro shows signs of degradation at ∼30 °C which severely limits its usability in biomimetic engineering. Notably, kinesin-1 functions robustly in animal cells at body temperatures as high as 40 °C which suggests that kinesin functioning can be stabilized beyond what is observed in vitro. The present study investigated the effect of trimethylamine N-oxide (TMAO) as a potential heat-protecting agent for kinesin function and microtubule stability. We show that at a concentration of 200 mM, TMAO can indeed stabilize kinesin-based motility up to a little over 50 °C and that such motility can be sustained for extended periods of time. Our results suggest that intracellular crowding (mimicked in vitro by TMAO) can indeed stabilize kinesin-1 at high temperatures and helps resolve a long standing discrepancy between thermal stability of kinesin-1 observed in vivo and in vitro. Moreover, when considered together with our previous report that kinesin-1 can function well down to near-freezing conditions, this study establishes kinesin-1/microtubule motility as a thermally viable engineering platform.
Collapse
|
19
|
Some of the most interesting things we know, and don't know, about the biochemistry and physiology of elasmobranch fishes (sharks, skates and rays). Comp Biochem Physiol B Biochem Mol Biol 2016; 199:21-28. [DOI: 10.1016/j.cbpb.2016.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/28/2015] [Accepted: 03/07/2016] [Indexed: 11/21/2022]
|
20
|
Yancey PH, Siebenaller JF. Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms. ACTA ACUST UNITED AC 2016; 218:1880-96. [PMID: 26085665 DOI: 10.1242/jeb.114355] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Organisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic 'piezolyte' or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation.
Collapse
Affiliation(s)
- Paul H Yancey
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Joseph F Siebenaller
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
21
|
Seldin MM, Meng Y, Qi H, Zhu W, Wang Z, Hazen SL, Lusis AJ, Shih DM. Trimethylamine N-Oxide Promotes Vascular Inflammation Through Signaling of Mitogen-Activated Protein Kinase and Nuclear Factor-κB. J Am Heart Assoc 2016; 5:JAHA.115.002767. [PMID: 26903003 PMCID: PMC4802459 DOI: 10.1161/jaha.115.002767] [Citation(s) in RCA: 550] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background The choline‐derived metabolite trimethylamine N‐oxide (TMAO) has been demonstrated to contribute to atherosclerosis and is associated with coronary artery disease risk. Methods and Results We explored the impact of TMAO on endothelial and smooth muscle cell function in vivo, focusing on disease‐relevant outcomes for atherogenesis. Initially, we observed that aortas of LDLR−/− mice fed a choline diet showed elevated inflammatory gene expression compared with controls. Acute TMAO injection at physiological levels was sufficient to induce the same inflammatory markers and activate the well‐known mitogen‐activated protein kinase, extracellular signal–related kinase, and nuclear factor‐κB signaling cascade. These observations were recapitulated in primary human aortic endothelial cells and vascular smooth muscle cells. We also found that TMAO promotes recruitment of activated leukocytes to endothelial cells. Through pharmacological inhibition, we further showed that activation of nuclear factor‐κB signaling was necessary for TMAO to induce inflammatory gene expression in both of these relevant cell types as well as endothelial cell adhesion of leukocytes. Conclusions Our results suggest a likely contributory mechanism for TMAO‐dependent enhancement in atherosclerosis and cardiovascular risks.
