1
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Dabin A, Stirnemann G. Toward a Molecular Mechanism of Complementary RNA Duplexes Denaturation. J Phys Chem B 2023. [PMID: 37389985 DOI: 10.1021/acs.jpcb.3c00908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
RNA duplexes are relatively rare but play very important biological roles. As an end-product of template-based RNA replication, they also have key implications for hypothetical primitive forms of life. Unless they are specifically separated by enzymes, these duplexes denature upon a temperature increase. However, mechanistic and kinetic aspects of RNA (and DNA) duplex thermal denaturation remain unclear at the microscopic level. We propose an in silico strategy that probes the thermal denaturation of RNA duplexes and allows for an extensive conformational space exploration along a wide temperature range with atomistic precision. We show that this approach first accounts for the strong sequence and length dependence of the duplexes melting temperature, reproducing the trends seen in the experiments and predicted by nearest-neighbor models. The simulations are then instrumental at providing a molecular picture of the temperature-induced strand separation. The textbook canonical "all-or-nothing" two-state model, very much inspired by the protein folding mechanism, can be nuanced. We demonstrate that a temperature increase leads to significantly distorted but stable structures with extensive base-fraying at the extremities, and that the fully formed duplexes typically do not form around melting. The duplex separation therefore appears as much more gradual than commonly thought.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
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2
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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3
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Bartoccini F, Retini M, Crinelli R, Menotta M, Fraternale A, Piersanti G. Dithiol Based on l-Cysteine and Cysteamine as a Disulfide-Reducing Agent. J Org Chem 2022; 87:10073-10079. [PMID: 35862282 PMCID: PMC9361291 DOI: 10.1021/acs.joc.2c01050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We report the synthesis, chemical properties, and disulfide
bond-reducing
performance of a dithiol called NACMEAA, conceived as a hybrid of
two biologically relevant thiols: cysteine and cysteamine. NACMEAA
is conveniently prepared from inexpensive l-cystine in an
efficient manner. As a nonvolatile, highly soluble, and neutral compound
at physiological pH with the first thiol pKa value of 8.0, NACMEAA is reactive and user-friendly. We also demonstrate
that NACMEAA reduces disulfide bonds in GSSG and lysozyme.
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Affiliation(s)
- Francesca Bartoccini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Michele Retini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Rita Crinelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Alessandra Fraternale
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
| | - Giovanni Piersanti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza Rinascimento 6, 61029 Urbino, PU, Italy
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4
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Stirnemann G. Molecular interpretation of single-molecule force spectroscopy experiments with computational approaches. Chem Commun (Camb) 2022; 58:7110-7119. [PMID: 35678696 DOI: 10.1039/d2cc01350a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single molecule force-spectroscopy techniques have granted access to unprecedented molecular-scale details about biochemical and biological mechanisms. However, the interpretation of the experimental data is often challenging. Computational and simulation approaches (all-atom steered MD simulations in particular) are key to provide molecular details about the associated mechanisms, to help test different hypotheses and to predict experimental results. In this review, particular recent efforts directed towards the molecular interpretation of single-molecule force spectroscopy experiments on proteins and protein-related systems (often in close collaboration with experimental groups) will be presented. These results will be discussed in the broader context of the field, highlighting the recent achievements and the ongoing challenges for computational biophysicists and biochemists. In particular, I will focus on the input gained from molecular simulations approaches to rationalize the origin of the unfolded protein elasticity and the protein conformational behavior under force, to understand how force denaturation differs from chemical, thermal or shear unfolding, and to unravel the molecular details of unfolding events for a variety of systems. I will also discuss the use of models based on Langevin dynamics on a 1-D free-energy surface to understand the effect of protein segmentation on the work exerted by a force, or, at the other end of the spectrum of computational techniques, how quantum calculations can help to understand the reactivity of disulfide bridges exposed to force.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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5
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Gil-Redondo JC, Weber A, Toca-Herrera JL. Measuring (biological) materials mechanics with atomic force microscopy. 3. Mechanical unfolding of biopolymers. Microsc Res Tech 2022; 85:3025-3036. [PMID: 35502131 PMCID: PMC9543778 DOI: 10.1002/jemt.24136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Biopolymers, such as polynucleotides, polypeptides and polysaccharides, are macromolecules that direct most of the functions in living beings. Studying the mechanical unfolding of biopolymers provides important information about their molecular elasticity and mechanical stability, as well as their energy landscape, which is especially important in proteins, since their three‐dimensional structure is essential for their correct activity. In this primer, we present how to study the mechanical properties of proteins with atomic force microscopy and how to obtain information about their stability and energetic landscape. In particular, we discuss the preparation of polyprotein constructs suitable for AFM single molecule force spectroscopy (SMFS), describe the parameters used in our force‐extension SMFS experiments and the models and equations employed in the analysis of the data. As a practical example, we show the effect of the temperature on the unfolding force, the distance to the transition state, the unfolding rate at zero force, the height of the transition state barrier, and the spring constant of the protein for a construct containing nine repeats of the I27 domain from the muscle protein titin.
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Affiliation(s)
- Juan Carlos Gil-Redondo
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Andreas Weber
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - José L Toca-Herrera
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
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6
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Stirnemann G. Recent Advances and Emerging Challenges in the Molecular Modeling of Mechanobiological Processes. J Phys Chem B 2022; 126:1365-1374. [PMID: 35143190 DOI: 10.1021/acs.jpcb.1c10715] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many biological processes result from the effect of mechanical forces on macromolecular structures and on their interactions. In particular, the cell shape, motion, and differentiation directly depend on mechanical stimuli from the extracellular matrix or from neighboring cells. The development of experimental techniques that can measure and characterize the tiny forces acting at the cellular scale and down to the single-molecule, biomolecular level has enabled access to unprecedented details about the involved mechanisms. However, because the experimental observables often do not provide a direct atomistic picture of the corresponding phenomena, particle-based simulations performed at various scales are instrumental in complementing these experiments and in providing a molecular interpretation. Here, we will review the recent key achievements in the field, and we will highlight and discuss the many technical challenges these simulations are facing, as well as suggest future directions for improvement.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
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7
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Han Z, Hilburg SL, Alexander-Katz A. Forced Unfolding of Protein-Inspired Single-Chain Random Heteropolymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zexiang Han
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shayna L. Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Devi S, Chaturvedi M, Fatima S, Priya S. Environmental factors modulating protein conformations and their role in protein aggregation diseases. Toxicology 2022; 465:153049. [PMID: 34818560 DOI: 10.1016/j.tox.2021.153049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/12/2021] [Accepted: 11/20/2021] [Indexed: 12/13/2022]
Abstract
The adverse physiological conditions have been long known to impact protein synthesis, folding and functionality. Major physiological factors such as the effect of pH, temperature, salt and pressure are extensively studied for their impact on protein structure and homeostasis. However, in the current scenario, the environmental risk factors (pollutants) have gained impetus in research because of their increasing concentrations in the environment and strong epidemiologic link with protein aggregation disorders. Here, we review the physiological and environmental risk factors for their impact on protein conformational changes, misfolding, aggregation, and associated pathological conditions, especially environmental risk factors associated pathologies.
