1
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Rajoub N, Gerard CJJ, Pantuso E, Fontananova E, Caliandro R, Belviso BD, Curcio E, Nicoletta FP, Pullen J, Chen W, Heng JYY, Ruane S, Liddell J, Alvey N, Ter Horst JH, Di Profio G. A workflow for the development of template-assisted membrane crystallization downstream processing for monoclonal antibody purification. Nat Protoc 2023; 18:2998-3049. [PMID: 37697106 DOI: 10.1038/s41596-023-00869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/06/2023] [Indexed: 09/13/2023]
Abstract
Monoclonal antibodies (mAbs) are commonly used biologic drugs for the treatment of diseases such as rheumatoid arthritis, multiple sclerosis, COVID-19 and various cancers. They are produced in Chinese hamster ovary cell lines and are purified via a number of complex and expensive chromatography-based steps, operated in batch mode, that rely heavily on protein A resin. The major drawback of conventional procedures is the high cost of the adsorption media and the extensive use of chemicals for the regeneration of the chromatographic columns, with an environmental cost. We have shown that conventional protein A chromatography can be replaced with a single crystallization step and gram-scale production can be achieved in continuous flow using the template-assisted membrane crystallization process. The templates are embedded in a membrane (e.g., porous polyvinylidene fluoride with a layer of polymerized polyvinyl alcohol) and serve as nucleants for crystallization. mAbs are flexible proteins that are difficult to crystallize, so it can be challenging to determine the optimal conditions for crystallization. The objective of this protocol is to establish a systematic and flexible approach for the design of a robust, economic and sustainable mAb purification platform to replace at least the protein A affinity stage in traditional chromatography-based purification platforms. The procedure provides details on how to establish the optimal parameters for separation (crystallization conditions, choice of templates, choice of membrane) and advice on analytical and characterization methods.
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Affiliation(s)
- Nazer Rajoub
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Charline J J Gerard
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Elvira Pantuso
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy
| | - Enrica Fontananova
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy
| | - Rocco Caliandro
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Cristallografia (IC), Bari, Italy
| | - Benny D Belviso
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Cristallografia (IC), Bari, Italy
| | - Efrem Curcio
- Department of Environmental Engineering, University of Calabria, Rende, Italy
| | - Fiore P Nicoletta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Edificio Polifunzionale, Rende, Italy
| | - James Pullen
- FUJIFILM Diosynth Biotechnologies, Billingham, UK
| | - Wenqian Chen
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Jerry Y Y Heng
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Sean Ruane
- Center for Process Innovation (CPI), Darlington, UK
| | - John Liddell
- Center for Process Innovation (CPI), Darlington, UK
| | | | - Joop H Ter Horst
- CMAC Future Manufacturing Research Hub, c/o Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Technology and Innovation Centre, Glasgow, UK
| | - Gianluca Di Profio
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Tecnologia delle Membrane (ITM), Rende, Italy.
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2
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Gerard CJ, Briuglia ML, Rajoub N, Mastropietro TF, Chen W, Heng JYY, Di Profio G, ter Horst JH. Template-Assisted Crystallization Behavior in Stirred Solutions of the Monoclonal Antibody Anti-CD20: Probability Distributions of Induction Times. CRYSTAL GROWTH & DESIGN 2022; 22:3637-3645. [PMID: 35673394 PMCID: PMC9164231 DOI: 10.1021/acs.cgd.1c01324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/14/2022] [Indexed: 05/14/2023]
Abstract
We present a method to determine the template crystallization behavior of proteins. This method is a statistical approach that accounts for the stochastic nature of nucleation. It makes use of batch-wise experiments under stirring conditions in volumes smaller than 0.3 mL to save material while mimicking larger-scale processes. To validate our method, it was applied to the crystallization of a monoclonal antibody of pharmaceutical interest, Anti-CD20. First, we determined the Anti-CD20 phase diagram in a PEG-400/Na2SO4/water system using the batch method, as, to date, no such data on Anti-CD20 solubility have been reported. Then, the probability distribution of induction times was determined experimentally, in the presence of various mesoporous silica template particles, and crystallization of Anti-CD20 in the absence of templates was compared to template-assisted crystallization. The probability distribution of induction times is shown to be a suitable method to determine the effect of template particles on protein crystallization. The induction time distribution allows for the determination of two key parameters of nucleation, the nucleation rate and the growth time. This study shows that the use of silica particles leads to faster crystallization and a higher nucleation rate. The template particle characteristics are shown to be critical parameters to efficiently promote protein crystallization.