Collapse
Affiliation(s)
- Marcus M Seldin
- Department of Medicine, Cardiology Division at the University of California, Los Angeles, CA
| | - Yonghong Meng
- Department of Medicine, Cardiology Division at the University of California, Los Angeles, CA
| | - Hongxiu Qi
- Department of Medicine, Cardiology Division at the University of California, Los Angeles, CA
| | - WeiFei Zhu
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH
| | - Zeneng Wang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH
| | - Stanley L Hazen
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH
| | - Aldons J Lusis
- Department of Medicine, Cardiology Division at the University of California, Los Angeles, CA
| | - Diana M Shih
- Department of Medicine, Cardiology Division at the University of California, Los Angeles, CA
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Rahman S, Rehman MT, Singh LR, Warepam M, Ahmad F, Dar TA. Salt potentiates methylamine counteraction system to offset the deleterious effects of urea on protein stability and function. PLoS One 2015; 10:e0119597. [PMID: 25793733 PMCID: PMC4368626 DOI: 10.1371/journal.pone.0119597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/14/2015] [Indexed: 11/21/2022] Open
Abstract
Cellular methylamines are osmolytes (low molecular weight organic compounds) believed to offset the urea’s harmful effects on the stability and function of proteins in mammalian kidney and marine invertebrates. Although urea and methylamines are found at 2:1 molar ratio in tissues, their opposing effects on protein structure and function have been questioned on several grounds including failure to counteraction or partial counteraction. Here we investigated the possible involvement of cellular salt, NaCl, in urea-methylamine counteraction on protein stability and function. We found that NaCl mediates methylamine counteracting system from no or partial counteraction to complete counteraction of urea’s effect on protein stability and function. These conclusions were drawn from the systematic thermodynamic stability and functional activity measurements of lysozyme and RNase-A. Our results revealed that salts might be involved in protein interaction with charged osmolytes and hence in the urea-methylamine counteraction.
Collapse
Affiliation(s)
- Safikur Rahman
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Tabish Rehman
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Laishram R. Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Marina Warepam
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Tanveer Ali Dar
- Clinical Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir, India
- * E-mail:
| |
Collapse
|
24
|
Luong TQ, Winter R. Combined pressure and cosolvent effects on enzyme activity – a high-pressure stopped-flow kinetic study on α-chymotrypsin. Phys Chem Chem Phys 2015; 17:23273-8. [DOI: 10.1039/c5cp03529e] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pressure enhances the hydrolysis of peptides catalysed by α-CT, which is efficiently and differently modulated by chaotropic and kosmotropic cosolvents.
Collapse
Affiliation(s)
- Trung Quan Luong
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44221 Dortmund
- Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44221 Dortmund
- Germany
| |
Collapse
|
25
|
Structural characteristic of the initial unfolded state on refolding determines catalytic efficiency of the folded protein in presence of osmolytes. PLoS One 2014; 9:e109408. [PMID: 25313668 PMCID: PMC4196897 DOI: 10.1371/journal.pone.0109408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/29/2014] [Indexed: 11/19/2022] Open
Abstract
Osmolytes are low molecular weight organic molecules accumulated by organisms to assist proper protein folding, and to provide protection to the structural integrity of proteins under denaturing stress conditions. It is known that osmolyte-induced protein folding is brought by unfavorable interaction of osmolytes with the denatured/unfolded states. The interaction of osmolyte with the native state does not significantly contribute to the osmolyte-induced protein folding. We have therefore investigated if different denatured states of a protein (generated by different denaturing agents) interact differently with the osmolytes to induce protein folding. We observed that osmolyte-assisted refolding of protein obtained from heat-induced denatured state produces native molecules with higher enzyme activity than those initiated from GdmCl- or urea-induced denatured state indicating that the structural property of the initial denatured state during refolding by osmolytes determines the catalytic efficiency of the folded protein molecule. These conclusions have been reached from the systematic measurements of enzymatic kinetic parameters (Km and kcat), thermodynamic stability (Tm and ΔHm) and secondary and tertiary structures of the folded native proteins obtained from refolding of various denatured states (due to heat-, urea- and GdmCl-induced denaturation) of RNase-A in the presence of various osmolytes.
Collapse
|
26
|
Levy-Sakin M, Berger O, Feibish N, Sharon N, Schnaider L, Shmul G, Amir Y, Buzhansky L, Gazit E. The influence of chemical chaperones on enzymatic activity under thermal and chemical stresses: common features and variation among diverse chemical families. PLoS One 2014; 9:e88541. [PMID: 24520396 PMCID: PMC3919781 DOI: 10.1371/journal.pone.0088541] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups.
