51
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Roy A, Das S, Manna D. Effect of Molecular Crowding Agents on the Activity and Stability of Immunosuppressive Enzyme Indoleamine 2,3‐Dioxygenase 1. ChemistrySelect 2018. [DOI: 10.1002/slct.201801366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ashalata Roy
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati-781039 Assam India
| | - Sreeparna Das
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati-781039 Assam India
| | - Debasis Manna
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati-781039 Assam India
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52
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Cheng RH, Chen JM, Chen YW, Cai H, Cui X, Hwang DW, Chen Z, Ding S. Macromolecular Crowding May Significantly Affect the Performance of an MRI Contrast Agent: A 1H NMR Spectroscopy, Microimaging, and Fast-Field-Cycling NMR Relaxometry Study. ChemistryOpen 2018; 7:288-296. [PMID: 29657915 PMCID: PMC5891664 DOI: 10.1002/open.201700192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Indexed: 11/09/2022] Open
Abstract
Contrast enhancement agents are often employed in magnetic resonance imaging (MRI) for clinical diagnosis and biomedical research. However, the current theory on MRI contrast generation does not consider the ubiquitous presence of macromolecular crowders in biological systems, which poses the risk of inaccurate data interpretation and misdiagnosis. To address this issue, herein the macromolecular crowding effects on MRI contrast agent are investigated with the 1H relaxation rate of water in aqueous solutions of Dotarem with different concentrations of macromolecules. Two representative macromolecular crowder systems are used: polyethylene glycol (with no specific secondary structure) and bovine serum albumin (with compact secondary and tertiary structures). The water 1H relaxation rates in various solutions are measured in a fixed magnetic field and in variable magnetic fields. The results show significant crowding effects for both crowders. The relaxation rate is proportional to the concentration of the MRI contrast agent but shows conspicuous superlinearity with respect to the concentration of the crowder. The size of polyethylene glycol does not affect the relaxivity of water in Dotarem solutions. The above effects are verified with T1- and T2-weighted NMR microimages. These results highlight the importance of the effect of macromolecular crowding on the MRI contrast agent and are valuable for understanding the mechanism of MRI contrast agents and designing new-generation MRI contrast agents.
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Affiliation(s)
- Ren-Hao Cheng
- Department of Chemistry and Center for Nanoscience & Nanotechnology National Sun Yat-sen University 70 Lien-Hai Road, Kaohsiung Taiwan 80424 Republic of China)
| | - Jie-Min Chen
- Department of Chemistry and Center for Nanoscience & Nanotechnology National Sun Yat-sen University 70 Lien-Hai Road, Kaohsiung Taiwan 80424 Republic of China)
| | - Yu-Wen Chen
- Institute of Biomedical Sciences Academia Sinica Taipei (Taiwan) 115 Republic of China
| | - Honghao Cai
- Department of Chemistry and Center for Nanoscience & Nanotechnology National Sun Yat-sen University 70 Lien-Hai Road, Kaohsiung Taiwan 80424 Republic of China).,Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University 422 Siming South Road Xiamen 361005 P.R. China.,School of Science Jimei University 183 Yinjiang Road Xiamen 361021 P.R. China
| | - Xiaohong Cui
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University 422 Siming South Road Xiamen 361005 P.R. China
| | - Dennis W Hwang
- Institute of Biomedical Sciences Academia Sinica Taipei (Taiwan) 115 Republic of China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University 422 Siming South Road Xiamen 361005 P.R. China
| | - Shangwu Ding
- Department of Chemistry and Center for Nanoscience & Nanotechnology National Sun Yat-sen University 70 Lien-Hai Road, Kaohsiung Taiwan 80424 Republic of China)
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53
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Zaslavsky BY, Uversky VN. In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles. Biochemistry 2018; 57:2437-2451. [PMID: 29303563 DOI: 10.1021/acs.biochem.7b01215] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.
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Affiliation(s)
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , United States.,Laboratory of New Methods in Biology , Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
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54
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Caccia S, Suffritti C, Carzaniga T, Berardelli R, Berra S, Martorana V, Fra A, Drouet C, Cicardi M. Intermittent C1-Inhibitor Deficiency Associated with Recessive Inheritance: Functional and Structural Insight. Sci Rep 2018; 8:977. [PMID: 29343682 PMCID: PMC5772639 DOI: 10.1038/s41598-017-16667-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022] Open
Abstract
C1-inhibitor is a serine protease inhibitor (serpin) controlling complement and contact system activation. Gene mutations result in reduced C1-inhibitor functional plasma level causing hereditary angioedema, a life-threatening disorder. Despite a stable defect, the clinical expression of hereditary angioedema is unpredictable, and the molecular mechanism underlying this variability remains undisclosed. Here we report functional and structural studies on the Arg378Cys C1-inhibitor mutant found in a patient presenting reduced C1-inhibitor levels, episodically undergoing normalization. Expression studies resulted in a drop in mutant C1-innhibitor secretion compared to wild-type. Notwithstanding, the purified proteins had similar features. Thermal denaturation experiments showed a comparable denaturation profile, but the mutant thermal stability decays when tested in conditions reproducing intracellular crowding.Our findings suggest that once correctly folded, the Arg378Cys C1-inhibitor is secreted as an active, although quite unstable, monomer. However, it could bear a folding defect, occasionally promoting protein oligomerization and interfering with the secretion process, thus accounting for its plasma level variability. This defect is exacerbated by the nature of the mutation since the acquired cysteine leads to the formation of non-functional homodimers through inter-molecular disulphide bonding. All the proposed phenomena could be modulated by specific environmental conditions, rendering this mutant exceptionally vulnerable to mild stress.
