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Negi KS, Das N, Khan T, Sen P. Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor. Phys Chem Chem Phys 2023; 25:32602-32612. [PMID: 38009208 DOI: 10.1039/d3cp03357k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.
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Affiliation(s)
- Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
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2
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Palladino P, Rainetti A, Lettieri M, Pieraccini G, Scarano S, Minunni M. Quantitative Colorimetric Sensing of Carbidopa in Anti-Parkinson Drugs Based on Selective Reaction with Indole-3-Carbaldehyde. SENSORS (BASEL, SWITZERLAND) 2023; 23:9142. [PMID: 38005530 PMCID: PMC10674578 DOI: 10.3390/s23229142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023]
Abstract
The quality of life of patients affected by Parkinson's disease is improved by medications containing levodopa and carbidopa, restoring the dopamine concentration in the brain. Accordingly, the affordable quality control of such pharmaceuticals is very important. Here is reported the simple and inexpensive colorimetric quantification of carbidopa in anti-Parkinson drugs by the selective condensation reaction between the hydrazine group from carbidopa and the formyl functional group of selected aldehydes in acidified hydroalcoholic solution. An optical assay was developed by using indole-3-carbaldehyde (I3A) giving a yellow aldazine in EtOH:H2O 1:1 (λmax~415 nm) at 70 °C for 4 h, as confirmed by LC-MS analysis. A filter-based plate reader was used for colorimetric data acquisition, providing superior results in terms of analytical performances for I3A, with a sensitivity ~50 L g-1 and LOD ~0.1 mg L-1 in comparison to a previous study based on vanillin, giving, for the same figures of merit values, about 13 L g-1 and 0.2-0.3 mg L-1, respectively. The calibration curves for the standard solution and drugs were almost superimposable, therefore excluding interference from the excipients and additives, with very good reproducibility (avRSD% 2-4%) within the linear dynamic range (10 mg L-1-50 mg L-1).
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Affiliation(s)
- Pasquale Palladino
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Alberto Rainetti
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Mariagrazia Lettieri
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 2, 53100 Siena, Italy
| | - Giuseppe Pieraccini
- CISM Mass Spectrometry Centre, University of Florence, Viale Gaetano Pieraccini 6, 50139 Florence, Italy
| | - Simona Scarano
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Maria Minunni
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 6, 56126 Pisa, Italy
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3
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Constantino-Jonapa LA, Espinoza-Palacios Y, Escalona-Montaño AR, Hernández-Ruiz P, Amezcua-Guerra LM, Amedei A, Aguirre-García MM. Contribution of Trimethylamine N-Oxide (TMAO) to Chronic Inflammatory and Degenerative Diseases. Biomedicines 2023; 11:biomedicines11020431. [PMID: 36830968 PMCID: PMC9952918 DOI: 10.3390/biomedicines11020431] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Trimethylamine N-oxide (TMAO) is a metabolite produced by the gut microbiota and has been mainly associated with an increased incidence of cardiovascular diseases (CVDs) in humans. There are factors that affect one's TMAO level, such as diet, drugs, age, and hormones, among others. Gut dysbiosis in the host has been studied recently as a new approach to understanding chronic inflammatory and degenerative diseases, including cardiovascular diseases, metabolic diseases, and Alzheimer's disease. These disease types as well as COVID-19 are known to modulate host immunity. Diabetic and obese patients have been observed to have an increase in their level of TMAO, which has a direct correlation with CVDs. This metabolite is attributed to enhancing the inflammatory pathways through cholesterol and bile acid dysregulation, promoting foam cell formation. Additionally, TMAO activates the transcription factor NF-κB, which, in turn, triggers cytokine production. The result can be an exaggerated inflammatory response capable of inducing endoplasmic reticulum stress, which is responsible for various diseases. Due to the deleterious effects that this metabolite causes in its host, it is important to search for new therapeutic agents that allow a reduction in the TMAO levels of patients and that, thus, allow patients to be able to avoid a severe cardiovascular event. The present review discussed the synthesis of TMAO and its contribution to the pathogenesis of various inflammatory diseases.