Collapse
Affiliation(s)
- Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Or Berger
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Nir Feibish
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Noa Sharon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Lee Schnaider
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shmul
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Yaniv Amir
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ludmila Buzhansky
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| |
Collapse
|
27
|
Khan S, Bano Z, Singh LR, Hassan MI, Islam A, Ahmad F. Testing the ability of non-methylamine osmolytes present in kidney cells to counteract the deleterious effects of urea on structure, stability and function of proteins. PLoS One 2013; 8:e72533. [PMID: 24039776 PMCID: PMC3767660 DOI: 10.1371/journal.pone.0072533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Human kidney cells are under constant urea stress due to its urine concentrating mechanism. It is believed that the deleterious effect of urea is counteracted by methylamine osmolytes (glycine betaine and glycerophosphocholine) present in kidney cells. A question arises: Do the stabilizing osmolytes, non-methylamines (myo-inositol, sorbitol and taurine) present in the kidney cells also counteract the deleterious effects of urea? To answer this question, we have measured structure, thermodynamic stability (ΔG D (o)) and functional activity parameters (K m and k cat) of different model proteins in the presence of various concentrations of urea and each non-methylamine osmolyte alone and in combination. We observed that (i) for each protein myo-inositol provides perfect counteraction at 1∶2 ([myo-inositol]:[urea]) ratio, (ii) any concentration of sorbitol fails to refold urea denatured proteins if it is six times less than that of urea, and (iii) taurine regulates perfect counteraction in a protein specific manner; 1.5∶2.0, 1.2∶2.0 and 1.0∶2.0 ([taurine]:[urea]) ratios for RNase-A, lysozyme and α-lactalbumin, respectively.
Collapse
Affiliation(s)
- Sheeza Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Zehra Bano
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Laishram R. Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- * E-mail:
| |
Collapse
|
28
|
Wang D, Zheng ZY, Feng J, Zhan XB, Zhang LM, Wu JR, Lin CC. A high salt tolerant neutral protease from Aspergillus Oryzae: Purification, characterization and kinetic properties. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683813040170] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
29
|
|
30
|
Trischitta F, Faggio C, Torre A. Living with high concentrations of urea: They can! ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojas.2012.21005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
31
|
Sagle LB, Cimatu K, Litosh VA, Liu Y, Flores SC, Chen X, Yu B, Cremer PS. Methyl groups of trimethylamine N-oxide orient away from hydrophobic interfaces. J Am Chem Soc 2011; 133:18707-12. [PMID: 21967088 DOI: 10.1021/ja205106e] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular orientation of trimethylamine N-oxide (TMAO), a powerful protein stabilizer, was explored at aqueous/hydrophobic interfaces using vibrational sum frequency spectroscopy (VSFS). The systems studied included the octadecyltrichlorosilane (OTS)/water interface, which represents an aqueous solution in direct contact with a hydrophobic medium. Surprisingly, the measurements revealed that the methyl groups of TMAO pointed into the aqueous phase and away from the OTS. This orientation may arise from the more hydrophilic nature of methyl groups attached to a strongly electron-withdrawing atom such as a quaternary nitrogen. Additional studies were performed at the air/water interface. This interface showed a high degree of TMAO alignment, but the dangling OH from water was present even at 5 M TAMO. Moreover, the addition of this osmolyte modestly increased the surface tension of the interface. This meant that this species was somewhat depleted at the interface compared to the bulk solution. These findings may have implications for the stabilizing effect of TMAO on proteins. Specifically, the strong hydration required for the methyl groups as well as the oxide moiety should be responsible for the osmolyte's depletion from hydrophobic/aqueous interfaces. Such depletion effects should help stabilize proteins in their folded and native conformations on entropic grounds, although orientational effects may play an additional role.