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Affiliation(s)
- Sonia Caccia
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, via GB Grassi 74, 20157, Milan, Italy.
| | - Chiara Suffritti
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, via GB Grassi 74, 20157, Milan, Italy
| | - Thomas Carzaniga
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, via GB Grassi 74, 20157, Milan, Italy
| | - Romina Berardelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Silvia Berra
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, via GB Grassi 74, 20157, Milan, Italy
| | - Vincenzo Martorana
- Institute of Biophysics, National Research Council of Italy, Palermo, Italy
| | - Annamaria Fra
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Christian Drouet
- GREPI EA7408, Universite Grenoble Alpes, and CREAK, CHU Grenoble, Grenoble, France
| | - Marco Cicardi
- "L. Sacco" Department of Biomedical and Clinical Sciences, University of Milan, via GB Grassi 74, 20157, Milan, Italy
- Luigi Sacco Hospital, Milan, Italy
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55
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Hong T, Iwashita K, Shiraki K. Viscosity Control of Protein Solution by Small Solutes: A Review. Curr Protein Pept Sci 2018; 19:746-758. [PMID: 29237380 PMCID: PMC6182935 DOI: 10.2174/1389203719666171213114919] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/22/2022]
Abstract
Viscosity of protein solution is one of the most troublesome issues for the high-concentration formulation of protein drugs. In this review, we summarize the practical methods that suppress the viscosity of protein solution using small molecular additives. The small amount of salts decreases the viscosity that results from electrostatic repulsion and attraction. The chaotrope suppresses the hydrophobic attraction and cluster formation, which can lower the solution viscosity. Arginine hydrochloride (ArgHCl) also suppresses the solution viscosity due to the hydrophobic and aromatic interactions between protein molecules. The small molecular additives are the simplest resolution of the high viscosity of protein solution as well as understanding of the primary cause in complex phenomena of protein interactions.
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Affiliation(s)
- Taehun Hong
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| | - Kazuki Iwashita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8573, Japan
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56
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Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA. Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments. Phys Chem Chem Phys 2018; 20:24045-24057. [DOI: 10.1039/c8cp03873b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.
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Affiliation(s)
- Hong Bok Lee
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Anh Cong
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Hannah Leopold
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Megan Currie
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | | | - Erin D. Sheets
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Ahmed A. Heikal
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
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57
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Schermeyer MT, Wöll AK, Kokke B, Eppink M, Hubbuch J. Characterization of highly concentrated antibody solution - A toolbox for the description of protein long-term solution stability. MAbs 2017; 9:1169-1185. [PMID: 28617076 PMCID: PMC5627599 DOI: 10.1080/19420862.2017.1338222] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
High protein titers are gaining importance in biopharmaceutical industry. A major challenge in the development of highly concentrated mAb solutions is their long-term stability and often incalculable viscosity. The complexity of the molecule itself, as well as the various molecular interactions, make it difficult to describe their solution behavior. To study the formulation stability, long- and short-range interactions and the formation of complex network structures have to be taken into account. For a better understanding of highly concentrated solutions, we combined established and novel analytical tools to characterize the effect of solution properties on the stability of highly concentrated mAb formulations. In this study, monoclonal antibody solutions in a concentration range of 50-200 mg/ml at pH 5-9 with and without glycine, PEG4000, and Na2SO4 were analyzed. To determine the monomer content, analytical size-exclusion chromatography runs were performed. ζ-potential measurements were conducted to analyze the electrophoretic properties in different solutions. The melting and aggregation temperatures were determined with the help of fluorescence and static light scattering measurements. Additionally, rheological measurements were conducted to study the solution viscosity and viscoelastic behavior of the mAb solutions. The so-determined analytical parameters were scored and merged in an analytical toolbox. The resulting scoring was then successfully correlated with long-term storage (40 d of incubation) experiments. Our results indicate that the sensitivity of complex rheological measurements, in combination with the applied techniques, allows reliable statements to be made with respect to the effect of solution properties, such as protein concentration, ionic strength, and pH shift, on the strength of protein-protein interaction and solution colloidal stability.
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Affiliation(s)
- Marie-Therese Schermeyer
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Anna K. Wöll
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Bas Kokke
- Synthon Biopharmaceuticals B.V., Nijmegen, The Netherlands
| | - Michel Eppink
- Synthon Biopharmaceuticals B.V., Nijmegen, The Netherlands
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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58
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Singh P, Choudhury S, Dutta S, Adhikari A, Bhattacharya S, Pal D, Pal SK. Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding. Int J Biol Macromol 2017; 103:395-402. [DOI: 10.1016/j.ijbiomac.2017.05.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/14/2017] [Indexed: 10/19/2022]
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59
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Protein aggregation: From background to inhibition strategies. Int J Biol Macromol 2017; 103:208-219. [DOI: 10.1016/j.ijbiomac.2017.05.048] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/01/2023]
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60
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Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
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61
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DeMott CM, Majumder S, Burz DS, Reverdatto S, Shekhtman A. Ribosome Mediated Quinary Interactions Modulate In-Cell Protein Activities. Biochemistry 2017; 56:4117-4126. [PMID: 28715177 DOI: 10.1021/acs.biochem.7b00613] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomes are present inside bacterial cells at micromolar concentrations and occupy up to 20% of the cell volume. Under these conditions, even weak quinary interactions between ribosomes and cytosolic proteins can affect protein activity. By using in-cell and in vitro NMR spectroscopy, and biophysical techniques, we show that the enzymes, adenylate kinase and dihydrofolate reductase, and the respective coenzymes, ATP and NADPH, bind to ribosomes with micromolar affinity, and that this interaction suppresses the enzymatic activities of both enzymes. Conversely, thymidylate synthase, which works together with dihydrofolate reductase in the thymidylate synthetic pathway, is activated by ribosomes. We also show that ribosomes impede diffusion of green fluorescent protein in vitro and contribute to the decrease in diffusion in vivo. These results strongly suggest that ribosome-mediated quinary interactions contribute to the differences between in vitro and in vivo protein activities and that ribosomes play a previously under-appreciated nontranslational role in regulating cellular biochemistry.