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Affiliation(s)
- Charline
J. J. Gerard
- EPSRC
Centre for Innovative Manufacturing in Continuous Manufacturing and
Crystallisation, Strathclyde Institute of Pharmacy and Biomedical
Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, U.K.
- SMS
Laboratory EA 3233, Place Emile Blondel, University of Rouen-Normandie, CEDEX, F-76821 Mont Saint Aignan, France
| | - Maria L. Briuglia
- EPSRC
Centre for Innovative Manufacturing in Continuous Manufacturing and
Crystallisation, Strathclyde Institute of Pharmacy and Biomedical
Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, U.K.
| | - Nazer Rajoub
- EPSRC
Centre for Innovative Manufacturing in Continuous Manufacturing and
Crystallisation, Strathclyde Institute of Pharmacy and Biomedical
Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, U.K.
| | - Teresa F. Mastropietro
- Consiglio
Nazionale delle Ricerche (CNR), Istituto
per la Tecnologia delle Membrane (ITM), Via P. Bucci, cubo 17/C, I-87036, Rende, Cosenza, Italy
| | - Wenqian Chen
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London, SW7 2AZ, U.K.
| | - Jerry Y. Y. Heng
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London, SW7 2AZ, U.K.
| | - Gianluca Di Profio
- Consiglio
Nazionale delle Ricerche (CNR), Istituto
per la Tecnologia delle Membrane (ITM), Via P. Bucci, cubo 17/C, I-87036, Rende, Cosenza, Italy
| | - Joop H. ter Horst
- EPSRC
Centre for Innovative Manufacturing in Continuous Manufacturing and
Crystallisation, Strathclyde Institute of Pharmacy and Biomedical
Sciences, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, U.K.
- SMS
Laboratory EA 3233, Place Emile Blondel, University of Rouen-Normandie, CEDEX, F-76821 Mont Saint Aignan, France
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3
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Calculated Terahertz Spectra of Glycine Oligopeptide Solutions Confined in Carbon Nanotubes. Polymers (Basel) 2019; 11:polym11020385. [PMID: 30960369 PMCID: PMC6419217 DOI: 10.3390/polym11020385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022] Open
Abstract
To reduce the intense terahertz (THz) wave absorption of water and increase the signal-to-noise ratio, the THz spectroscopy detection of biomolecules usually operates using the nanofluidic channel technologies in practice. The effects of confinement due to the existence of nanofluidic channels on the conformation and dynamics of biomolecules are well known. However, studies of confinement effects on the THz spectra of biomolecules are still not clear. In this work, extensive all-atom molecular dynamics simulations are performed to investigate the THz spectra of the glycine oligopeptide solutions in free and confined environments. THz spectra of the oligopeptide solutions confined in carbon nanotubes (CNTs) with different radii are calculated and compared. Results indicate that with the increase of the degree of confinement (the reverse of the radius of CNT), the THz absorption coefficient decreases monotonically. By analyzing the diffusion coefficient and dielectric relaxation dynamics, the hydrogen bond life, and the vibration density of the state of the water molecules in free solution and in CNTs, we conclude that the confinement effects on the THz spectra of biomolecule solutions are mainly to slow down the dynamics of water molecules and hence to reduce the THz absorption of the whole solution in confined environments.
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4
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Artusio F, Pisano R. Surface-induced crystallization of pharmaceuticals and biopharmaceuticals: A review. Int J Pharm 2018; 547:190-208. [PMID: 29859921 DOI: 10.1016/j.ijpharm.2018.05.069] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 01/18/2023]
Abstract
Despite the wide occurrence of crystallization in the pharmaceutical industry, deep understanding and fine control of the process remain a tricky issue. Nevertheless, the successful manufacturing of finished pharmaceutical products, as well as the structural determination of biopharmaceuticals, depend on the size, form, shape and purity of the crystals. The ability of substrates with precise chemistry and topological features to induce nucleation has been thoroughly assessed during the recent years. This paper reviews the major advances and discoveries in controlling small molecule drug and protein crystallization by means of engineered surfaces. By designing superficial properties and morphology, it has been possible to tune the polymorph outcome, shorten the nucleation induction time, impose specific crystal shapes, control the crystal size and carry out crystallization at very low supersaturation levels. Such achievements underline the potential of surface-induced crystallization to provide an ideal platform for the study of the nucleation process and gain control over its stochastic nature.
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Affiliation(s)
- Fiora Artusio
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy.