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Affiliation(s)
- Shweta Devi
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Minal Chaturvedi
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Siraj Fatima
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Smriti Priya
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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9
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Pang X, Yuan C, Sun R, Wang K, Tang B. Revealing the Underestimated Anticancer Effect of Azurin by Mechanical Unfolding. ACS Biomater Sci Eng 2021; 7:4809-4818. [PMID: 34558912 DOI: 10.1021/acsbiomaterials.1c00934] [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] [Indexed: 11/30/2022]
Abstract
As a potential anticancer agent, azurin has attracted extensive attraction among chemists, physicists, and material scientists. Its structural and unfolding/folding information has been partially understood, but some detailed information, such as the difference in the unfolding processes between apo-azurin and holo-azurin, the mechanical stability, and the role of the copper cluster in its stability, has not been addressed adequately, especially at the single-molecule level. Here, we employed AFM-based single-molecule force spectroscopy to investigate the unfolding process of azurin in the apo and holo forms under an external force. The results indicated that the unfolding processes of apo-azurin and holo-azurin are different, and holo-azurin requires a stronger force to unfold than does apo-azurin. The copper cluster exhibited a more significant impact on the stability and the folding process of holo-azurin: the copper cluster was completely broken, and the copper ion left the unfolded azurin during the unfolding process of azurin. We suspected that the presence of the disulfide bond in azurin made the unfolding of the copper cluster different from that in pseudoazurin, which is also a type I copper protein like azurin. Rarely reported in previous studies, the mechanical strength of the Cu-N(His) bond of the copper cluster was obtained in this study, which is weaker than that of most metal-S(Cys) bonds but higher than that of the Fe-N(His) bond. Altogether, our results offer a possible new scenario for azurin to widely extend its anticancer activity.
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Affiliation(s)
- Xiangchao Pang
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, PR China.,Hunan Province Key Laboratory of Materials Surface & Interface Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China.,Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Caijie Yuan
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, PR China
| | - Rui Sun
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Kui Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Bin Tang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.,Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, Guangdong P.R. China.,Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, Guangdong, P.R. China
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10
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Kelly C, Gage MJ. Protein Unfolding: Denaturant vs. Force. Biomedicines 2021; 9:biomedicines9101395. [PMID: 34680512 PMCID: PMC8533514 DOI: 10.3390/biomedicines9101395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods.
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Affiliation(s)
- Colleen Kelly
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA;
| | - Matthew J. Gage
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA;
- UMass Movement Center (UMOVE), University of Massachusetts Lowell, Lowell, MA 01854, USA
- Correspondence:
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11
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Raab SA, El-Baba TJ, Laganowsky A, Russell DH, Valentine SJ, Clemmer DE. Protons Are Fast and Smart; Proteins Are Slow and Dumb: On the Relationship of Electrospray Ionization Charge States and Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1553-1561. [PMID: 34151568 PMCID: PMC9003666 DOI: 10.1021/jasms.1c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present simple considerations of how differences in time scales of motions of protons, the lightest and fastest chemical moiety, and the much longer time scales associated with the dynamics of proteins, among the heaviest and slowest analytes, may allow many protein conformations from solution to be kinetically trapped during the process of electrospraying protein solutions into the gas phase. In solution, the quantum nature of protons leads them to change locations by tunneling, an instantaneous process; moreover, the Grotthuss mechanism suggests that these small particles can respond nearly instantaneously to the dynamic motions of proteins that occur on much longer time scales. A conformational change is accompanied by favorable or unfavorable variations in the free energy of the system, providing the impetus for solvent ↔ protein proton exchange. Thus, as thermal distributions of protein conformations interconvert, protonation states rapidly respond, as specific acidic and basic sites are exposed or protected. In the vacuum of the mass spectrometer, protons become immobilized in locations that are specific to the protein conformations from which they were incorporated. In this way, conformational states from solution are preserved upon electrospraying them into the gas phase. These ideas are consistent with the exquisite sensitivity of electrospray mass spectra to small changes of the local environment that alter protein structure in solution. We might remember this approximation for the protonation of proteins in solution with the colloquial expression-protons are fast and smart; proteins are slow and dumb.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Stephen J Valentine
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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12
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Dhabal D, Jiang Z, Pallath A, Patel AJ. Characterizing the Interplay between Polymer Solvation and Conformation. J Phys Chem B 2021; 125:5434-5442. [PMID: 33978411 DOI: 10.1021/acs.jpcb.1c02191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhitong Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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13
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Lyu J, Wang Y, Ruan C, Zhang X, Li K, Ye M. Mechanical stress induced protein precipitation method for drug target screening. Anal Chim Acta 2021; 1168:338612. [PMID: 34051997 DOI: 10.1016/j.aca.2021.338612] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022]
Abstract
The process of protein precipitation can be used to decipher the interaction of ligand and protein. For example, the classic Thermal Proteome Profiling (TPP) method uses heating as the driving force for protein precipitation, to discover the drug target protein. Under heating or other denature forces, the target protein that binds with the drug compound will be more resistant to precipitation than the free protein. Similar to thermal stress, mechanical stress can also induce protein precipitation. Upon mechanical stress, protein will gradually precipitate along with protein conformational changes, which can be exploited for the study of the ligand-protein interaction. Herein, we proposed a Mechanical Stress Induced Protein Precipitation (MSIPP) method for drug target deconvolution. Its streamlined workflow allows in situ sample preparation on the surface of microparticles, from protein precipitation to digestion. The mechanical stress was generated by vortexing the slurry of protein solution and microparticle materials. The mechanical stress induced protein precipitate was captured by the microparticles, which guarantees the MSIPP method to be scalable and user-friendly. The MSIPP method was successfully applied to four drug compounds, Methotrexate, Raltitrexed, SHP099, Geldanamycin and a pan-inhibitor of protein kinases, Staurosporine. Besides, DHFR was demonstrated to be a target of Raltitrexed, which has not been revealed by any other modification-free drug target discovery method yet. Thus, MSIPP is a complementary method to other drug target screening methods.
