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Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. J Mol Model 2021; 27:261. [PMID: 34432183 DOI: 10.1007/s00894-021-04882-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while only partial denaturation occurs at the concentration slightly below 0.1 M. In large part, protein denaturation is structurally manifested by disappearance of helical segments and loss of tertiary interactions. The computational prediction of the extent of burial of cysteine residues was experimentally validated by measuring the accessibility of the respective sulfhydryl groups. Overall, our work indicates an interesting synergy between electrostatic and hydrophobic contributions to lysozyme's denaturation process by anionic surfactants. In fact, first disulfide bridges and hydrogen bonds from protein surface to SPDS head groups loosen the protein globule followed by fuller denaturation via insertion of the surfactant's hydrophobic tails into the protein core.
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Affiliation(s)
- Armen H Poghosyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia.
| | - Aram A Shahinyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia
| | - Gayane R Kirakosyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | - Naira M Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | | | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
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Poghosyan AH, Schafer NP, Lyngsø J, Shahinyan AA, Pedersen JS, Otzen DE. Molecular dynamics study of ACBP denaturation in alkyl sulfates demonstrates possible pathways of unfolding through fused surfactant clusters. Protein Eng Des Sel 2019; 32:175-190. [DOI: 10.1093/protein/gzz037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 11/15/2022] Open
Abstract
AbstractAnionic surfactants denature proteins at low millimolar concentrations, yet little is known about the underlying molecular mechanisms. Here, we undertake 1-μs-long atomistic molecular dynamics simulations of the denaturation of acyl coenzyme A binding protein (ACBP) and compare our results with previously published and new experimental data. Since increasing surfactant chain length is known to lead to more rapid denaturation, we studied denaturation using both the medium-length alkyl chain surfactant sodium dodecyl sulfate (SDS) and the long alkyl chain surfactant sodium hexadecyl sulfate (SHS). In silico denaturation on the microsecond timescale was not achieved using preformed surfactant micelles but required ACBP to be exposed to monomeric surfactant molecules. Micellar self-assembly occurred together with protein denaturation. To validate our analyses, we calculated small-angle X-ray scattering spectra of snapshots from the simulations. These agreed well with experimental equilibrium spectra recorded on ACBP-SDS mixtures with similar compositions. Protein denaturation occurs through the binding of partial micelles to multiple preferred binding sites followed by the accretion of surfactant monomers until these partial micelles merge to form a mature micelle and the protein chain is left disordered on the surface of the micelle. While the two surfactants attack in a similar fashion, SHS’s longer alkyl chain leads to a more efficient denaturation through the formation of larger clusters that attack ACBP, a more rapid drop in native contacts, a greater expansion in size, as well as a more thorough rearrangement of hydrogen bonds and disruption of helices.
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Affiliation(s)
- Armen H Poghosyan
- International Scientific-Educational Center of National Academy of Sciences of Armenia, 24d Marshal Baghramyan Ave, Yerevan 0019, Armenia
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
- Center for Theoretical Biological Physics, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Jeppe Lyngsø
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 120, 8000 Aarhus, Denmark
| | - Aram A Shahinyan
- International Scientific-Educational Center of National Academy of Sciences of Armenia, 24d Marshal Baghramyan Ave, Yerevan 0019, Armenia
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 120, 8000 Aarhus, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
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Ahmed MF, Molla MR, Saha M, Shahriar I, Rahman MS, Halim MA, Rub MA, Hoque MA, Asiri AM. Aggregation behavior of cetyldimethylethylammonium bromide under the influence of bovine serum albumin in aqueous/electrolyte solutions at various temperatures and compositions: conductivity and molecular dynamics study. RSC Adv 2019; 9:6556-6567. [PMID: 35518479 PMCID: PMC9060940 DOI: 10.1039/c9ra00070d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/15/2019] [Indexed: 11/21/2022] Open
Abstract