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5
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Wang Z, Liu YF, Yan H, Tong H, Mei Z. Theoretical Investigations of the Chiral Transition of α-Amino Acid Confined in Various Sized Armchair Boron-Nitride Nanotubes. J Phys Chem A 2017; 121:1833-1840. [PMID: 28139928 DOI: 10.1021/acs.jpca.7b00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We computationally study the chiral transition process of the α-Ala molecule under confined different sizes of armchair SWBNNTs to explore the confinement effect. We find that the influence of a confinement environment (in armchair SWBNNTs) on the α-Ala molecule would lead to different reaction pathways. Meanwhile, the preferred reaction pathway is also different in various sizes of armchair SWBNNTs, and their energy barriers for the rate-limiting step decrease rapidly with the decreasing of the diameters of the nanotubes. It is obvious that significant decrease of the chiral transition energy barrier occurs compared with the isolated α-Ala molecule chirality conversion mechanism, by ∼15.6 kcal mol-1, highlighting the improvement in the activity the enantiomers of α-Ala molecule. We concluded that the confinement environment has a significant impact at the nanoscale on the enantiomer transformation process of the chiral molecule.
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Affiliation(s)
- Zuocheng Wang
- The Department of Physics, Baicheng Normal University , Baicheng 137000, P.R. China.,The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Yan Fang Liu
- The Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, P.R. China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101, Shandong, P.R. China
| | - Honyan Yan
- The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China.,Department of Computer Science, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Hua Tong
- The Department of Physics, Baicheng Normal University , Baicheng 137000, P.R. China.,The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Zemin Mei
- The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China.,Department of Chemistry, Baicheng Normal University , Baicheng 137000, P.R. China
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6
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Echeverria C, Kapral R. Enzyme kinetics and transport in a system crowded by mobile macromolecules. Phys Chem Chem Phys 2015; 17:29243-50. [DOI: 10.1039/c5cp05056a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of an elastic network model for the enzyme 4-oxalocrotonate tautomerase is studied in a system crowded by mobile macromolecules, also modeled by elastic networks.
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Affiliation(s)
- Carlos Echeverria
- Chemical Physics Theory Group
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
| | - Raymond Kapral
- Chemical Physics Theory Group
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
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7
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Meng Y, Dai X, Xin M, Tian C, Liu H, Jin M, Wang Z, Zhang RQ. Environmental-confinement-induced stability enhancement of chiral molecules. Chemphyschem 2014; 15:2672-5. [PMID: 24954782 DOI: 10.1002/cphc.201402104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 11/12/2022]
Abstract
We computationally study the transition process of a chiral difluorobenzo[c]phenanthrene (DFBcPh) molecule within non-polar fullerene C(260) to explore the confinement effect. We find blue-shifts in the infrared and Raman spectra of the molecule inside the fullerene relative to those of isolated systems. Six types of spectrum features of the molecule appear in the 0-60 cm(-1) band. Interestingly, the energy barrier of the chiral transformation of the molecule is elevated by 15.88 kcal mol(-1) upon the confinement by the fullerene, indicating improvement in the stability of the enantiomers. The protection by C(260) lowers the highest occupied molecular orbital energy level and lifts the lowest unoccupied molecular orbital energy level of the chiral molecule such that the chiral molecule is further chemically stabilized. We concluded that the confinement environment has an impact at the nanoscale on the enantiomer transformation process of the chiral molecule.
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Affiliation(s)
- Yan Meng
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China)
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8
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Feig M, Sugita Y. Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model 2013; 45:144-56. [PMID: 24036504 DOI: 10.1016/j.jmgm.2013.08.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 12/21/2022]
Abstract
An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States; RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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9
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Affiliation(s)
- Tristan Giesa
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and
- Center for Computational Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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10
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Saha R, Rakshit S, Verma PK, Mitra RK, Pal SK. Protein-cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles. J Mol Recognit 2013; 26:59-66. [DOI: 10.1002/jmr.2246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ranajay Saha
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Surajit Rakshit
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Pramod Kumar Verma
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
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11
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Su G, Czader A, Homouz D, Bernardes G, Mateen S, Cheung MS. Multiscale Simulation on a Light-Harvesting Molecular Triad. J Phys Chem B 2012; 116:8460-73. [DOI: 10.1021/jp212273n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guoxiong Su
- Department of Physics, University of Houston, Houston, Texas 77204, United
States
| | - Arkadiusz Czader
- Department of Chemistry, University of Houston, Houston, Texas 77204, United
States
| | - Dirar Homouz
- Department of Applied
Math and
Sciences, Khalifa University, Abu Dhabi,
United Arab Emirates
| | - Gabriela Bernardes
- Department of Physics, University of Houston, Houston, Texas 77204, United
States
| | - Sana Mateen
- Department of Physics, University of Houston, Houston, Texas 77204, United
States
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United
States
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12
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Samiotakis A, Cheung MS. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I. J Chem Phys 2012; 135:175101. [PMID: 22070323 DOI: 10.1063/1.3656691] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.