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Affiliation(s)
- Jiawen Lyu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejia Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Schäfer K, Diezemann G. Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1743886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ken Schäfer
- Institut für Physikalische Chemie, Universität Mainz, Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Mainz, Germany
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15
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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16
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Maffucci I, Laage D, Sterpone F, Stirnemann G. Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature. Chemistry 2020; 26:10045-10056. [DOI: 10.1002/chem.202001973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Irene Maffucci
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
- Present address: Centre de recherche Royallieu Université de Technologie de Compiègne, UPJV CNRS, Enzyme and Cell Engineering CS 60319-60203 Compiègne Cedex France
| | - Damien Laage
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
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17
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Song W, Jing Z, Meng L, Zhou R. Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains. ACS OMEGA 2020; 5:11005-11012. [PMID: 32455221 PMCID: PMC7241039 DOI: 10.1021/acsomega.0c00822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Tungsten oxide nanodot (WO3-x ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO3-x and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations. Our results show that WO3-x interacts only weakly with the key residues at the putative proline-rich motif (PRM) ligand-binding site of both domains. More importantly, our free energy landscape calculations reveal that the binding strength between WO3-x and WW/SH3 is weaker than that of the native PRM ligand with WW/SH3, implying that WO3-x has a limited inhibitory effect over PRM on both the WW and SH3 domains. These findings suggest that the cytotoxic effects of WO3-x on the key modular protein domains could be very mild, which provides new insights for the future potential biomedical applications of this nanomaterial.
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Affiliation(s)
- Wei Song
- Institute of Quantitative
Biology, Zhejiang University, Hangzhou 310027, China
| | - Zhifeng Jing
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Lijun Meng
- Institute of Quantitative
Biology, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative
Biology, Zhejiang University, Hangzhou 310027, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
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18
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Kelly CM, Manukian S, Kim E, Gage MJ. Differences in stability and calcium sensitivity of the Ig domains in titin's N2A region. Protein Sci 2020; 29:1160-1171. [PMID: 32112607 DOI: 10.1002/pro.3848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/11/2022]
Abstract
Titin is a large filamentous protein that spans half a sarcomere, from Z-disk to M-line. The N2A region within the titin molecule exists between the proximal immunoglobulin (Ig) region and the PEVK region and protein-protein interactions involving this region are required for normal muscle function. The N2A region consists of four Ig domains (I80-I83) with a 105 amino acid linker region between I80 and I81 that has a helical nature. Using chemical stability measurements, we show that predicted differences between the adjacent Ig domains (I81-I83) correlate with experimentally determined differences in chemical stability and refolding kinetics. Our work further shows that I83 has the lowest ΔGunfolding , which is increased in the presence of calcium (pCa 4.3), indicating that Ca2+ plays a role in stabilizing this immunoglobulin domain. The characteristics of N2A's three Ig domains provide insight into the stability of the binding sites for proteins that interact with the N2A region. This work also provides insights into how Ca2+ might influence binding events involving N2A.
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Affiliation(s)
- Colleen M Kelly
- Chemistry Department, University of Massachusetts Lowell, Lowell, Massachusetts, USA.,UMass Movement Center, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Sophia Manukian
- Chemistry Department, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Emily Kim
- Chemistry Department, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Matthew J Gage
- Chemistry Department, University of Massachusetts Lowell, Lowell, Massachusetts, USA.,UMass Movement Center, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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19
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Zhang W, Chen Y, Huynh T, Yang Y, Yang X, Zhou R. Directional extraction and penetration of phosphorene nanosheets to cell membranes. NANOSCALE 2020; 12:2810-2819. [PMID: 31961358 DOI: 10.1039/c9nr09577b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recently, phosphorene, a novel two-dimensional nanomaterial with a puckered surface morphology, was shown to exhibit cytotoxicity, but its underlying molecular mechanisms remain unknown. Herein, using large scale molecular dynamics simulations, we show that phosphorene nanosheets can penetrate into and extract large amounts of phospholipids from the cell membranes due to the strong dispersion interaction between phosphorene and lipid molecules, which would reduce cell viability. The extracted phospholipid molecules are aligned along the wrinkle direction of the phosphorene nanosheet because of its unique puckered structure. Our results also reveal that small phosphorene nanosheets penetrate into the cell membrane in a specific direction which is determined by the size and surface topography of phosphorene and the thickness of the membrane. These findings might shed light on understanding phosphorene's cytotoxicity and would be helpful for the future potential biomedical applications of phosphorene, such as biosensors and antibacterial agents.
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Affiliation(s)
- Wei Zhang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Yezhe Chen
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Tien Huynh
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
| | - Yunqiu Yang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Xianqing Yang
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, China.
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA. and Department of Chemistry, Columbia University, New York, New York 10027, USA
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20
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Zou A, Lee S, Li J, Zhou R. Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp Structure. J Phys Chem B 2020; 124:701-707. [DOI: 10.1021/acs.jpcb.9b06428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Sangyun Lee
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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21
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Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering. Biophys J 2020; 118:1076-1089. [PMID: 32027822 DOI: 10.1016/j.bpj.2020.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.
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22
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Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Phys Chem Chem Phys 2020; 22:18361-18373. [DOI: 10.1039/d0cp02738c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
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Affiliation(s)
- Irene Maffucci
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Damien Laage
- PASTEUR
- Département de chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
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23
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Mandal M, Das A, Mukhopadhyay C. Ubiquitin folds via a flip-twist-lock mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140299. [DOI: 10.1016/j.bbapap.2019.140299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 01/08/2023]
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24
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Mora M, Stannard A, Garcia-Manyes S. The nanomechanics of individual proteins. Chem Soc Rev 2020; 49:6816-6832. [DOI: 10.1039/d0cs00426j] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review provides an overview of the single protein force spectroscopy field, including the main techniques and the basic tools for analysing the data obtained from the single molecule experiments.