Collapse
Affiliation(s)
- Laura B Sagle
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77843, USA
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Zhadin N, Callender R. Effect of osmolytes on protein dynamics in the lactate dehydrogenase-catalyzed reaction. Biochemistry 2011; 50:1582-9. [PMID: 21306147 DOI: 10.1021/bi1018545] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Laser-induced temperature jump relaxation spectroscopy was used to probe the effect of osmolytes on the microscopic rate constants of the lactate dehydrogenase-catalyzed reaction. NADH fluorescence and absorption relaxation kinetics were measured for the lactate dehydrogenase (LDH) reaction system in the presence of varying amounts of trimethylamine N-oxide (TMAO), a protein-stabilizing osmolyte, or urea, a protein-destabilizing osmolyte. Trimethylamine N-oxide (TMAO) at a concentration of 1 M strongly increases the rate of hydride transfer, nearly nullifies its activation energy, and also slightly increases the enthalpy of hydride transfer. In 1 M urea, the hydride transfer enthalpy is almost nullified, but the activation energy of the step is not affected significantly. TMAO increases the preference of the closed conformation of the active site loop in the LDH·NAD(+)·lactate complex; urea decreases it. The loop opening rate in the LDH·NADH·pyruvate complex changes its temperature dependence to inverse Arrhenius with TMAO. In this complex, urea accelerates the loop motion, without changing the loop opening enthalpy. A strong, non-Arrhenius decrease in the pyruvate binding rate in the presence of TMAO offers a decrease in the fraction of the open loop, pyruvate binding competent form at higher temperatures. The pyruvate off rate is not affected by urea but decreases with TMAO. Thus, the osmolytes strongly affect the rates and thermodynamics of specific events along the LDH-catalyzed reaction: binding of substrates, loop closure, and the chemical event. Qualitatively, these results can be understood as an osmolyte-induced change in the energy landscape of the protein complexes, shifting the conformational nature of functional substates within the protein ensemble.
Collapse
Affiliation(s)
- Nickolay Zhadin
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | | |
Collapse
|
33
|
Somero GN, Yancey PH. Osmolytes and Cell‐Volume Regulation: Physiological and Evolutionary Principles. Compr Physiol 2011. [DOI: 10.1002/cphy.cp140110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
34
|
Chang YC, Oas TG. Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand. Biochemistry 2010; 49:5086-96. [PMID: 20476778 DOI: 10.1021/bi100222h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.
Collapse
Affiliation(s)
- Yu-Chu Chang
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | |
Collapse
|
35
|
An overview of the importance of conformational flexibility in gene regulation by the transcription factors. JOURNAL OF BIOPHYSICS 2010; 2009:210485. [PMID: 20169123 PMCID: PMC2821642 DOI: 10.1155/2009/210485] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 11/18/2009] [Accepted: 11/30/2009] [Indexed: 11/18/2022]
Abstract
A number of proteins with intrinsically disordered (ID) regions/domains are reported to be found disproportionately higher in transcription factors. Available evidences suggest that presence of ID region/domain within a transcription factor plays an important role in its biological functions. These ID sequences provide large flexible surfaces that can allow them to make more efficient physical and functional interactions with their target partners. Since transcription factors regulate expression of target genes by interacting with specific coregulatory proteins, these ID regions/domains can be used as a platform for such large macromolecular interactions, and may represent a mechanism for regulation of cellular processes. The precise structural basis for the function of these ID regions/domains of the transcription factors remains to be determined. In the recent years there has been growing evidence suggesting that an induced fit-like process leads to imposition of folded functional structure in these ID domains on which large multiprotein complexes are built. These multiprotein complexes may eventually dictate the final outcome of the gene regulation by the transcription factors.