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Affiliation(s)
- Luis A. Constantino-Jonapa
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Yoshua Espinoza-Palacios
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Alma R. Escalona-Montaño
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Paulina Hernández-Ruiz
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Luis M. Amezcua-Guerra
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Interdisciplinary Internal Medicine Unit, Careggi University Hospital, 50134 Florence, Italy
| | - María M. Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5573-2911 (ext. 27316)
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4
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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.
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5
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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.
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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
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6
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Song X, An L, Wang M, Chen J, Liu Z, Yao L. Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions. ACS Chem Biol 2021; 16:864-871. [PMID: 33843182 DOI: 10.1021/acschembio.1c00024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although numerous in vitro studies have shown that osmolytes are capable of stabilizing proteins, their effect on protein folding in vivo has been less understood. In this work, we investigated the effect of osmolytes, including glycerol, sorbitol, betaine, and taurine, on the folding of a protein GB3 variant in E. coli cells using NMR spectroscopy. 400 mM osmolytes were added to E. coli cells; only glycerol stabilizes the folded protein, whereas betaine and taurine considerably destabilize the protein through modulating folding and unfolding rates. Further investigation indicates that betaine and taurine can enhance the quinary interaction between the protein and cellular environment and manifestly weaken the electrostatic attraction in protein salt bridges. The combination of the two factors causes destabilization of the protein in E. coli cells. These factors counteract the preferential exclusion mechanism that is adopted by osmolytes to stabilize proteins.
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Affiliation(s)
- Xiangfei Song
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengting Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhijun Liu
- National Facility for Protein Science, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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7
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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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8
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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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9
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Inayathullah M, Rajadas J. Conformational dynamics of a hydrophobic prion fragment (113-127) in different pH and osmolyte solutions. Neuropeptides 2016; 57:9-14. [PMID: 26919915 DOI: 10.1016/j.npep.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/09/2016] [Accepted: 02/14/2016] [Indexed: 01/17/2023]
Abstract
Prion diseases are characterized by a conformational change in prion protein from its native state into beta-sheet rich aggregates that are neurotoxic. The central domain that contain a highly conserved hydrophobic region of the protein play an important role in the toxicity. The conformation of the proteins is largely influenced by various solvent environments. Here we report results of study of hydrophobic prion fragment peptide PrP(113-127) under different pH and osmolytes solution conditions. The secondary structure and the folding of PrP(113-127) was determined using circular dichroism and fluorescence spectroscopic methods. The results indicate that PrP(113-127) adopts a random coil conformation in aqueous buffer at neutral pH and that converted into beta sheet on aging. Even though the initial random coil conformation was similar in different pH conditions, the acidic as well as basic pH conditions delays the conformational transition to beta sheet. FRET results indicate that the distance between N and C-terminal regions increased on aging due to unfolding by self-assembly of the peptide into an organized beta sheet structure. Presence of osmolytes, prevented or decelerated the aggregation process of PrP(113-127) peptide.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, Tamil Nadu 600020, India; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakumar Rajadas
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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10
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Rani A, Jayaraj A, Jayaram B, Pannuru V. Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation. Sci Rep 2016; 6:23656. [PMID: 27025561 PMCID: PMC4812290 DOI: 10.1038/srep23656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