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Affiliation(s)
- Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
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25
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Gu Z, Chen SH, Ding Z, Song W, Wei W, Liu S, Ma G, Zhou R. The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide. NANOSCALE 2019; 11:22293-22304. [PMID: 31746904 DOI: 10.1039/c9nr04358f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molybdenum disulfide (MoS2), a representative hexagonal transition metal dichalcogenide (TMD), has been extensively exploited in biomedical applications due to its unique physicochemical properties and biocompatibility. However, the lack of adequate data regarding how MoS2 activates immunological responses of macrophages remains a key concern for its risk assessment. Here, we employ a combined theoretical and experimental approach to investigate the interactions of MoS2 and PEGylated MoS2 (MoS2-PEG) with macrophages. We first perform molecular dynamics simulations to examine the atomic-detailed interactions of MoS2 and MoS2-PEG nanoflakes with a realistic model of the macrophage membrane. We show that a small MoS2 nanoflake (edge length of 2.86 nm) is capable of penetrating the macrophage membrane independent of its concentration. We also demonstrate that when initiated with a corner point-on configuration, the surface-bound PEG chains of MoS2-PEG hinder its membrane insertion process, leading to a prolonged passage through the membrane. Moreover, when placed in a face-on arrangement initially, the MoS2-PEG exhibits a lower binding free energy than pristine MoS2 after its adsorption on the membrane surface. The PEG chains can even insert and get buried in the outer leaflet of the membrane, providing additional contact for membrane adsorption. Our flow cytometric experiments then show that the responses of macrophages to either MoS2-PEG or MoS2 are significantly higher than that of the control (no nanomaterial stimulus), with MoS2-PEG eliciting stronger cytokine secretion than the pristine MoS2. The characteristics of slower/prolonged membrane penetration and stronger membrane adsorption of MoS2-PEG compared to pristine MoS2 explain why it triggers more sustained stimulation and higher cytokine secretion in macrophages as observed in our experiments. Our findings reveal the underlying molecular mechanism of how MoS2-PEG influences the immune responses and suggest its potential applications in nanomedicine involving immune stimulation.
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Affiliation(s)
- Zonglin Gu
- Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
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26
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Perez-Aguilar JM, Kang SG, Zhang L, Zhou R. Modeling and Structural Characterization of the Sweet Taste Receptor Heterodimer. ACS Chem Neurosci 2019; 10:4579-4592. [PMID: 31553164 DOI: 10.1021/acschemneuro.9b00438] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sweet taste receptor, a heterodimer belonging to the class C G-protein coupled receptor (GPCR) family and composed of the T1R2 and T1R3 subunits, is responsible for the perception of natural sugars, sweet proteins, various d-amino acids, as well as artificial sweeteners. Despite the critical importance of the sweet receptor not only in mediating gustation but also in its role in the food industry, the architecture of the T1R2-T1R3 complex and the mechanism by which extracellular stimuli induce conformational changes that are propagated to the intracellular milieu, i.e., the signal transduction pathway, remain largely unknown. Here, we constructed and characterized a full-length structural model of the T1R2-T1R3 receptor, including both the transmembrane (TM) and extracellular (EC) domains of the heterodimer, using comparative modeling and extensive all-atom molecular dynamics simulations. Several heterodimer interfaces were first examined for the TM domain, and conformational changes occurring at the intracellular side and associated with the receptor's activation were characterized. From the analysis on the simulated data, putative allosteric binding sites for ligands, ions, and cholesterol were proposed. Also, insights into the protein interface of the TM domain upon activation are provided. The EC domain of the heterodimer, including both the Venus flytrap and cysteine-rich domains, was also investigated. Several important intersubunit interactions located at regions responsible for the receptor's proper function were observed, which resemble those recently identified in other class C GPCR members. Integration of the results from the TM and EC domains facilitates the generation of a full-length T1R2-T1R3 receptor. These findings along with the full-length structural model of the T1R2-T1R3 receptor provide a structural framework that may assist in understanding the mechanistic details associated with the receptor activation process for the sweet T1R2-T1R3 receptor as well as other members of the same family.
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Affiliation(s)
- Jose Manuel Perez-Aguilar
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Seung-gu Kang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Leili Zhang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
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27
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Tapia-Rojo R, Mazo JJ, Falo F. Thermal versus mechanical unfolding in a model protein. J Chem Phys 2019; 151:185105. [PMID: 31731855 DOI: 10.1063/1.5126071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to the information obtained using other denaturants since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is not likely to be meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is unfolded first mechanically through typical force spectroscopy-like protocols and next thermally. When unfolded by nonequilibrium force extension and constant force protocols, we recover a simple two-barrier landscape as the protein reaches the extended conformation through a metastable intermediate. Interestingly, folding-unfolding equilibrium simulations at low forces suggested a totally different scenario, where this metastable state plays little role in the unfolding mechanism, and the protein unfolds through two competing pathways [R. Tapia-Rojo et al., J. Chem. Phys. 141, 135102 (2014)]. Finally, we use Markov state models to describe the configurational space of the unperturbed protein close to the critical temperature. The thermal dynamics is well understood by a one-dimensional landscape along an appropriate reaction coordinate, however it is very different from the mechanical picture. In this sense, the results of our protein model for the mechanical and thermal descriptions provide incompatible views of the folding/unfolding landscape of the system, and the estimated quantities to zero force result are hard to interpret.
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Affiliation(s)
- Rafael Tapia-Rojo
- Departamento de Física de la Materia Condensada, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Juan J Mazo
- Departamento de Física de la Materia Condensada, Instituto de Ciencia de Materiales de Aragón, CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Fernando Falo
- Departamento de Física de la Materia Condensada, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain
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28
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Liu S, Yin X, Zhou H, Zhou B, Shao Q, Yang Z, Zhou R. Different platinum crystal surfaces show very distinct protein denaturation capabilities. NANOSCALE 2019; 11:19352-19361. [PMID: 31620747 DOI: 10.1039/c9nr03682b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications.
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Affiliation(s)
- Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Bo Zhou
- School of Electronic Engineering, Chengdu Technological University, Chengdu 611730, China
| | - Qiwen Shao
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China. and IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA and Department of Chemistry, Columbia University, New York, NY 10027, USA
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29
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He Z, Li J, Chen SH, Zhou R. Surface Inhomogeneity of Graphene Oxide Influences Dissociation of Aβ 16-21 Peptide Assembly. J Phys Chem B 2019; 123:9098-9103. [PMID: 31566974 DOI: 10.1021/acs.jpcb.9b07359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal peptide assembly and aggregation is associated with an array of neurodegenerative diseases including Alzheimer's disease (AD). A detailed understanding of how nanostructured materials such as oxidized graphene perturb the peptide assembly and subsequently induce fibril dissociation may open new directions for the development of potential AD treatments. Here, we investigate the impact of surface inhomogeneity of graphene oxide (GO) on the assembly of amyloid-beta Aβ16-21 peptides on GO surfaces with different degrees of oxidation using molecular dynamics simulations. Interestingly, nonuniform GO nanosheets (in terms of oxidation sites) have a much stronger perturbation effect on the structure of Aβ16-21 assembly. The Aβ peptides exhibit a remarkable tendency in binding to the scattered interfaces between unoxidized and oxidized regions, which induces the dissociation of Aβ amyloid fibril. These findings should deepen our understanding of surface-induced peptide dissociation and stimulate discovery of alternative AD treatments.