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Affiliation(s)
- Christopher M DeMott
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Subhabrata Majumder
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
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62
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Chen E, Kliger DS. Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments. J Phys Chem B 2017; 121:7064-7074. [PMID: 28703591 DOI: 10.1021/acs.jpcb.7b04107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved linear dichroism spectroscopy. The results of these studies offer simple empirically determined linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells.
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Affiliation(s)
- Eefei Chen
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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63
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Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies. J Phys Chem B 2017; 121:5688-5698. [DOI: 10.1021/acs.jpcb.7b01306] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Megan Currie
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Hannah Leopold
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Jacob Schwarz
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Erin D. Sheets
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Ahmed A. Heikal
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
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64
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Zaak H, Siar EH, Kornecki JF, Fernandez-Lopez L, Pedrero SG, Virgen-Ortíz JJ, Fernandez-Lafuente R. Effect of immobilization rate and enzyme crowding on enzyme stability under different conditions. The case of lipase from Thermomyces lanuginosus immobilized on octyl agarose beads. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.02.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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65
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Effect of protein load on stability of immobilized enzymes. Enzyme Microb Technol 2017; 98:18-25. [DOI: 10.1016/j.enzmictec.2016.12.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/24/2022]
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66
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Protein aggregation under high concentration/density state during chromatographic and ultrafiltration processes. Int J Biol Macromol 2017; 95:1153-1158. [DOI: 10.1016/j.ijbiomac.2016.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022]
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67
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Ferreira LA, Uversky VN, Zaslavsky BY. Role of solvent properties of water in crowding effects induced by macromolecular agents and osmolytes. MOLECULAR BIOSYSTEMS 2017; 13:2551-2563. [DOI: 10.1039/c7mb00436b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dipolarity/polarizability of water in polymer mixtures may be additive, reduced or enhanced depending on the composition of the mixture.
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Affiliation(s)
| | - V. N. Uversky
- Department of Molecular Medicine
- Morsant College of Medicine
- University of South Florida
- Tampa
- USA
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68
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Impact of additives on the formation of protein aggregates and viscosity in concentrated protein solutions. Int J Pharm 2016; 516:82-90. [PMID: 27836754 DOI: 10.1016/j.ijpharm.2016.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
In concentrated protein solutions attractive protein interactions may not only cause the formation of undesired aggregates but also of gel-like networks with elevated viscosity. To guarantee stable biopharmaceutical processes and safe formulations, both phenomenons have to be avoided as these may hinder regular processing steps. This work screens the impact of additives on both phase behavior and viscosity of concentrated protein solutions. For this purpose, additives known for stabilizing proteins in solution or modulating the dynamic viscosity were selected. These additives were PEG 300, PEG 1000, glycerol, glycine, NaCl and ArgHCl. Concentrated lysozyme and glucose oxidase solutions at pH 3 and 9 served as model systems. Fourier-transformed-infrared spectroscopy was chosen to determine the conformational stability of selected protein samples. Influencing protein interactions, the impact of additives was strongly dependent on pH. Of all additives investigated, glycine was the only one that maintained protein conformational and colloidal stability while decreasing the dynamic viscosity. Low concentrations of NaCl showed the same effect, but increasing concentrations resulted in visible protein aggregation.
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69
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Reščič J. Effect of excluded volume and chain flexibility on depletion interaction between proteins. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.03.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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70
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Zinchenko A. DNA conformational behavior and compaction in biomimetic systems: Toward better understanding of DNA packaging in cell. Adv Colloid Interface Sci 2016; 232:70-79. [PMID: 26976700 DOI: 10.1016/j.cis.2016.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/05/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
In a living cell, long genomic DNA is strongly compacted and exists in the environment characterized by a dense macromolecular crowding, high concentrations of mono- and divalent cations, and confinement of ca. 10μm size surrounded by a phospholipid membrane. Experimental modelling of such complex biological system is challenging but important to understand spatiotemporal dynamics and functions of the DNA in cell. The accumulated knowledge about DNA condensation/compaction in conditions resembling those in the real cell can be eventually used to design and construct partly functional "artificial cells" having potential applications in drug delivery systems, gene therapy, and production of synthetic cells. In this review, I would like to overview the past progress in our understanding of the DNA conformational behavior and, in particular, DNA condensation/compaction phenomenon and its relation to the DNA biological activity. This understanding was gained by designing relevant experimental models mimicking DNA behavior in the environment of living cell. Starting with a brief summary of classic experimental systems to study DNA condensation/compaction, in later parts, I highlight recent experimental methodologies to address the effects of macromolecular crowding and nanoscale and microscale confinements on DNA conformation dynamics. All the studies are discussed in the light of their relevance to DNA behavior in living cells, and future prospects of the field are outlined.
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71
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Mourão MA, Hakim JB, Schnell S. Connecting the dots: the effects of macromolecular crowding on cell physiology. Biophys J 2016; 107:2761-2766. [PMID: 25517143 DOI: 10.1016/j.bpj.2014.10.051] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/17/2014] [Accepted: 10/23/2014] [Indexed: 10/25/2022] Open
Abstract
The physicochemical properties of cellular environments with a high macromolecular content have been systematically characterized to explain differences observed in the diffusion coefficients, kinetics parameters, and thermodynamic properties of proteins inside and outside of cells. However, much less attention has been given to the effects of macromolecular crowding on cell physiology. Here, we review recent findings that shed some light on the role of crowding in various cellular processes, such as reduction of biochemical activities, structural reorganization of the cytoplasm, cytoplasm fluidity, and cellular dormancy. We conclude by presenting some unresolved problems that require the attention of biophysicists, biochemists, and cell physiologists. Although it is still underappreciated, macromolecular crowding plays a critical role in life as we know it.