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13
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Echeverria C, Kapral R. Molecular crowding and protein enzymatic dynamics. Phys Chem Chem Phys 2012; 14:6755-63. [DOI: 10.1039/c2cp40200a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Shental-Bechor D, Levy Y. Communication: Folding of glycosylated proteins under confinement. J Chem Phys 2011; 135:141104. [DOI: 10.1063/1.3650700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Aguilar X, F. Weise C, Sparrman T, Wolf-Watz M, Wittung-Stafshede P. Macromolecular Crowding Extended to a Heptameric System: The Co-chaperonin Protein 10. Biochemistry 2011; 50:3034-44. [DOI: 10.1021/bi2002086] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ximena Aguilar
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Christoph F. Weise
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Tobias Sparrman
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Magnus Wolf-Watz
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
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16
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Christiansen A, Wang Q, Samiotakis A, Cheung MS, Wittung-Stafshede P. Factors Defining Effects of Macromolecular Crowding on Protein Stability: An in Vitro/in Silico Case Study Using Cytochrome c. Biochemistry 2010; 49:6519-30. [DOI: 10.1021/bi100578x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Christiansen
- Department of Chemistry, Chemical Biological Center, Umeå University, 901 87 Umeå, Sweden
| | - Qian Wang
- Department of Physics, University of Houston, Houston, Texas 77204
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17
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Abstract
The structural and dynamical properties of macromolecules in confining or crowded environments are different from those in simple bulk liquids. In this paper, both the conformational and diffusional dynamics of globular polymers are studied in solutions containing fixed spherical obstacles. These properties are studied as a function of obstacle volume fraction and size, as well as polymer chain length. The results are obtained using a hybrid scheme that combines multiparticle collision dynamics of the solvent with molecular dynamics that includes the interactions among the polymer monomers and between the polymer beads and obstacles and solvent molecules. The dynamics accounts for hydrodynamic interactions among the polymer beads and intermolecular forces with the solvent molecules. We consider polymers in poor solvents where the polymer chain adopts a compact globular structure in solution. Our results show that the collapse of the polymer chain to a compact globular state is strongly influenced by the obstacle array. A nonmonotonic variation in the radius of gyration with time is observed and the collapse time scale is much longer than that in simple solutions without obstacles. Hydrodynamic interactions are important at low obstacle volume fractions but are screened at high volume fractions. The diffusion of the globular polymer chain among the obstacles is subdiffusive in character on intermediate time scales where the dynamics explores the local structure of the heterogeneous environment. For large polymer chains in systems with high obstacle volume fractions, the chain adopts bloblike conformations that arise from trapping of portions of the chain in voids among the obstacles.
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Affiliation(s)
- Carlos Echeverria
- Laboratorio de Física Aplicada y Computacional, Universidad Nacional Experimental del Táchira, San Cristóbal 5001, Venezuela.
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18
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Wang Z, Wang C, Xiu P, Qi W, Tu Y, Shen Y, Zhou R, Zhang R, Fang H. Size Dependence of Nanoscale Confinement on Chiral Transformation. Chemistry 2010; 16:6482-7. [DOI: 10.1002/chem.200903383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Jewett AI, Shea JE. Reconciling theories of chaperonin accelerated folding with experimental evidence. Cell Mol Life Sci 2010; 67:255-76. [PMID: 19851829 PMCID: PMC11115962 DOI: 10.1007/s00018-009-0164-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/14/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
For the last 20 years, a large volume of experimental and theoretical work has been undertaken to understand how chaperones like GroEL can assist protein folding in the cell. The most accepted explanation appears to be the simplest: GroEL, like most other chaperones, helps proteins fold by preventing aggregation. However, evidence suggests that, under some conditions, GroEL can play a more active role by accelerating protein folding. A large number of models have been proposed to explain how this could occur. Focused experiments have been designed and carried out using different protein substrates with conclusions that support many different mechanisms. In the current article, we attempt to see the forest through the trees. We review all suggested mechanisms for chaperonin-mediated folding and weigh the plausibility of each in light of what we now know about the most stringent, essential, GroEL-dependent protein substrates.