In adaptation biology of the discovery of the intracellular osmolytes, the osmolytes are found to play a central role in cellular homeostasis and stress response. A number of models using these molecules are now poised to address a wide range of problems in biology. Here, a combination of biophysical measurements and molecular dynamics (MD) simulation method is used to examine the effect of trimethylamine-N-oxide (TMAO) on stem bromelain (BM) structure, stability and function. From the analysis of our results, we found that TMAO destabilizes BM hydrophobic pockets and active site as a result of concerted polar and non-polar interactions which is strongly evidenced by MD simulation carried out for 250 ns. This destabilization is enthalpically favourable at higher concentrations of TMAO while entropically unfavourable. However, to the best of our knowledge, the results constitute first detailed unambiguous proof of destabilizing effect of most commonly addressed TMAO on the interactions governing stability of BM and present plausible mechanism of protein unfolding by TMAO.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Abhilash Jayaraj
- Department of Chemistry, Indian Institute of Technology, New Delhi-110 016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology, New Delhi-110 016, India.,Supercomputing Facility for Bioinformatics &Computational Biology, Indian Institute of Technology, New Delhi-110 016, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi-110 016, India
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11
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Galm L, Morgenstern J, Hubbuch J. Manipulation of lysozyme phase behavior by additives as function of conformational stability. Int J Pharm 2015; 494:370-80. [PMID: 26302861 DOI: 10.1016/j.ijpharm.2015.08.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/15/2015] [Indexed: 11/18/2022]
Abstract
Undesired protein aggregation in general and non-native protein aggregation in particular need to be inhibited during bio-pharmaceutical processing to ensure patient safety and to maintain product activity. In this work the potency of different additives, namely glycerol, PEG 1000, and glycine, to prevent lysozyme aggregation and selectively manipulate lysozyme phase behavior was investigated. The results revealed a strong pH dependency of the additive impact on lysozyme phase behavior, lysozyme solubility, crystal size and morphology. This work aims to link this pH dependent impact to a protein-specific parameter, the conformational stability of lysozyme. At pH 3 the addition of 10% (w/v) glycerol, 10% (w/v) PEG 1000, and 1 M glycine stabilized or destabilized lysozymes' native conformation resulting in a modified size of the crystallization area without influencing lysozyme solubility, crystal size and morphology. Addition of 1 M glycine even promoted non-native aggregation at pH 3 whereas addition of PEG 1000 completely inhibited non-native aggregation. At pH 5 the addition of 10% (w/v) glycerol, 10% (w/v) PEG 1000, and 1 M glycine did not influence lysozymes' native conformation, but strongly influenced the position of the crystallization area, lysozyme solubility, crystal size and morphology. The observed pH dependent impact of the additives could be linked to a differing lysozyme conformational stability in the binary systems without additives at pH 3 and pH 5. However, in any case lysozyme phase behavior could selectively be manipulated by addition of glycerol, PEG 1000 and glycine. Furthermore, at pH 5 crystal size and morphology could selectively be manipulated.
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Affiliation(s)
- Lara Galm
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Josefine Morgenstern
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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12
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Wawer J, Krakowiak J, Szociński M, Lustig Z, Olszewski M, Szostak K. Inhibition of amyloid fibril formation of hen egg white lysozyme by trimethylamine N-oxide at low pH. Int J Biol Macromol 2014; 70:214-21. [DOI: 10.1016/j.ijbiomac.2014.06.057] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 10/25/2022]
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13
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Jain R, Sharma D, Kumar S, Kumar R. Factor Defining the Effects of Glycine Betaine on the Thermodynamic Stability and Internal Dynamics of Horse Cytochrome c. Biochemistry 2014; 53:5221-35. [DOI: 10.1021/bi500356c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rishu Jain
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Deepak Sharma
- Council
of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Sandeep Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Rajesh Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
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14
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Macchi F, Eisenkolb M, Kiefer H, Otzen DE. The effect of osmolytes on protein fibrillation. Int J Mol Sci 2012; 13:3801-3819. [PMID: 22489184 PMCID: PMC3317744 DOI: 10.3390/ijms13033801] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/10/2012] [Accepted: 03/13/2012] [Indexed: 11/24/2022] Open
Abstract
Osmolytes are small molecules that are exploited by cells as a protective system against stress conditions. They favour compact protein states which makes them stabilize globular proteins in vitro and promote folding. Conversely, this preference for compact states promotes aggregation of unstructured proteins. Here we combine a brief review of the effect of osmolytes on protein fibrillation with a report of the effect of osmolytes on the unstructured peptide hormone glucagon. Our results show that osmolytes either accelerate the fibrillation kinetics or leave them unaffected, with the exception of the osmolyte taurine. Furthermore, the osmolytes that affected the shape of the fibrillation time profile led to fibrils with different structure as revealed by CD. The structural changes induced by Pro, Ser and choline-O-sulfate could be due to specific osmolytes binding to the peptides, stabilizing an otherwise labile fibrillation intermediate.