Collapse
|
36
|
Jamal S, Poddar NK, Singh LR, Dar TA, Rishi V, Ahmad F. Relationship between functional activity and protein stability in the presence of all classes of stabilizing osmolytes. FEBS J 2009; 276:6024-32. [PMID: 19765077 DOI: 10.1111/j.1742-4658.2009.07317.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the effects of stabilizing osmolytes (low molecular mass organic compounds that raise the midpoint of thermal denaturation) on the stability and function of RNase-A under physiological conditions (pH 6.0 and 25 degrees C). Measurements of Gibbs free energy change at 25 degrees C (DeltaG(D) degrees ) and kinetic parameters, Michaelis constant (K(m)) and catalytic constant (k(cat)) of the enzyme mediated hydrolysis of cytidine monophosphate, enabled us to classify stabilizing osmolytes into three different classes based on their effects on kinetic parameters and protein stability. (a) Polyhydric alcohols and amino acids and their derivatives do not have significant effects on DeltaG(D) degrees and functional activity (K(m) and k(cat)). (b) Methylamines increase DeltaG(D) degrees and k(cat), but decrease K(m). (c) Sugars increase DeltaG(D) degrees , but decrease both K(m) and k(cat). These findings suggest that, among the stabilizing osmolytes, (a) polyols, amino acids and amino acid derivatives are compatible solutes in terms of both stability and function, (b) methylamines are the best refolders (stabilizers), and (c) sugar osmolytes stabilize the protein, but they apparently do not yield functionally active folded molecules.
Collapse
Affiliation(s)
- Shazia Jamal
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | | | | | | | | | | |
Collapse
|
37
|
|
38
|
Vasudevamurthy MK, Weatherley LR, Lever M. Enzyme stabilization using synthetic compensatory solutes. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500190795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
39
|
Muir TJ, Costanzo JP, Lee RE. Metabolic depression induced by urea in organs of the wood frog, Rana sylvatica: effects of season and temperature. ACTA ACUST UNITED AC 2008; 309:111-6. [PMID: 18273861 DOI: 10.1002/jez.436] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It has long been suspected that urea accumulation plays a key role in the induction or maintenance of metabolic suppression during extended dormancy in animals from diverse taxa. However, little evidence supporting that hypothesis in living systems exists. We measured aerobic metabolism of isolated organs from the wood frog (Rana sylvatica) in the presence or absence of elevated urea at various temperatures using frogs acclimatized to different seasons. The depressive effect of urea on metabolism was not consistent across organs, seasons, or temperatures. None of the organs from summer frogs, which were tested at 20 degrees C, or from winter frogs tested at 4 degrees C were affected by urea treatment. However, liver, stomach, and heart from spring frogs tested at 4 degrees C had significantly lower metabolic rates when treated with urea as compared with control samples. Additionally, when organs from winter frogs were tested at 10 degrees C, metabolism was significantly decreased in urea-treated liver and stomach by approximately 15% and in urea-treated skeletal muscle by approximately 50%. Our results suggest that the presence of urea depresses the metabolism of living organs, and thereby reduces energy expenditure, but its effect varies with temperature and seasonal acclimatization. The impact of our findings may be wide ranging owing to the number of diverse organisms that accumulate urea during dormancy.
Collapse
Affiliation(s)
- Timothy J Muir
- Department of Zoology, Miami University, Oxford, Ohio 45056, USA.