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Affiliation(s)
- Márcio A Mourão
- Mathematical Biosciences Institute, Ohio State University, Columbus, Ohio
| | - Joe B Hakim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan.
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72
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Grime JMA, Dama JF, Ganser-Pornillos BK, Woodward CL, Jensen GJ, Yeager M, Voth GA. Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly. Nat Commun 2016; 7:11568. [PMID: 27174390 PMCID: PMC4869257 DOI: 10.1038/ncomms11568] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 04/07/2016] [Indexed: 12/23/2022] Open
Abstract
The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies. Significant morphological changes occur during the conversion of the immature HIV virion into a mature infectious form. Here the authors use coarse-grained molecular dynamics simulations to model HIV-1 capsid self-assembly and disassembly events that suggests several metastable capsid intermediates sensitive to local conditions.
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Affiliation(s)
- John M A Grime
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - James F Dama
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Cora L Woodward
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.,Center for Membrane Biology, Cardiovascular Research Center, and Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA
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73
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Patra S, Erwin N, Winter R. Translational Dynamics of Lipidated Ras Proteins in the Presence of Crowding Agents and Compatible Osmolytes. Chemphyschem 2016; 17:2164-9. [PMID: 27028423 DOI: 10.1002/cphc.201600179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/07/2022]
Abstract
Ras proteins are small GTPases and are involved in transmitting signals that control cell growth, differentiation, and proliferation. Since the cell cytoplasm is crowded with different macromolecules, understanding the translational dynamics of Ras proteins in crowded environments is crucial to yielding deeper insight into their reactivity and function. Herein, the translational dynamics of lipidated N-Ras and K-Ras4B is studied in the bulk and in the presence of a macromolecular crowder (Ficoll) and the compatible osmolyte and microcrowder sucrose by fluorescence correlation spectroscopy. The results reveal that N-Ras forms dimers due to the presence of its lipid moiety in the hypervariable region, whereas K-Ras4B remains in its monomeric form in the bulk. Addition of a macromolecular crowding agent gradually favors clustering of the Ras proteins. In 20 wt % Ficoll N-Ras forms trimers and K-Ras4B dimers. Concentrations of sucrose up to 10 wt % foster formation of N-Ras trimers and K-Ras dimers as well. The results can be rationalized in terms of the excluded-volume effect, which enhances the association of the proteins, and, for the higher concentrations, by limited-hydration conditions. The results of this study shed new light on the association state of these proteins in a crowded environment. This is of particular interest for the Ras proteins, because their solution state-monomeric or clustered-influences their membrane-partitioning behavior and their interplay with cytosolic interaction partners.
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Affiliation(s)
- Satyajit Patra
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Nelli Erwin
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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74
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Metzler R, Jeon JH, Cherstvy AG. Non-Brownian diffusion in lipid membranes: Experiments and simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2451-2467. [PMID: 26826272 DOI: 10.1016/j.bbamem.2016.01.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/21/2016] [Accepted: 01/23/2016] [Indexed: 12/14/2022]
Abstract
The dynamics of constituents and the surface response of cellular membranes-also in connection to the binding of various particles and macromolecules to the membrane-are still a matter of controversy in the membrane biophysics community, particularly with respect to crowded membranes of living biological cells. We here put into perspective recent single particle tracking experiments in the plasma membranes of living cells and supercomputing studies of lipid bilayer model membranes with and without protein crowding. Special emphasis is put on the observation of anomalous, non-Brownian diffusion of both lipid molecules and proteins embedded in the lipid bilayer. While single component, pure lipid bilayers in simulations exhibit only transient anomalous diffusion of lipid molecules on nanosecond time scales, the persistence of anomalous diffusion becomes significantly longer ranged on the addition of disorder-through the addition of cholesterol or proteins-and on passing of the membrane lipids to the gel phase. Concurrently, experiments demonstrate the anomalous diffusion of membrane embedded proteins up to macroscopic time scales in the minute time range. Particular emphasis will be put on the physical character of the anomalous diffusion, in particular, the occurrence of ageing observed in the experiments-the effective diffusivity of the measured particles is a decreasing function of time. Moreover, we present results for the time dependent local scaling exponent of the mean squared displacement of the monitored particles. Recent results finding deviations from the commonly assumed Gaussian diffusion patterns in protein crowded membranes are reported. The properties of the displacement autocorrelation function of the lipid molecules are discussed in the light of their appropriate physical anomalous diffusion models, both for non-crowded and crowded membranes. In the last part of this review we address the upcoming field of membrane distortion by elongated membrane-binding particles. We discuss how membrane compartmentalisation and the particle-membrane binding energy may impact the dynamics and response of lipid membranes. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- R Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany; Department of Physics, Tampere University of Technology, 33101 Tampere, Finland.
| | - J-H Jeon
- Korea Institute for Advanced Study (KIAS), Seoul, Republic of Korea
| | - A G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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75
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Wu S, Ding Y, Zhang G. Mechanic Insight into Aggregation of Lysozyme by Ultrasensitive Differential Scanning Calorimetry and Sedimentation Velocity. J Phys Chem B 2015; 119:15789-95. [PMID: 26633732 DOI: 10.1021/acs.jpcb.5b08190] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Folding and aggregation of proteins profoundly influence their functions. We have investigated the effects of thermal history, concentration and pH on the denaturation and refolding of lysozyme by using ultrasensitive differential scanning calorimetry (US-DSC) and sedimentation velocity (SV) via analytical ultracentrifugation (AUC). The former is sensitive to small energy change whereas the latter can differentiate the oligomers such as dimer and trimer from individual protein molecules. Our studies reveal that the degree of denaturation irreversibility increases as heating times increases. The denaturation temperature (Td) and enthalpy change (ΔH) are influenced by heating rate since the denaturation is not in equilibrium during the heating. We can obtain Td and ΔH in equilibrium by extrapolation of heating rate to zero. In a dilute solution, no aggregation but unfolding happens in the denaturation. However, when the concentration is above a critical value (∼15.0 mg/mL), lysozyme molecules readily form trimers or other oligomers. Lysozyme molecules unfold into stretched chains at pH > 6.0, which would further forms large aggregates. The formation of aggregates makes the refolding of lysozyme impossible.