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Affiliation(s)
| | | | - Serena H Chen
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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30
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Zhou H, Yang Z, Tian X, Chen L, Lee S, Huynh T, Ge C, Zhou R. Lanosterol Disrupts the Aggregation of Amyloid-β Peptides. ACS Chem Neurosci 2019; 10:4051-4060. [PMID: 31369236 DOI: 10.1021/acschemneuro.9b00285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lanosterol, an amphipathic molecule, was discovered only very recently to effectively hinder the aggregation of lens proteins and dissolve the extremely stable fibrillar aggregates in cataracts. Here, we combined computational and experimental approaches to study how lanosterol disrupts the aggregation of another important peptide, amyloid-β (Aβ) peptide, associated with the Alzheimer's Disease (AD). Molecular dynamics simulations using the core amyloidogenic segment (KLVFFA) of Aβ peptide revealed that lanosterol exhibits at least two types of inhibition mechanism on the self-assembly of Aβ peptides. First, lanosterol entangles with peptides and forms a hydrophobic core with residues Phe-19 and Phe-20 in particular. Second, it interferes with the steric zipper interaction at the β-sheet-β-sheet interface. These simulation data suggest that lanosterol induces the unfolding of the Aβ peptide and the separation of the β-sheet layers. This predicted inhibition effect of lanosterol was then confirmed by an in vitro ThT fluorescence assay and AFM imaging. The cell toxicity assay also showed that the treatment of lanosterol indeed mitigates the cytotoxicity of the Aβ peptide in PC-12 cells. Moreover, lanosterol shows a stronger suppression effect on Aβ peptides' aggregation than cholesterol because of its higher hydrophobicity. This result establishes a foundation for the development of lanosterol-based potential therapies for AD and other protein conformational diseases.
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Affiliation(s)
- Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Xin Tian
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Lei Chen
- East District of Suzhou Municipal Hospital, Suzhou, Jiangsu 215001, China
| | - Sangyun Lee
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Tien Huynh
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Cuicui Ge
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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31
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Zhang L, Luan B, Zhou R. Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method. J Phys Chem B 2019; 123:7243-7252. [PMID: 31369702 DOI: 10.1021/acs.jpcb.9b02797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS2), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS2 contact angles in the literature depending on the aging process on the surface of a MoS2 nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS2 with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS2 with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS2-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS2. We conclude that to describe both fresh and aged MoS2 surfaces it is convenient to only adjust the Lennard-Jones parameter εS (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Binquan Luan
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biology Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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32
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Kato T, Schäfer K, Jaschonek S, Gauss J, Diezemann G. Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations. J Chem Phys 2019; 151:045102. [DOI: 10.1063/1.5111717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Takashi Kato
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Ken Schäfer
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Stefan Jaschonek
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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33
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Yang KC, Cui FC, Shi C, Chen WD, Li YQ. Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-019-2238-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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34
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Duan G, Chen L, Jing Z, De Luna P, Wen L, Zhang L, Zhao L, Xu J, Li Z, Yang Z, Zhou R. Robust Antibacterial Activity of Tungsten Oxide (WO 3-x) Nanodots. Chem Res Toxicol 2019; 32:1357-1366. [PMID: 31251039 DOI: 10.1021/acs.chemrestox.8b00399] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antibacterial agents are an important tool in the prevention of bacterial infections. Inorganic materials are attractive due to their high stability under a variety of conditions compared to organic antibacterial agents. Herein tungsten oxide nanodots (WO3-x), synthesized by a simple one-pot synthetic approach, were found to exhibit strong antibacterial capabilities. The analyses with colony-forming units (CFU) showed an excellent antibacterial activity of WO3-x against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus) strains. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed clear damages to the bacterial cell membranes, which was further confirmed by molecular dynamics simulations. Additionally, exposure to simulated sunlight was found to further increase the germicidal activity of WO3-x nanodots, a 30 min exposure to sunlight combined with 50 μg/mL WO3-x nanodots showed a 70% decrease in E. coli viability compared to without exposure. Electron spin resonance spectroscopy (ESR) was used to elucidate the underlying mechanism of this photocatalytic activity through the generation of hydroxyl radical species. The cell counting kit-8 (CCK-8) and the live/dead assay were further employed to evaluate the cytotoxicity of WO3-x nanodots on eukaryotic cells, which demonstrated their general biocompatibility. In summary, our results suggest WO3-x nanodots have considerable potential in antibacterial applications, while also being biocompatible at large.
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Affiliation(s)
- Guangxin Duan
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China.,Center of Burn & Trauma , Affiliated Suzhou Hospital of Nanjing Medical University , Suzhou 215008 , China
| | - Lu Chen
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Zhifeng Jing
- IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Phil De Luna
- IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ling Wen
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Leili Zhang
- IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Lin Zhao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Jiaying Xu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Zhen Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Zaixing Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China
| | - Ruhong Zhou
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions , Soochow University , Suzhou 215123 , China.,IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States.,Department of Chemistry , Columbia University , New York , New York 10027 , United States
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35
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Muttathukattil AN, Singh PC, Reddy G. Role of Disulfide Bonds and Topological Frustration in the Kinetic Partitioning of Lysozyme Folding Pathways. J Phys Chem B 2019; 123:3232-3241. [PMID: 30913878 DOI: 10.1021/acs.jpcb.9b00739] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disulfide bonds in proteins can strongly influence the folding pathways by constraining the conformational space. Lysozyme has four disulfide bonds and is widely studied for its antibacterial properties. Experiments on lysozyme infer that the protein folds through a fast and a slow pathway. However, the reasons for the kinetic partitioning in the folding pathways are not completely clear. Using a coarse-grained protein model and simulations, we show that two out of the four disulfide bonds, which are present in the α-domain of lysozyme, are responsible for the slow folding pathway. In this pathway, a kinetically trapped intermediate state, which is close to the native state, is populated. In this state, the orientations of α-helices present in the α-domain are misaligned relative to each other. The protein in this state has to partially unfold by breaking down the interhelical contacts between the misaligned helices to fold to the native state. However, the topological constraints due to the two disulfide bonds present in the α-domain make the protein less flexible, and it is trapped in this conformation for hundreds of milliseconds. On disabling these disulfide bonds, we find that the kinetically trapped intermediate state and the slow folding pathway disappear. Simulations mimicking the folding of protein without disulfide bonds under oxidative conditions show that the native disulfide bonds are formed as the protein folds, indicating that folding guides the formation of disulfide bonds. The sequence of formation of the disulfide bonds is Cys64-Cys80 → Cys76-Cys94 → Cys30-Cys115 → Cys6-Cys127. Any disulfide bond that forms before its precursor in the sequence has to break and follow the sequence for the protein to fold. These results show that lysozyme also serves as a very good model system to probe the role of disulfide bonds and topological frustration in protein folding. The predictions from the simulations can be verified by single-molecule fluorescence resonance energy transfer or single-molecule pulling experiments, which can probe heterogeneity in the folding pathways.