| | | | | |
Collapse
|
40
|
Ortiz-Costa S, Sorenson MM, Sola-Penna M. Betaine protects urea-induced denaturation of myosin subfragment-1. FEBS J 2008; 275:3388-96. [DOI: 10.1111/j.1742-4658.2008.06487.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
Chebotareva NA. Effect of molecular crowding on the enzymes of glycogenolysis. BIOCHEMISTRY (MOSCOW) 2007; 72:1478-90. [DOI: 10.1134/s0006297907130056] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
42
|
Singh LR, Ali Dar T, Haque I, Anjum F, Moosavi-Movahedi AA, Ahmad F. Testing the paradigm that the denaturing effect of urea on protein stability is offset by methylamines at the physiological concentration ratio of 2:1 (urea:methylamines). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1555-62. [DOI: 10.1016/j.bbapap.2007.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 09/14/2007] [Accepted: 09/17/2007] [Indexed: 11/27/2022]
|
43
|
Gulotta M, Qiu L, Desamero R, Rösgen J, Bolen DW, Callender R. Effects of cell volume regulating osmolytes on glycerol 3-phosphate binding to triosephosphate isomerase. Biochemistry 2007; 46:10055-62. [PMID: 17696453 PMCID: PMC2533736 DOI: 10.1021/bi700990d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
During cell volume regulation, intracellular concentration changes occur in both inorganic and organic osmolytes in order to balance the extracellular osmotic stress and maintain cell volume homeostasis. Generally, salt and urea increase the Km's of enzymes and trimethylamine N-oxide (TMAO) counteracts these effects by decreasing Km's. The hypothesis to account for these effects is that urea and salt shift the native state ensemble of the enzyme toward conformers that are substrate-binding incompetent (BI), while TMAO shifts the ensemble toward binding competent (BC) species. Km's are often complex assemblies of rate constants involving several elementary steps in catalysis, so to better understand osmolyte effects we have focused on a single elementary event, substrate binding. We test the conformational shift hypothesis by evaluating the effects of salt, urea, and TMAO on the mechanism of binding glycerol 3-phosphate, a substrate analogue, to yeast triosephosphate isomerase. Temperature-jump kinetic measurements promote a mechanism consistent with osmolyte-induced shifts in the [BI]/[BC] ratio of enzyme conformers. Importantly, salt significantly affects the binding constant through its effect on the activity coefficients of substrate, enzyme, and enzyme-substrate complex, and it is likely that TMAO and urea affect activity coefficients as well. Results indicate that the conformational shift hypothesis alone does not account for the effects of osmolytes on Km's.
Collapse
Affiliation(s)
- Miriam Gulotta
- Department of Biochemistry, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx NY 10461
| | - Linlin Qiu
- Department of Biochemistry, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx NY 10461
| | - Ruel Desamero
- Department of Chemistry, York College, City University of New York, 94-20 Guy R. Brewer Blvd., Jamaica, NY 11451
| | - Jörg Rösgen
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, 5.154 Medical Research Building, Galveston, TX 77555-1052
| | - D. Wayne Bolen
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, 5.154 Medical Research Building, Galveston, TX 77555-1052
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx NY 10461
| |
Collapse
|
44
|
Eronina TB, Chebotareva NA, Kurganov BI. Influence of Osmolytes on Inactivation and Aggregation of Muscle Glycogen Phosphorylase b by Guanidine Hydrochloride. Stimulation of Protein Aggregation under Crowding Conditions. BIOCHEMISTRY (MOSCOW) 2005; 70:1020-6. [PMID: 16266274 DOI: 10.1007/s10541-005-0219-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The effects of the osmolytes trimethylamine-N-oxide (TMAO), betaine, proline, and glycine on the kinetics of inactivation and aggregation of rabbit skeletal muscle glycogen phosphorylase b by guanidine hydrochloride (GuHCl) have been studied. It is shown that the osmolytes TMAO and betaine exhibit the highest protective efficacy against phosphorylase b inactivation. A test system for studying the effects of macromolecular crowding induced by osmolytes on aggregation of proteins is proposed. TMAO and glycine increase the rate of phosphorylase b aggregation induced by GuHCl.