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Affiliation(s)
- Francesca Macchi
- iNANO, Center for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; E-Mail:
| | - Maike Eisenkolb
- Hochschule Biberach, Pharmaceutical Biotechnology, Hubertus-Liebrecht-Str. 35, D-88400 Biberach, Germany; E-Mails: ;
| | - Hans Kiefer
- Hochschule Biberach, Pharmaceutical Biotechnology, Hubertus-Liebrecht-Str. 35, D-88400 Biberach, Germany; E-Mails: ;
| | - Daniel E. Otzen
- iNANO, Center for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +45-87-41-54-41; Fax: +45-86-12-31-78
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15
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Protein and DNA destabilization by osmolytes: The other side of the coin. Life Sci 2011; 88:117-25. [DOI: 10.1016/j.lfs.2010.10.020] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 09/26/2010] [Accepted: 10/19/2010] [Indexed: 01/23/2023]
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16
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Abstract
This article defines protein stability, emphasizes its importance and surveys some notable recent publications (2004-2008) in the field of protein stability/stabilization. Knowledge of the factors stabilizing proteins has emerged from denaturation studies and from study of thermophilic (and other extremophilic) proteins. One can enhance stability by protein engineering strategies, the judicious use of solutes and additives, immobilization, and chemical modification in solution. General protocols are set out on how to measure the kinetic thermal stability of a given protein and how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán O'Fágáin
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland.
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17
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van der Kamp MW, Daggett V. Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations. Top Curr Chem (Cham) 2011; 305:169-97. [PMID: 21526434 DOI: 10.1007/128_2011_158] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes can be simulated, including the initial steps of misfolding. By introducing mutations in silico, the effect of pathogenic mutations on PrP conformation and dynamics can be assessed. Here, we briefly introduce molecular dynamics methods and review the application of molecular dynamics simulations to obtain insight into various aspects of the PrP, including the mechanism of misfolding, the response to changes in the environment, and the influence of disease-related mutations.
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Affiliation(s)
- Marc W van der Kamp
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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18
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The Unfolded State of the Murine Prion Protein and Properties of Single-point Mutants Related to Human Prion Diseases. J Mol Biol 2010; 401:7-12. [DOI: 10.1016/j.jmb.2010.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/12/2010] [Accepted: 06/03/2010] [Indexed: 01/18/2023]
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Hu CY, Lynch GC, Kokubo H, Pettitt BM. Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model. Proteins 2010; 78:695-704. [PMID: 19790265 DOI: 10.1002/prot.22598] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of organic osmolytes has been pivotal in demonstrating the role of solvent effects on the protein backbone in the folding process. Although a thermodynamic description of the interactions between the protein backbone and osmolyte has been well defined, the structural analysis of the effect of osmolyte on the protein backbone has been incomplete. Therefore, we have performed simulations of a peptide backbone model, glycine(15), in protecting osmolyte trimethylamine N-oxide (TMAO) solution, in order to determine the effect of the solution structure on the conformation of the peptide backbone. We show that the models chosen show that the ensemble of backbone structures shifts toward a more collapsed state in TMAO solution as compared with pure water solution. The collapse is consistent with preferential exclusion of the osmolyte caused by unfavorable interactions between osmolyte and peptide backbone. The exclusion is caused by strong triplet correlations of osmolyte, water, and peptide backbone. This provides a clear mechanism showing that even a modest concentration of TMAO forces the protein backbone to adopt a more collapsed structure in the absence of side chain effects.
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Affiliation(s)
- Char Y Hu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USA
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Singh LR, Dar TA, Rahman S, Jamal S, Ahmad F. Glycine betaine may have opposite effects on protein stability at high and low pH values. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:929-35. [DOI: 10.1016/j.bbapap.2009.02.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2008] [Revised: 02/14/2009] [Accepted: 02/17/2009] [Indexed: 11/26/2022]
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Pappalardo M, Milardi D, Grasso D, La Rosa C. Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species. NEW J CHEM 2007. [DOI: 10.1039/b700764g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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