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Affiliation(s)
- Aswathy N Muttathukattil
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru 560012 , Karnataka , India
| | - Prashant Chandra Singh
- School of Chemical Science , Indian Association for the Cultivation of Science , 2A & 2B, Raja S.C. Mullick Road , Jadavpur, Kolkata 700032 , India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru 560012 , Karnataka , India
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36
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Mechanobiology: protein refolding under force. Emerg Top Life Sci 2018; 2:687-699. [PMID: 33530665 DOI: 10.1042/etls20180044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023]
Abstract
The application of direct force to a protein enables to probe wide regions of its energy surface through conformational transitions as unfolding, extending, recoiling, collapsing, and refolding. While unfolding under force typically displayed a two-state behavior, refolding under force, from highly extended unfolded states, displayed a more complex behavior. The first recording of protein refolding at a force quench step displayed an initial rapid elastic recoil, followed by a plateau phase at some extension, concluding with a collapse to a final state, at which refolding occurred. These findings stirred a lively discussion, which led to further experimental and theoretical investigation of this behavior. It was demonstrated that the polymeric chain of the unfolded protein is required to fully collapse to a globular conformation for the maturation of native structure. This behavior was modeled using one-dimensional free energy landscape over the end-to-end length reaction coordinate, the collective measured variable. However, at low forces, conformational space is not well captured by such models, and using two-dimensional energy surfaces provides further insight into the dynamics of this process. This work reviews the main concepts of protein refolding under constant force, which is essential for understanding how mechanotransducing proteins operate in vivo.
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37
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Languin-Cattoën O, Melchionna S, Derreumaux P, Stirnemann G, Sterpone F. Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses. J Phys Chem B 2018; 122:11922-11930. [PMID: 30444631 DOI: 10.1021/acs.jpcb.8b08711] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The perturbation of a protein conformation by a physiological fluid flow is crucial in various biological processes including blood clotting and bacterial adhesion to human tissues. Investigating such mechanisms by computer simulations is thus of great interest, but it requires development of ad hoc strategies to mimic the complex hydrodynamic interactions acting on the protein from the surrounding flow. In this study, we apply the Lattice Boltzmann Molecular Dynamics (LBMD) technique built on the implicit solvent coarse-grained model for protein Optimized Potential for Efficient peptide structure Prediction (OPEP) and a mesoscopic representation of the fluid solvent, to simulate the unfolding of a small globular cold-shock protein in shear flow and to compare it to the unfolding mechanisms caused either by mechanical or thermal perturbations. We show that each perturbation probes a specific weakness of the protein and causes the disruption of the native fold along different unfolding pathways. Notably, the shear flow and the thermal unfolding exhibit very similar pathways, while because of the directionality of the perturbation, the unfolding under force is quite different. For force and thermal disruption of the native state, the coarse-grained simulations are compared to all-atom simulations in explicit solvent, showing an excellent agreement in the explored unfolding mechanisms. These findings encourage the use of LBMD based on the OPEP model to investigate how a flow can affect the function of larger proteins, for example, in catch-bond systems.
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Affiliation(s)
- Olivier Languin-Cattoën
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | | | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Guillaume Stirnemann
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique , CNRS, Institut de Biologie Physico-Chimique, Sorbonne Paris Cité, PSL University , 13 rue Pierre et Marie Curie , 75005 Paris , France
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38
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Raskar T, Koh CY, Niebling S, Kini RM, Hosur MV. X-ray crystallographic analysis of time-dependent binding of guanidine hydrochloride to HEWL: First steps during protein unfolding. Int J Biol Macromol 2018; 122:903-913. [PMID: 30412756 DOI: 10.1016/j.ijbiomac.2018.11.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/24/2018] [Accepted: 11/05/2018] [Indexed: 01/02/2023]
Abstract
Time-dependent binding of guanidine hydrochloride (GuHCl) to hen egg-white lysozyme (HEWL), and effects of this binding on the protein structure have been investigated by solving X-ray structures of crystalline complexes. The complexes have been prepared by soaking, for different periods of time, native lysozyme crystals in solutions containing 2.5M GuHCl. In the refined structures, the number of water molecules in the protein's first solvent shell has progressively decreased from 152 to 115, showing protein's preference for guanidinium over water. Guanidinium ions preferentially hydrogen bond with the backbone carbonyl oxygen atoms. In their van der Waals interactions, they do not show any preference for apolar residues. Guanidinium ions have replaced water molecules that form cages around exposed hydrophobic residues. Guanidinium binding has decreased the average length of water-water hydrogen bond by 0.1Å. The hydrogen bonds between main chain atoms have been weakened by GuHCl, and this may be the reason for increased potency of GuHCl compared to urea. Guanidinium binding destabilizes the β-domain by causing loss of hydrogen bonds involving Asn 59 side chain. Interestingly, this loss is almost identical to that observed in structures of amyloidogenic variants of human lysozyme. Compounds preventing this loss could be anti-amyloidogenic.
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Affiliation(s)
- Tushar Raskar
- Ultrafast Molecular Dynamics Group, Centre for Hybrid Nanostructures (ChyN), University of Hamburg, Germany
| | - Cho Yeow Koh
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Stephan Niebling
- Ultrafast Molecular Dynamics Group, Centre for Hybrid Nanostructures (ChyN), University of Hamburg, Germany
| | - R M Kini
- Department of Biological Sciences, National University of Singapore, Singapore
| | - M V Hosur
- National Institute of Advanced Studies, IISc campus, Bengaluru 560012, India.