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Affiliation(s)
- Sha Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China , Hefei, 230026, China
| | - Yanwei Ding
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China , Hefei, 230026, China
| | - Guangzhao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China , Hefei, 230026, China.,Faculty of Materials Science and Engineering, South China University of Technology , Guangzhou, P. R. China 510640
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76
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Chiang YL, Chang YC, Chiang IC, Mak HM, Hwang IS, Shih YL. Atomic Force Microscopy Characterization of Protein Fibrils Formed by the Amyloidogenic Region of the Bacterial Protein MinE on Mica and a Supported Lipid Bilayer. PLoS One 2015; 10:e0142506. [PMID: 26562523 PMCID: PMC4642933 DOI: 10.1371/journal.pone.0142506] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils play a crucial role in many human diseases and are found to function in a range of physiological processes from bacteria to human. They have also been gaining importance in nanotechnology applications. Understanding the mechanisms behind amyloid formation can help develop strategies towards the prevention of fibrillation processes or create new technological applications. It is thus essential to observe the structures of amyloids and their self-assembly processes at the nanometer-scale resolution under physiological conditions. In this work, we used highly force-sensitive frequency-modulation atomic force microscopy (FM-AFM) to characterize the fibril structures formed by the N-terminal domain of a bacterial division protein MinE in solution. The approach enables us to investigate the fibril morphology and protofibril organization over time progression and in response to changes in ionic strength, molecular crowding, and upon association with different substrate surfaces. In addition to comparison of the fibril structure and behavior of MinE1-31 under varying conditions, the study also broadens our understanding of the versatile behavior of amyloid-substrate surface interactions.
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Affiliation(s)
- Ya-Ling Chiang
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yuan-Chih Chang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - I-Chen Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Huey-Ming Mak
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ing-Shouh Hwang
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (ISH), (YLS)
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- * E-mail: (ISH), (YLS)
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77
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Pindrus M, Shire SJ, Kelley RF, Demeule B, Wong R, Xu Y, Yadav S. Solubility Challenges in High Concentration Monoclonal Antibody Formulations: Relationship with Amino Acid Sequence and Intermolecular Interactions. Mol Pharm 2015; 12:3896-907. [PMID: 26407030 DOI: 10.1021/acs.molpharmaceut.5b00336] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The purpose of this work was to elucidate the molecular interactions leading to monoclonal antibody self-association and precipitation and utilize biophysical measurements to predict solubility behavior at high protein concentration. Two monoclonal antibodies (mAb-G and mAb-R) binding to overlapping epitopes were investigated. Precipitation of mAb-G solutions was most prominent at high ionic strength conditions and demonstrated strong dependence on ionic strength, as well as slight dependence on solution pH. At similar conditions no precipitation was observed for mAb-R solutions. Intermolecular interactions (interaction parameter, kD) related well with high concentration solubility behavior of both antibodies. Upon increasing buffer ionic strength, interactions of mAb-R tended to weaken, while those of mAb-G became more attractive. To investigate the role of amino acid sequence on precipitation behavior, mutants were designed by substituting the CDR of mAb-R into the mAb-G framework (GM-1) or deleting two hydrophobic residues in the CDR of mAb-G (GM-2). No precipitation was observed at high ionic strength for either mutant. The molecular interactions of mutants were similar in magnitude to those of mAb-R. The results suggest that presence of hydrophobic groups in the CDR of mAb-G may be responsible for compromising its solubility at high ionic strength conditions since deleting these residues mitigated the solubility issue.
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Affiliation(s)
- Mariya Pindrus
- Summer Intern from Department of Pharmaceutical Sciences, University of Connecticut , Storrs, Connecticut 06269, United States
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78
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Herhut M, Brandenbusch C, Sadowski G. Inclusion of mPRISM potential for polymer-induced protein interactions enables modeling of second osmotic virial coefficients in aqueous polymer-salt solutions. Biotechnol J 2015; 11:146-54. [PMID: 26250594 DOI: 10.1002/biot.201500086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/15/2015] [Accepted: 08/04/2015] [Indexed: 11/07/2022]
Abstract
The downstream processing of therapeutic proteins is a challenging task. Key information needed to estimate applicable workup strategies (e.g. crystallization) are the interactions of the proteins with other components in solution. This information can be deduced from the second osmotic virial coefficient B22 , measurable by static light scattering. Thermodynamic models are very valuable for predicting B22 data for different process conditions and thus decrease the experimental effort. Available B22 models consider aqueous salt solutions but fail for the prediction of B22 if an additional polymer is present in solution. This is due to the fact that depending on the polymer concentration protein-protein interactions are not rectified as assumed within these models. In this work, we developed an extension of the xDLVO model to predict B22 data of proteins in aqueous polymer-salt solutions. To show the broad applicability of the model, lysozyme, γ-globulin and D-xylose ketol isomerase in aqueous salt solution containing polyethylene glycol were considered. For all proteins considered, the modified xDLVO model was able to predict the experimentally observed non-monotonical course in B22 data with high accuracy. When used in an early stage in process development, the model will contribute to an efficient and cost effective downstream processing development.
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Affiliation(s)
- Marcel Herhut
- Department of Biochemical and Chemical Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Dortmund, Nordrhein-Westfalen, Germany
| | - Christoph Brandenbusch
- Department of Biochemical and Chemical Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Dortmund, Nordrhein-Westfalen, Germany
| | - Gabriele Sadowski
- Department of Biochemical and Chemical Engineering, Laboratory of Thermodynamics, Technische Universität Dortmund, Dortmund, Nordrhein-Westfalen, Germany.