Collapse
Affiliation(s)
- T B Eronina
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
| | | | | |
Collapse
|
45
|
do Couto SG, Oliveira MDS, Alonso A. Dynamics of proteins and lipids in the stratum corneum: Effects of percutaneous permeation enhancers. Biophys Chem 2005; 116:23-31. [PMID: 15911079 DOI: 10.1016/j.bpc.2005.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2004] [Revised: 01/26/2005] [Accepted: 01/26/2005] [Indexed: 10/25/2022]
Abstract
We have spin labeled the stratum corneum (SC) with a lysine specific reagent, succinimidyl-2,2,5,5-tetramethyl-3-pirroline-1-oxyl-carboxylate spin label (SSL), to assess the dynamics and hydration degree of SC proteins by electron paramagnetic resonance (EPR) spectroscopy taking measurements directly from the intact tissue. Treating the SC with two percutaneous penetration enhancers, 8 M urea or 20% (v/v) 1-methyl-2-pyrrolidone (1 MP), destabilizes the proteins thus promoting more mobile and solvent-exposed protein conformations. Upon SC lipid depletion the nitroxide side chain becomes more solvent exposed, suggesting that the removal of hygroscopic substances in the extraction process favors more hydrated protein conformations. On the other hand, the treatments with 8 M urea or 40% (v/v) 1 MP did not alter significantly the fluidity in the SC lipid domain as assessed by the probe 5-doxyl stearic acid; these permeation enhancers, specially 1 MP, seem to increase the probe solubility in the solvent leading to a considerable fraction of spin label to be removed from the lipid domain.
Collapse
|
46
|
Chebotareva NA, Kurganov BI, Livanova NB. Biochemical effects of molecular crowding. BIOCHEMISTRY (MOSCOW) 2005; 69:1239-51. [PMID: 15627378 DOI: 10.1007/s10541-005-0070-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell cytoplasm contains high concentrations of high-molecular-weight components that occupy a substantial part of the volume of the medium (crowding conditions). The effect of crowding on biochemical processes proceeding in the cell (conformational transitions of biomacromolecules, assembling of macromolecular structures, protein folding, protein aggregation, etc.) is discussed in this review. The excluded volume concept, which allows the effects of crowding on biochemical reactions to be quantitatively described, is considered. Experimental data demonstrating the biochemical effects of crowding imitated by both low-molecular-weight and high-molecular-weight crowding agents are summarized.
Collapse
Affiliation(s)
- N A Chebotareva
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia.
| | | | | |
Collapse
|
47
|
Park C, Marqusee S. Probing the high energy states in proteins by proteolysis. J Mol Biol 2004; 343:1467-76. [PMID: 15491624 DOI: 10.1016/j.jmb.2004.08.085] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 08/24/2004] [Accepted: 08/26/2004] [Indexed: 11/29/2022]
Abstract
Unless the native conformation has an unstructured region, proteases cannot effectively digest a protein under native conditions. Digestion must occur from a higher energy form, when at least some part of the protein is exposed to solvent and becomes accessible by proteases. Monitoring the kinetics and denaturant dependence of proteolysis under native conditions yields insight into the mechanism of proteolysis as well as these high-energy conformations. We propose here a generalized approach to exploit proteolysis as a tool to probe high-energy states in proteins. This "native state proteolysis" experiment was carried out on Escherichia coli ribonuclease HI. Mass spectrometry and N-terminal sequencing showed that thermolysin cleaves the peptide bond between Thr92 and Ala93 in an extended loop region of the protein. By comparing the proteolysis rate of the folded protein and a peptidic substrate mimicking the sequence at the cleavage site, the energy required to reach the susceptible state (Delta G(proteolysis)) was determined. From the denaturant dependence of Delta G(proteolysis), we determined that thermolysin digests this protein through a local fluctuation, i.e. localized unfolding with minimal change in solvent assessable surface area. Proteolytic susceptibilities of proteins are discussed based on the finding of this local fluctuation mechanism for proteolysis under native conditions.