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39
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Izadi D, Chen Y, Whitmore ML, Slivka JD, Ching K, Lapidus LJ, Comstock MJ. Combined Force Ramp and Equilibrium High-Resolution Investigations Reveal Multipath Heterogeneous Unfolding of Protein G. J Phys Chem B 2018; 122:11155-11165. [DOI: 10.1021/acs.jpcb.8b06199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dena Izadi
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yujie Chen
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Miles L. Whitmore
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joseph D. Slivka
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin Ching
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lisa J. Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthew J. Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
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40
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Abstract
A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo. REVIEWERS This article was reviewed by Eugene Koonin and Frank Eisenhaber.
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41
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Knoch F, Schäfer K, Diezemann G, Speck T. Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding. J Chem Phys 2018; 148:044109. [PMID: 29390802 DOI: 10.1063/1.5010435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.
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Affiliation(s)
- Fabian Knoch
- Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Ken Schäfer
- Institut für Physikalische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Thomas Speck
- Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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42
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Abstract
Up to 40% of intracellular water is confined due to the dense packing of macromolecules, ions, and osmolytes. Despite the large body of work concerning the effect of additives on the biomolecular structure and stability, the role of crowding and heterogeneity in these interactions is not well understood. Here, infrared spectroscopy and molecular dynamics simulations are used to describe the mechanisms by which crowding modulates hydrogen bonding interactions between water and dimethyl sulfoxide (DMSO). Specifically, we use formamide and dimethylformamide (DMF) as molecular crowders and show that the S═O hydrogen bond populations in aqueous mixtures are increased by both amides. These additives increase the amount of water within the DMSO first solvation shell through two mechanisms: (a) directly stabilizing water-DMSO hydrogen bonds; (b) increasing water exposure by destabilizing DMSO-DMSO self-interactions. Further, we quantified the hydrogen bond enthalpies between the different components: DMSO-water (61 kJ/mol) > DMSO-formamide (32 kJ/mol) > water-water (23 kJ/mol) ≫ formamide-water (4.7 kJ/mol). Spectra of carbonyl stretching vibrations show that DMSO induces the dehydration of amides as a result of strong DMSO-water interactions, which has been suggested as the main mechanism of protein destabilization.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry , University of Texas at Austin , 105 E 24th St. Stop A5300 , Austin , TX 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , University of Texas at Austin , 105 E 24th St. Stop A5300 , Austin , TX 78712 , United States
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43
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Weber JK, Kang SG, Zhou R. Rare Dissipative Transitions Punctuate the Initiation of Chemical Denaturation in Proteins. Biophys J 2018; 114:812-821. [PMID: 29490243 DOI: 10.1016/j.bpj.2017.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/18/2017] [Accepted: 12/27/2017] [Indexed: 10/17/2022] Open
Abstract
Protein unfolding dynamics are bound by their degree of entropy production, a quantity that relates the amount of heat dissipated by a nonequilibrium process to a system's forward and time-reversed trajectories. We here explore the statistics of heat dissipation that emerge in protein molecules subjected to a chemical denaturant. Coupling large molecular dynamics datasets and Markov state models with the theory of entropy production, we demonstrate that dissipative processes can be rigorously characterized over the course of the urea-induced unfolding of the protein chymotrypsin inhibitor 2. By enumerating full entropy production probability distributions as a function of time, we first illustrate that distinct passive and dissipative regimes are present in the denaturation dynamics. Within the dissipative dynamical region, we next find that chymotrypsin inhibitor 2 is strongly driven into unfolded states in which the protein's hydrophobic core has been penetrated by urea molecules and disintegrated. Detailed analyses reveal that urea's interruption of key hydrophobic contacts between core residues causes many of the protein's native structural features to dissolve.
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Affiliation(s)
- Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York
| | - Seung-Gu Kang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York; Department of Chemistry, Columbia University, New York, New York.
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44
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Perales-Calvo J, Giganti D, Stirnemann G, Garcia-Manyes S. The force-dependent mechanism of DnaK-mediated mechanical folding. SCIENCE ADVANCES 2018; 4:eaaq0243. [PMID: 29487911 PMCID: PMC5817926 DOI: 10.1126/sciadv.aaq0243] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/09/2018] [Indexed: 05/27/2023]
Abstract
It is well established that chaperones modulate the protein folding free-energy landscape. However, the molecular determinants underlying chaperone-mediated mechanical folding remain largely elusive, primarily because the force-extended unfolded conformation fundamentally differs from that characterized in biochemistry experiments. We use single-molecule force-clamp spectroscopy, combined with molecular dynamics simulations, to study the effect that the Hsp70 system has on the mechanical folding of three mechanically stiff model proteins. Our results demonstrate that, when working independently, DnaJ (Hsp40) and DnaK (Hsp70) work as holdases, blocking refolding by binding to distinct substrate conformations. Whereas DnaK binds to molten globule-like forms, DnaJ recognizes a cryptic sequence in the extended state in an unanticipated force-dependent manner. By contrast, the synergetic coupling of the Hsp70 system exhibits a marked foldase behavior. Our results offer unprecedented molecular and kinetic insights into the mechanisms by which mechanical force finely regulates chaperone binding, directly affecting protein elasticity.
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Affiliation(s)
- Judit Perales-Calvo
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
| | - David Giganti
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
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45
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Luan B, Zhou S, Wang D, Zhou R. Detecting Interactions between Nanomaterials and Cell Membranes by Synthetic Nanopores. ACS NANO 2017; 11:12615-12623. [PMID: 29161017 DOI: 10.1021/acsnano.7b07005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Engineered nanomaterials have been increasingly utilized in industry for various consumer products, environmental treatments, energy storage, and biomedical applications. Meanwhile, it has been established that certain nanomaterials can be toxic to biological cells from extensive experimental and theoretical studies. Despite that the exact molecular mechanisms of this nanomaterial toxicity are still not well understood, it is ubiquitous that their interactions with cell membranes, through either endocytosis or penetration (and thus potential lysis), act as the first step toward the inflammation or even the death of a cell. To facilitate the study of nanomaterial-membrane interactions, here we demonstrate a nanopore-based single-molecule approach that can be applied to monitor a specific nanomaterial-membrane interaction in real time. Combined with molecular dynamics and experimental approaches, we show how an ionic current can be used to detect membrane damage by a graphene nanosheet and illustrate the underlying molecular mechanism. More generally, we expect that measured transmembrane ionic currents (both DC and AC) can signify many particle-induced membrane modifications, such as hole formation, particle adsorption, and protein insertion.