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79
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Ishrat M, Imtaiyaz Hassan M, Ahmad F, Moosavi-Movahedi AA, Islam A. Effect of dextran on the thermodynamic stability and structure of ribonuclease A. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2015. [DOI: 10.1007/s13738-015-0726-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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80
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Kalwarczyk T, Sozanski K, Ochab-Marcinek A, Szymanski J, Tabaka M, Hou S, Holyst R. Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model. Adv Colloid Interface Sci 2015; 223:55-63. [PMID: 26189602 DOI: 10.1016/j.cis.2015.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/27/2015] [Accepted: 06/27/2015] [Indexed: 01/12/2023]
Abstract
This paper deals with the recent phenomenological model of the motion of nanoscopic objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We analysed motion in polymer, micellar, colloidal and protein solutions and the cytoplasm of living cells using the length-scale dependent viscosity model. Viscosity monotonically approaches macroscopic viscosity as the size of the object increases and thus gives a single, coherent picture of motion at the nano and macro scale. The model includes interparticle interactions (solvent-solute), temperature and the internal structure of a complex liquid. The depletion layer ubiquitously occurring in complex liquids is also incorporated into the model. We also discuss the biological aspects of crowding in terms of the length-scale dependent viscosity model.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Sozanski
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Anna Ochab-Marcinek
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jedrzej Szymanski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; State Key Laboratory of Medicinal Chemical Biology, Nankai University, China
| | - Robert Holyst
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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81
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Murray B, Rosenthal J, Zheng Z, Isaacson D, Zhu Y, Belfort G. Cosolute effects on amyloid aggregation in a nondiffusion limited regime: intrinsic osmolyte properties and the volume exclusion principle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4246-4254. [PMID: 25803421 DOI: 10.1021/acs.langmuir.5b00254] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The effects of cosolutes on amyloid aggregation kinetics in vivo are critical and not fully understood. To explore the effects of cosolute additives, the in vitro behavior of destabilizing and stabilizing osmolytes with polymer cosolutes on the aggregation of a model amyloid, human insulin, is probed using experiments coupled with an amyloid aggregation reaction model. The destabilizing osmolyte, guanidine hydrochloride (GuHCl), induces biphasic behavior on the amyloid aggregation rate exhibited by an enhancement of the aggregation kinetics at low concentrations of GuHCl (<0.6 M) and a reduction in kinetics at higher GuHCl concentrations. Stabilizing osmolytes, glycerol, sorbitol and trimethylamine N-oxide, slow the rate of aggregation by reducing the rate of monomer unfolding. Polymer cosolutes, polyvinylpyrrolidone 3.5 kDa and 40 kDa, delay amyloid aggregation mainly through a decrease in the nucleation reaction. These results are in good agreement with the volume exclusion principle for polymer crowding and supports the need to include conformational rearrangement of monomers prior to nucleation. Using fluorescence correlation spectroscopy, we demonstrate that amyloid aggregation is nondiffusion limited, except during fibril accumulation in the presence of high concentrations of long chain polymers. Lastly, the neutral surface area of osmolytes correlates well with the time to initiate fibril formation, tlag, which implicates an intrinsic osmolyte property underlying preferential interactions.
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Affiliation(s)
| | | | - Zhongli Zheng
- §Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | | | - Yingxi Zhu
- §Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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82
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Acosta H, Cáceres A, González-Marcano E, Quiñones W, Avilán L, Dubourdieu M, Concepción JL. Hysteresis and positive cooperativity as possible regulatory mechanisms of Trypanosoma cruzi hexokinase activity. Mol Biochem Parasitol 2015; 198:82-91. [PMID: 25683029 DOI: 10.1016/j.molbiopara.2015.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 10/24/2022]
Abstract
In Trypanosoma cruzi, the causal agent of Chagas disease, the first six or seven steps of glycolysis are compartmentalized in glycosomes, which are authentic but specialized peroxisomes. Hexokinase (HK), the first enzyme in the glycolytic pathway, has been an important research object, particularly as a potential drug target. Here we present the results of a specific kinetics study of the native HK from T. cruzi epimastigotes; a sigmoidal behavior was apparent when the velocity of the reaction was determined as a function of the concentration of its substrates, glucose and ATP. This behavior was only observed at low enzyme concentration, while at high concentration classical Michaelis-Menten kinetics was displayed. The progress curve of the enzyme's activity displays a lag phase of which the length is dependent on the protein concentration, suggesting that HK is a hysteretic enzyme. The hysteretic behavior may be attributed to slow changes in the conformation of T. cruzi HK as a response to variations of glucose and ATP concentrations in the glycosomal matrix. Variations in HK's substrate concentrations within the glycosomes may be due to variations in the trypanosome's environment. The hysteretic and cooperative behavior of the enzyme may be a form of regulation by which the parasite can more readily adapt to these environmental changes, occurring within each of its hosts, or during the early phase of transition to a new host.
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Affiliation(s)
- Héctor Acosta
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela.