Collapse
Affiliation(s)
- Chiwook Park
- Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, CA 94720, USA
| | | |
Collapse
|
48
|
|
49
|
Sebollela A, Louzada PR, Sola-Penna M, Sarone-Williams V, Coelho-Sampaio T, Ferreira ST. Inhibition of yeast glutathione reductase by trehalose: possible implications in yeast survival and recovery from stress. Int J Biochem Cell Biol 2004; 36:900-8. [PMID: 15006642 DOI: 10.1016/j.biocel.2003.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2003] [Revised: 10/09/2003] [Accepted: 10/14/2003] [Indexed: 11/22/2022]
Abstract
Accumulation of trehalose has been implicated in the tolerance of yeast cells to several forms of stress, including heat-shock and high ethanol levels. However, yeast lacking trehalase, the enzyme that degrades trehalose, exhibit poor survival after exposure to stress conditions. This suggests that optimal cell viability also depends on the capacity to rapidly degrade the high levels of trehalose that build up under stress. Here, we initially examined the effects of trehalose on the activity of an important antioxidant enzyme, glutathione reductase (GR), from Saccharomyces cerevisiae. At 25 degrees C, GR was inhibited by trehalose in a dose-dependent manner, with 70% inhibition at 1.5M trehalose. The inhibition was practically abolished at 40 degrees C, a temperature that induces a physiological response of trehalose accumulation in yeast. The inhibition of GR by trehalose was additive to the inhibition caused by ethanol, indicating that enzyme function is drastically affected upon ethanol-induced stress. Moreover, two other yeast enzymes, cytosolic pyrophosphatase and glucose 6-phosphate dehydrogenase, showed temperature dependences on inhibition by trehalose that were similar to the temperature dependence of GR inhibition. These results are discussed in terms of the apparent paradox represented by the induction of enzymes involved in both synthesis and degradation of trehalose under stress, and suggest that the persistence of high levels of trehalose after recovery from stress could lead to the inactivation of important yeast enzymes.
Collapse
Affiliation(s)
- Adriano Sebollela
- Departamento de Bioquímica Médica, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.
| | | | | | | | | | | |
Collapse
|
50
|
Ortiz-Costa S, Sorenson MM, Sola-Penna M. Counteracting effects of urea and methylamines in function and structure of skeletal muscle myosin. Arch Biochem Biophys 2002; 408:272-8. [PMID: 12464281 DOI: 10.1016/s0003-9861(02)00565-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Myosin is an asymmetric protein that comprises two globular heads (S1) and a double-stranded alpha-helical rod. We have investigated the effects of urea and the methylamines trimethylamine oxide (TMA-O) and glycine betaine (betaine) on activity and structure of skeletal muscle myosin. K(+) EDTA ATPase activity of myosin was almost completely inhibited by urea (2M); TMA-O stimulated myosin activity, whereas betaine had no effect. When combined with urea (0-2M), TMA-O or betaine (1 M) effectively protected the ATPase activity of myosin against inhibition. Intrinsic fluorescence measurements showed that in urea or TMA-O (0-2M), there were no shifts in the center of mass of the fluorescence spectrum of myosin, despite a decrease in fluorescence intensity. However, these osmolytes at concentrations above 2M produced a red shift in the emission spectrum. Betaine alone did not alter the center of mass at any concentration tested up to 5.2M. Thus, modifications in ATPase activity induced by low concentrations of solutes (<2M) are not directly correlated with the modifications in myosin structure detected by fluorescence. Both methylamines (>or=1M) were also able to protect myosin structure against urea-induced effects (2-8M). Protection was not observed for S1, supporting the hypothesis that these osmolytes have a biphasic effect on myosin: at lower concentrations there is an effect on the globular portion (S1), and at higher concentrations there is an effect on the coiled-coil (rod) portion of myosin.
Collapse
Affiliation(s)
- Susana Ortiz-Costa
- Laboratório de Enzimologia e Controle do Metabolismo (LabECoM), Departamento de Fármacos, Faculdade de Farmácia/CCS/UFRJ, Rio de Janeiro, Brazil
| | | | | |
Collapse
|