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Affiliation(s)
- Binquan Luan
- Computational Biology Center, IBM Thomas J. Watson Research , Yorktown Heights, New York 10598, United States
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714, China
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research , Yorktown Heights, New York 10598, United States
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46
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Abstract
Inspired by Somero's corresponding state principle that relates protein enhanced thermal stability with mechanical rigidity, we deployed state of the art computational techniques (based on atomistic steered molecular dynamics and Hamiltonian-replica exchange simulations) to study the in silico realization of mechanical and thermal unfolding of two homologous Csp proteins that have evolved to thrive in different thermal environments. By complementing recent single-molecule experiments, we unambiguously show that, for these homologues whose structures are very similar, the increased thermal resistance of the thermophilic variant is not associated with an increased mechanical stability. Our approach provides microscopic insights that are otherwise inaccessible to experimental techniques, and explains why the protein weak spots for thermal and mechanical denaturation are distinct.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
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47
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Zhao X, Zeng X, Lu C, Yan J. Studying the mechanical responses of proteins using magnetic tweezers. NANOTECHNOLOGY 2017; 28:414002. [PMID: 28766506 DOI: 10.1088/1361-6528/aa837e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mechanical stability of proteins has been extensively studied using AFM as a single-molecule force spectroscopy method. While this has led to many important results, these studies have been mainly limited to fast unfolding at a high-force regime due to the rapid mechanical drift in most AFM stretching experiments. Therefore, there is a gap between the knowledge obtained at a high-force regime and the mechanical properties of proteins at a lower force regime which is often more physiologically relevant. Recent studies have demonstrated that this gap can be addressed by stretching single protein molecules using magnetic tweezers, due to the excellent mechanical stability this technology offers. Here we review magnetic tweezers technology and its current application in studies of the force-dependent stability and interactions of proteins.
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Affiliation(s)
- Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
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48
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Huston S, Collins J, Sun F, Zhang T, Vaden TD, Zhang YHP, Fu J. An activity transition from NADH dehydrogenase to NADH oxidase during protein denaturation. Biotechnol Appl Biochem 2017; 65:286-293. [PMID: 28881090 DOI: 10.1002/bab.1607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/14/2017] [Accepted: 09/02/2017] [Indexed: 11/07/2022]
Abstract
A decrease in the specific activity of an enzyme is commonly observed when the enzyme is inappropriately handled or is stored over an extended period. Here, we reported a functional transition of an FMN-bound diaphorase (FMN-DI) that happened during the long-term storage process. It was found that FMN-DI did not simply lose its β-nicotinamide adenine diphosphate (NADH) dehydrogenase activity after a long-time storage, but obtained a new enzyme activity of NADH oxidase. Further mechanistic studies suggested that the alteration of the binding strength of an FMN cofactor with a DI protein could be responsible for this functional switch of the enzyme.
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Affiliation(s)
- Scott Huston
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, USA
| | - John Collins
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, USA
| | - Fangfang Sun
- Cell Free Bioinnovations Inc., Blacksburg, VA, USA
| | - Ting Zhang
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, USA
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, USA
| | - Y-H Percival Zhang
- Cell Free Bioinnovations Inc., Blacksburg, VA, USA
- Department of Biological Systems Engineering, Virginia Tech, VA, USA
| | - Jinglin Fu
- Department of Chemistry, Rutgers University-Camden, Camden, NJ, USA
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
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49
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Macgregor M, Williams R, Downes J, Bachhuka A, Vasilev K. The Role of Controlled Surface Topography and Chemistry on Mouse Embryonic Stem Cell Attachment, Growth and Self-Renewal. MATERIALS (BASEL, SWITZERLAND) 2017; 10:E1081. [PMID: 28906470 PMCID: PMC5615735 DOI: 10.3390/ma10091081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022]
Abstract
The success of stem cell therapies relies heavily on our ability to control their fate in vitro during expansion to ensure an appropriate supply. The biophysical properties of the cell culture environment have been recognised as a potent stimuli influencing cellular behaviour. In this work we used advanced plasma-based techniques to generate model culture substrates with controlled nanotopographical features of 16 nm, 38 nm and 68 nm in magnitude, and three differently tailored surface chemical functionalities. The effect of these two surface properties on the adhesion, spreading, and self-renewal of mouse embryonic stem cells (mESCs) were assessed. The results demonstrated that physical and chemical cues influenced the behaviour of these stem cells in in vitro culture in different ways. The size of the nanotopographical features impacted on the cell adhesion, spreading and proliferation, while the chemistry influenced the cell self-renewal and differentiation.
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Affiliation(s)
- Melanie Macgregor
- School of Engineering, Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Rachel Williams
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.
| | - Joni Downes
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.
| | - Akash Bachhuka
- Institute for Photonics and Advanced Sensing, University of Adelaide, Adelaide, SA 5000, Australia.
| | - Krasimir Vasilev
- School of Engineering, Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
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50
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Exploring the Denatured State Ensemble by Single-Molecule Chemo-Mechanical Unfolding: The Effect of Force, Temperature, and Urea. J Mol Biol 2017; 430:450-464. [PMID: 28782558 DOI: 10.1016/j.jmb.2017.07.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 11/22/2022]
Abstract
While it is widely appreciated that the denatured state of a protein is a heterogeneous conformational ensemble, there is still debate over how this ensemble changes with environmental conditions. Here, we use single-molecule chemo-mechanical unfolding, which combines force and urea using the optical tweezers, together with traditional protein unfolding studies to explore how perturbants commonly used to unfold proteins (urea, force, and temperature) affect the denatured-state ensemble. We compare the urea m-values, which report on the change in solvent accessible surface area for unfolding, to probe the denatured state as a function of force, temperature, and urea. We find that while the urea- and force-induced denatured states expose similar amounts of surface area, the denatured state at high temperature and low urea concentration is more compact. To disentangle these two effects, we use destabilizing mutations that shift the Tm and Cm. We find that the compaction of the denatured state is related to changing temperature as the different variants of acyl-coenzyme A binding protein have similar m-values when they are at the same temperature but different urea concentration. These results have important implications for protein folding and stability under different environmental conditions.
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