| | - Ana Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | | | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Luisana Avilán
- Laboratorio de Fisiología Animal, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Michel Dubourdieu
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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83
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Piedmonte DM, Hair A, Baker P, Brych L, Nagapudi K, Lin H, Cao W, Hershenson S, Ratnaswamy G. Sorbitol Crystallization-Induced Aggregation in Frozen mAb Formulations. J Pharm Sci 2015; 104:686-97. [DOI: 10.1002/jps.24141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/31/2014] [Accepted: 08/06/2014] [Indexed: 12/27/2022]
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84
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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85
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Liu J, Yadav S, Andya J, Demeule B, Shire SJ. Analytical Ultracentrifugation and Its Role in Development and Research of Therapeutical Proteins. Methods Enzymol 2015; 562:441-76. [DOI: 10.1016/bs.mie.2015.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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86
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Liebner R, Meyer M, Hey T, Winter G, Besheer A. Head to head comparison of the formulation and stability of concentrated solutions of HESylated versus PEGylated anakinra. J Pharm Sci 2014; 104:515-26. [PMID: 25445200 DOI: 10.1002/jps.24253] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/12/2014] [Accepted: 10/17/2014] [Indexed: 12/31/2022]
Abstract
Although PEGylation of biologics is currently the gold standard for half-life extension, the technology has a number of limitations, most importantly the non-biodegradability of PEG and the extremely high viscosity at high concentrations. HESylation is a promising alternative based on coupling to the biodegradable polymer hydroxyethyl starch (HES). In this study, we are comparing HESylation with PEGylation regarding the effect on the protein's physicochemical properties, as well as on formulation at high concentrations, where protein stability and viscosity can be compromised. For this purpose, the model protein anakinra is coupled to HES or PEG by reductive amination. Results show that coupling of HES or PEG had practically no effect on the protein's secondary structure, and that it reduced protein affinity by one order of magnitude, with HESylated anakinra more affine than the PEGylated protein. The viscosity of HESylated anakinra at protein concentrations up to 75 mg/mL was approximately 40% lower than that of PEG-anakinra. Both conjugates increased the apparent melting temperature of anakinra in concentrated solutions. Finally, HESylated anakinra was superior to PEG-anakinra regarding monomer recovery after 8 weeks of storage at 40°C. These results show that HESylating anakinra offers formulation advantages compared with PEGylation, especially for concentrated protein solutions.
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Affiliation(s)
- Robert Liebner
- Department of Pharmacy, Pharmaceutical Technology & Biopharmaceutics, Ludwig-Maximillians-University Munich, Munich, 81377, Germany
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87
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Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol Model 2014; 20:2530. [DOI: 10.1007/s00894-014-2530-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/12/2014] [Indexed: 01/25/2023]
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88
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Hasnain S, McClendon CL, Hsu MT, Jacobson MP, Bandyopadhyay P. A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion. PLoS One 2014; 9:e106466. [PMID: 25180859 PMCID: PMC4152264 DOI: 10.1371/journal.pone.0106466] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 07/30/2014] [Indexed: 01/07/2023] Open
Abstract
A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.
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Affiliation(s)
- Sabeeha Hasnain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Christopher L. McClendon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, United States of America
| | - Monica T. Hsu
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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89
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Naik S, Kumru OS, Cullom M, Telikepalli SN, Lindboe E, Roop TL, Joshi SB, Amin D, Gao P, Middaugh CR, Volkin DB, Fisher MT. Probing structurally altered and aggregated states of therapeutically relevant proteins using GroEL coupled to bio-layer interferometry. Protein Sci 2014; 23:1461-78. [PMID: 25043635 DOI: 10.1002/pro.2515] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 11/09/2022]
Abstract
The ability of a GroEL-based bio-layer interferometry (BLI) assay to detect structurally altered and/or aggregated species of pharmaceutically relevant proteins is demonstrated. Assay development included optimizing biotinylated-GroEL immobilization to streptavidin biosensors, combined with biophysical and activity measurements showing native and biotinylated GroEL are both stable and active. First, acidic fibroblast growth factor (FGF-1) was incubated under conditions known to promote (40°C) and inhibit (heparin addition) molten globule formation. Heat exposed (40°C) FGF-1 exhibited binding to GroEL-biosensors, which was significantly diminished in the presence of heparin. Second, a polyclonal human IgG solution containing 6-8% non-native dimer showed an increase in higher molecular weight aggregates upon heating by size exclusion chromatography (SEC). The poly IgG solution displayed binding to GroEL-biosensors initially with progressively increased binding upon heating. Enriched preparations of the IgG dimers or monomers showed significant binding to GroEL-biosensors. Finally, a thermally treated IgG1 monoclonal antibody (mAb) solution also demonstrated increased GroEL-biosensor binding, but with different kinetics. The bound complexes could be partially to fully dissociated after ATP addition (i.e., specific GroEL binding) depending on the protein, environmental stress, and the assay's experimental conditions. Transmission electron microscopy (TEM) images of GroEL-mAb complexes, released from the biosensor, also confirmed interaction of bound complexes at the GroEL binding site with heat-stressed mAb. Results indicate that the GroEL-biosensor-BLI method can detect conformationally altered and/or early aggregation states of proteins, and may potentially be useful as a rapid, stability-indicating biosensor assay for monitoring the structural integrity and physical stability of therapeutic protein candidates.
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Affiliation(s)
- Subhashchandra Naik
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
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90
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The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study. PLoS One 2014; 9:e98618. [PMID: 24915485 PMCID: PMC4051634 DOI: 10.1371/journal.pone.0098618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/05/2014] [Indexed: 02/02/2023] Open
Abstract
Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
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91
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Concentration dependent viscosity of monoclonal antibody solutions: explaining experimental behavior in terms of molecular properties. Pharm Res 2014; 31:3161-78. [PMID: 24906598 DOI: 10.1007/s11095-014-1409-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/06/2014] [Indexed: 01/18/2023]
Abstract
PURPOSE Early identification of monoclonal antibody candidates whose development, as high concentration (≥100 mg/mL) drug products, could prove challenging, due to high viscosity, can help define strategies for candidate engineering and selection. METHODS Concentration dependent viscosities of 11 proprietary mAbs were measured. Sequence and structural features of the variable (Fv) regions were analyzed to understand viscosity behavior of the mAbs. Coarse-grained molecular simulations of two problematic mAbs were compared with that of a well behaved mAb. RESULTS Net charge, ξ-potential and pI of Fv regions were found to correlate with viscosities of highly concentrated antibody solutions. Negative net charges on the Fv regions of two mAbs with poor viscosity behaviors facilitate attractive self-associations, causing them to diffuse slower than a well-behaved mAb with positive net charge on its Fv region. An empirically derived equation that connects aggregation propensity and pI of the Fv region with high concentration viscosity of the whole mAb was developed. CONCLUSIONS An Fv region-based qualitative screening profile was devised to flag mAb candidates whose development, as high concentration drug products, could prove challenging. This screen can facilitate developability risk assessment and mitigation strategies for antibody based therapeutics via rapid high throughput material-free screening.