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Affiliation(s)
- Andrew I. Jewett
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Department of Physics, University of California, Santa Barbara, CA 93106 USA
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Homouz D, Hoffman B, Cheung MS. Hydrophobic interactions of hexane in nanosized water droplets. J Phys Chem B 2009; 113:12337-42. [PMID: 19725588 DOI: 10.1021/jp907318d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use all-atomistic molecular dynamics simulations to study hydrophobic interactions of hexane in nanosized water droplets where the hydrogen bonding network of water molecules is disrupted at the surface. As a result of the competition between the energetics of a hexane molecule and the distribution of water molecules that lost the ability to form hydrogen bonds at the boundary, all-trans-hexane molecules are statistically favored at the surface of a nanosized water droplet and such a statistical trend increases as the size of a nano water droplet decreases. Changes in the radial distribution and the orientation of water molecules surrounding hexane in nanosized water droplets over bulk water are indicative of the finite-size effects on the structural distribution of a short, topologically complex hydrocarbon chain.
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Affiliation(s)
- Dirar Homouz
- Department of Physics, University of Houston, 4800 Calhoun Road, Houston, Texas 77204, USA
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Wu Z, Dong F, Zhao W, Wang H, Liu Y, Guan B. The fabrication and characterization of novel carbon doped TiO2 nanotubes, nanowires and nanorods with high visible light photocatalytic activity. NANOTECHNOLOGY 2009; 20:235701. [PMID: 19451679 DOI: 10.1088/0957-4484/20/23/235701] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Novel carbon doped TiO(2) nanotubes, nanowires and nanorods were fabricated by utilizing the nanoconfinement of hollow titanate nanotubes (TNTs). The fabrication process included adsorption of ethanol molecules in the inner space of TNTs and thermal treatment of the complex in inert N(2) atmosphere. The structural morphology of carbon doped TiO(2) nanostructures can be tuned using the calcination temperature. X-ray diffraction, Raman and Brunauer-Emmett-Teller studies proved that the doped carbon promoted the crystallization and phase transition by acting as nucleation seeds. X-ray photoelectron spectroscopy (XPS) showed that O-Ti-C and Ti-O-C bonds were formed in the nanostructures. Additional electronic states from the XPS valence band due to carbon doping were observed. This evidence indicated the electronic origin of the band gap narrowing and visible light absorption. The differences in chemical and electronic states between the surface and bulk of as-prepared samples confirmed that carbon was doped into the lattice of TiO(2) nanostructure through an inner doping process. The as-prepared catalysts exhibited enhanced photocatalytic activity for degradation of toluene in gas phase under both visible and simulated solar light irradiation compared with that of commercial Degussa P25. This novel fabrication approach can valuably contribute to designing nanostructured photocatalytic materials and modifying various nanotube materials.
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Affiliation(s)
- Zhongbiao Wu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China.
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Lucent D, England J, Pande V. Inside the chaperonin toolbox: theoretical and computational models for chaperonin mechanism. Phys Biol 2009; 6:015003. [DOI: 10.1088/1478-3975/6/1/015003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Xiu P, Zhou B, Qi W, Lu H, Tu Y, Fang H. Manipulating Biomolecules with Aqueous Liquids Confined within Single-Walled Nanotubes. J Am Chem Soc 2009; 131:2840-5. [DOI: 10.1021/ja804586w] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Peng Xiu
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Bo Zhou
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Wenpeng Qi
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Hangjun Lu
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Yusong Tu
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Haiping Fang
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
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Abstract
Understanding the effects of confinement on protein stability and folding kinetics is important for describing protein folding in the cellular environment. We have investigated the effects of confinement on two structurally distinct proteins as a function of the dimension d(c) and characteristic size R of the confining boundary. We find that the stabilization of the folded state relative to bulk conditions is quantitatively described by R(-gamma(c)), where the exponent gamma(c) is approximately 5/3 independent of the dimension of confinement d(c) (cylindrical, planar, or spherical). Moreover, we find that the logarithm of the folding rates also scale as R(-gamma(c)), with deviations only being seen for very small confining geometries, where folding is downhill; for both stability and kinetics, the dominant effect is the change in the free energy of the unfolded state. A secondary effect on the kinetics is a slight destabilization of the transition state by confinement, although the contacts present in the confined transition state are essentially identical to the bulk case. We investigate the effect of confinement on the position-dependent diffusion coefficients D(Q) for dynamics along the reaction coordinate Q (fraction of native contacts). The diffusion coefficients only change in the unfolded state basin, where they are increased because of compaction.
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