Herein, we have investigated the interaction of bovine serum albumin (BSA), the most abundant globular protein, with a conventional cationic surfactant, cetyldimethylethylammonium bromide (CDMEAB), through a conductivity technique in the absence/presence of electrolyte solutions at various temperatures (298.15-323.15 K). The interaction of the protein with drugs/surfactants and other additives plays a crucial role in the body. Hence, the main concern of the study is to extract the impact of BSA on surfactant molecules and vice versa. From the specific conductivity versus concentration of surfactant plots, three different noticeable critical micelle concentration (c*) values were obtained for pure CDMEAB and its mixture with protein/protein + salts. The presence of BSA and electrolytes altered the c* values of CDMEAB revealing interactions among the studied constituents where the salt solutions reduced the c* values and created a convenient environment for favorable micellization. The negative magnitudes achieved for standard free energy changes (ΔG 0 m) suggest spontaneity of micellization while the values of ΔH 0 m and ΔS 0 m signified the existence of some electrostatic and hydrophobic interactions. The values of molar heat capacity (ΔC 0 m) were positive as well as small which was an indication of less structural deformation. Molecular Dynamics (MD) simulation for all atoms revealed that the salt ions promoted non-covalent interaction between BSA and CDMEAB, and such interactions were not observed in the absence of the salt. Protein structure remained nearly same in spite of strong interaction with CDMEAB as evident from the overall RMSD (root-mean-square deviation) values of the alpha carbons and backbone of the protein and RMSF (root-mean-square fluctuation) values of the amino acid residues present in BSA. In this work thermodynamic parameters of transfer (such as ΔG 0 m.tr., ΔH 0 m.tr., and ΔC 0 p.m.tr.) were also evaluated and the results are discussed in detail. Besides, contributions of enthalpy and entropy to free energy changes were also analyzed.
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Affiliation(s)
- Md Farid Ahmed
- Department of Chemistry, Jahangirnagar University Savar Dhaka-1342 Bangladesh +880-2-7791052 PABX: +880-2-7791045-51 extn 1437
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Dhaka Bangladesh
| | - Mohammad Robel Molla
- Department of Chemistry, Jahangirnagar University Savar Dhaka-1342 Bangladesh +880-2-7791052 PABX: +880-2-7791045-51 extn 1437
- Bangladesh Council of Scientific and Industrial Research (BCSIR) Dhaka Bangladesh
| | - Mousumi Saha
- Division of Quantum Chemistry, The Red-Green Research Centre, BICCB Dhaka Bangladesh
| | - Imrul Shahriar
- Division of Quantum Chemistry, The Red-Green Research Centre, BICCB Dhaka Bangladesh
| | - Mohammad Saidur Rahman
- Department of Chemistry, Jahangirnagar University Savar Dhaka-1342 Bangladesh +880-2-7791052 PABX: +880-2-7791045-51 extn 1437
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya 50603 Kuala Lumpur Malaysia
| | - Mohammad A Halim
- Division of Quantum Chemistry, The Red-Green Research Centre, BICCB Dhaka Bangladesh
| | - Malik Abdul Rub
- Chemistry Department, Faculty of Science, King Abdulaziz University Jeddah-21589 Saudi Arabia
- Center of Excellence for Advanced Materials Research, King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Md Anamul Hoque
- Department of Chemistry, Jahangirnagar University Savar Dhaka-1342 Bangladesh +880-2-7791052 PABX: +880-2-7791045-51 extn 1437
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University Jeddah-21589 Saudi Arabia
- Center of Excellence for Advanced Materials Research, King Abdulaziz University Jeddah 21589 Saudi Arabia
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Nedergaard Pedersen J, Frederix PWJM, Skov Pedersen J, Marrink SJ, Otzen DE. Role of Charge and Hydrophobicity in Liprotide Formation: A Molecular Dynamics Study with Experimental Constraints. Chembiochem 2018; 19:263-271. [PMID: 29156084 DOI: 10.1002/cbic.201700496] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Indexed: 12/15/2022]
Abstract
Bovine α-lactalbumin (aLA) and oleate (OA) form a complex that has been intensively studied for its tumoricidal activity. Small-angle X-ray scattering (SAXS) has revealed that this complex consists of a lipid core surrounded by partially unfolded protein. We call this type of complex a liprotide. Little is known of the molecular interactions between OA and aLA, and no technique has so far provided any high-resolution structure of a liprotide. Here we have used coarse-grained (CG) molecular dynamics (MD) simulations, isothermal titration calorimetry (ITC) and SAXS to investigate the interactions between aLA and OA during the process of liprotide formation. With ITC we found that the strongest enthalpic interactions occurred at a molar ratio of 12.0±1.4:1 OA/aLA. Liprotides formed between OA and aLA at several OA/aLA ratios in silico were stable both in CG and in all-atom simulations. From the simulated structures we calculated SAXS spectra that show good agreement with experimentally measured patterns of matching liprotides. The simulations showed that aLA assumes a molten globular (MG) state, exposing several hydrophobic patches involved in interactions with OA. Initial binding of aLA to OA occurs in an area of aLA in which a high amount of positive charge is located, and only later do hydrophobic interactions become important. The results reveal how unfolding of aLA to expose hydrophobic residues is important for complex formation between aLA and OA. Our findings suggest a general mechanism for liprotide formation and might explain the ability of a large number of proteins to form liprotides with OA.
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Affiliation(s)
- Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Pim Wilhelmus Johannes Maria Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Siewert Jan Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
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Dominguez H. Interaction of the interleukin 8 protein with a sodium dodecyl sulfate micelle: A computer simulation study. J Mol Model 2017. [DOI: 10.1007/s00894-017-3386-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Manjunath S, Satish Rao BS, Satyamoorthy K, Mahato KK. Laser induced autofluorescence in the monitoring of β-mercaptoethanol mediated photo induced proton coupled electron transfer in proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 149:607-614. [PMID: 25985124 DOI: 10.1016/j.saa.2015.04.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/18/2015] [Accepted: 04/22/2015] [Indexed: 06/04/2023]
Abstract
Photo induced proton coupled electron transfer (PCET) is an important process that many organisms use for progression of catalytic reactions leading to energy conversion. In the present study, the influence of SDS and BME on the redox properties of tyrosine and tryptophan for five different globular proteins, BSA, HSA, RNase-A, trypsin and lysozyme were studied using laser induced autofluorescence. The proteins were subjected to denaturation under SDS, SDS plus heat and SDS plus β-mercaptoethanol (BME) plus heat and the corresponding fluorescence were recorded. The influence of BME on the autofluorescence properties of the proteins were evaluated upon tris-2-corboxy-ethyl phosphine (TCEP) denaturation. The BSA and HSA when exposed to SDS alone, exhibited hydrophobic collapse around their tryptophan moieties. However, these proteins when treated with SDS plus BME plus heat, an unusual red shift in the emission was observed, may be due to proton transfer from hydroxyl group of the excited tyrosine residues to the local microenvironments. The observation was further confirmed with similar proton transfer in absence of tryptophan in RNase-A showing involvement of tyrosine in the process. A drastic quenching of fluorescence in all of the proteins under study were also observed, may be due to photo-induced electron transfer (PET) from BME to the intrinsic fluorophores resulting in radical ions formation, evaluated upon DCFDA measurements.
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Affiliation(s)
- S Manjunath
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, India
| | - B S Satish Rao
- Department of Radiation Biology and Toxicology, School of Life Sciences, Manipal University, Manipal, India
| | - K Satyamoorthy
- School of Life Sciences, Manipal University, Manipal 576104, Karnataka, India
| | - K K Mahato
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, India.
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Lu D, Yang C, Liu Z. How hydrophobicity and the glycosylation site of glycans affect protein folding and stability: a molecular dynamics simulation. J Phys Chem B 2011; 116:390-400. [PMID: 22118044 DOI: 10.1021/jp203926r] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Glycosylation is one of the most common post-translational modifications in the biosynthesis of protein, but its effect on the protein conformational transitions underpinning folding and stabilization is poorly understood. In this study, we present a coarse-grained off-lattice 46-β barrel model protein glycosylated by glycans with different hydrophobicity and glycosylation sites to examine the effect of glycans on protein folding and stabilization using a Langevin dynamics simulation, in which an H term was proposed as the index of the hydrophobicity of glycan. Compared with its native counterpart, introducing glycans of suitable hydrophobicity (0.1 < H < 0.4) at flexible peptide residues of this model protein not only facilitated folding of the protein but also increased its conformation stability significantly. On the contrary, when glycans were introduced at the restricted peptide residues of the protein, only those hydrophilic (H = 0) or very weak hydrophobic (H < 0.2) ones contributed slightly to protein stability but hindered protein folding due to increased free energy barriers. The glycosylated protein retained the two-step folding mechanism in terms of hydrophobic collapse and structural rearrangement. Glycan chains located in a suitable site with an appropriate hydrophobicity facilitated both collapse and rearrangement, whereas others, though accelerating collapse, hindered rearrangement. In addition to entropy effects, that is, narrowing the space of the conformations of the unfolded state, the presence of glycans with suitable hydrophobicity at suitable glycosylation site strengthened the folded state via hydrophobic interaction, that is, the enthalpy effect. The simulations have shown both the stabilization and the destabilization effects of glycosylation, as experimentally reported in the literature, and provided molecular insight into glycosylated proteins. The understanding of the effects of glycans with different hydrophobicities on the folding and stability of protein, as attempted by the present work, is helpful not only to explain the stabilization and destabilization effect of real glycoproteins but also to design protein-polymer conjugates for biotechnological purposes.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
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Chen X, Dong W, Zhang X. Self-assembly of amphiphilic molecules: A review on the recent computer simulation results. Sci China Chem 2010. [DOI: 10.1007/s11426-010-4064-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kudou M, Yumioka R, Ejima D, Arakawa T, Tsumoto K. A novel protein refolding system using lauroyl-l-glutamate as a solubilizing detergent and arginine as a folding assisting agent. Protein Expr Purif 2010; 75:46-54. [PMID: 20817098 DOI: 10.1016/j.pep.2010.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/23/2010] [Accepted: 08/26/2010] [Indexed: 11/26/2022]
Abstract
More than 50 detergents, including acylated amino acid derivatives, were screened for their ability to solubilize and refold recombinant proteins expressed as inclusion bodies. Two model proteins, human interleukin-6 and microbial transglutaminase, were solubilized by these detergents and the solubilized proteins were rapidly diluted for testing their solubilization and refolding effectiveness. Long chain-acylated amino acid derivatives having dicarboxylic acid moieties were found to be superior to others under the conditions tested. In particular, lauroyl-l-glutamate (C12-l-Glu) showed the highest recovery of the native proteins. The effectiveness of dilution refolding was greatly improved by adding aggregation suppressive arginine into the refolding solvents. To gain understanding how this detergent works, interactions between detergents and proteins were examined using spectroscopic and native gel electrophoretic analyses, showing ideal properties for C12-l-Glu as a solubilzing agent, i.e. highly reversible nature of the detergent binding to the model globular proteins and of the conformational changes. These properties most likely have contributed to the effective protein solubilzation and refolding of inclusion bodies using C12-l-Glu and arginine.
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Affiliation(s)
- Motonori Kudou
- Department of Medical Genome Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
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Lu D, Wu J, Liu Z. Dynamic Control of Protein Folding Pathway with a Polymer of Tunable Hydrophobicity. J Phys Chem B 2007; 111:12303-9. [PMID: 17914802 DOI: 10.1021/jp076043k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the knowledge of protein folding in a dilute solution is now well-advanced, little is known of the influence of surrounding conditions on the folding kinetics, in particular when the protein is in a dynamically responsive environment. Here we report a new procedure to control the pathways of protein folding by using a thermally responsive polymer that varies its hydrophobicity concomitant with the protein structural changes. The advantages of folding in a dynamic environment have been demonstrated first by Langevin dynamics simulations on the basis of coarse-grained models for both the protein and polymer and then by experiments for lysozyme refolding in the presence of poly(N-isopropylacrylamide-co-N-tert-butylacrylamide), a thermal responsive polymer that varies its hydrophobicity in response to temperature. The simulation suggests that decreasing the polymer hydrophobicity during the folding process may result in an optimized free-energy landscape that enhances both the folding yield and kinetics. The experiments affirm that an optimal folding condition can be identified when structural transitions of the protein collaborate with the polymer hydrophobicity tuned by variation of temperature.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 10084
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