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92
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Balcells C, Pastor I, Vilaseca E, Madurga S, Cascante M, Mas F. Macromolecular crowding effect upon in vitro enzyme kinetics: mixed activation-diffusion control of the oxidation of NADH by pyruvate catalyzed by lactate dehydrogenase. J Phys Chem B 2014; 118:4062-8. [PMID: 24660904 DOI: 10.1021/jp4118858] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Enzyme kinetics studies have been usually designed as dilute solution experiments, which differ substantially from in vivo conditions. However, cell cytosol is crowded with a high concentration of molecules having different shapes and sizes. The consequences of such crowding in enzymatic reactions remain unclear. The aim of the present study is to understand the effect of macromolecular crowding produced by dextran of different sizes and at diverse concentrations in the well-known reaction of oxidation of NADH by pyruvate catalyzed by L-lactate dehydrogenase (LDH). Our results indicate that the reaction rate is determined by both the occupied volume and the relative size of dextran obstacles with respect to the enzyme present in the reaction. Moreover, we analyzed the influence of macromolecular crowding on the Michaelis-Menten constants, vmax and Km. The obtained results show that only high concentrations and large sizes of dextran reduce both constants suggesting a mixed activation-diffusion control of this enzymatic reaction due to the dextran crowding action. From our knowledge, this is the first experimental study that depicts mixed activation-diffusion control in an enzymatic reaction due to the effect of crowding.
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Affiliation(s)
- Cristina Balcells
- Department of Physical Chemistry and Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona (UB) , 08028 Barcelona, Spain
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93
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Yearley EJ, Zarraga IE, Shire SJ, Scherer TM, Gokarn Y, Wagner NJ, Liu Y. Small-angle neutron scattering characterization of monoclonal antibody conformations and interactions at high concentrations. Biophys J 2014; 105:720-31. [PMID: 23931320 DOI: 10.1016/j.bpj.2013.06.043] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 06/15/2013] [Accepted: 06/24/2013] [Indexed: 12/27/2022] Open
Abstract
Small-angle neutron scattering (SANS) is used to probe the solution structure of two protein therapeutics (monoclonal antibodies 1 and 2 (MAb1 and MAb2)) and their protein-protein interaction (PPI) at high concentrations. These MAbs differ by small sequence alterations in the complementarity-determining region but show very large differences in solution viscosity. The analyses of SANS patterns as a function of different solution conditions suggest that the average intramolecular structure of both MAbs in solution is not significantly altered over the studied protein concentrations and experimental conditions. Even though a strong repulsive interaction is expected for both MAbs due to their net charges and low solvent ionic strength, analysis of the SANS data shows that the effective PPI for MAb1 is dominated by a very strong attraction at small volume fraction that becomes negligible at large concentrations. The MAb1 PPI cannot be modeled simply by a spherically symmetric central forces model. It is proposed that an anisotropic attraction strongly affects the local interprotein structure and leads to an anomalously large viscosity of concentrated MAb1 solutions. Conversely, MAb2 displays a repulsive interaction potential throughout the concentration series probed and a comparatively small solution viscosity.
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Affiliation(s)
- Eric J Yearley
- Department of Chemical and Biomolecular Engineering, Center for Neutron Science, University of Delaware, Newark, USA
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94
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Role of posttranslational protein modifications in epididymal sperm maturation and extracellular quality control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 759:159-80. [PMID: 25030764 DOI: 10.1007/978-1-4939-0817-2_8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The epididymal lumen is a complex microenvironment in which spermatozoa acquire motility and fertility. Spermatozoa are synthetically inactive and therefore the maturation process requires their interaction with proteins that are synthesized and secreted in a highly regionalized manner by the epididymal epithelium. In addition to the integration of epididymal secretory proteins, posttranslational modifications of existing sperm proteins are important for sperm maturation and acquisition of fertilizing potential. Phosphorylation, glycosylation, and processing are several of the posttranslational modifications that sperm proteins undergo during epididymal transit resulting in changes in protein function and localization ultimately leading to mature spermatozoa. In addition to these well-characterized modifications, protein aggregation and cross-linking also occur within the epididymal lumen and may represent unique mechanisms for controlling protein function including that for maturation as well as for extracellular quality control.
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95
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Greese B, Hülskamp M, Fleck C. Quantification of variability in trichome patterns. FRONTIERS IN PLANT SCIENCE 2014; 5:596. [PMID: 25431575 PMCID: PMC4230044 DOI: 10.3389/fpls.2014.00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/13/2014] [Indexed: 05/02/2023]
Abstract
While pattern formation is studied in various areas of biology, little is known about the noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to, e.g., the abundance of cell components or environmental conditions. To elevate the understanding of regulatory processes underlying the pattern formation it is crucial to quantitatively analyze the variability in naturally occurring patterns. Here, we review recent approaches toward characterization of noise on trichome initiation. We present methods for the quantification of spatial patterns, which are the basis for data-driven mathematical modeling and enable the analysis of noise from different sources. Besides the insight gained on trichome formation, the examination of observed trichome patterns also shows that highly regulated biological processes can be substantially affected by variability.
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Affiliation(s)
- Bettina Greese
- Computational Biology and Biological Physics, Faculty for Theoretical Physics and Astronomy, Lund UniversityLund, Sweden
| | - Martin Hülskamp
- Molecular Cell Biology and Developmental Genetics, Biocenter, Botanical Institute, Cologne UniversityCologne, Germany
| | - Christian Fleck
- Laboratory for Systems and Synthetic Biology, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Christian Fleck, Laboratory for Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands e-mail:
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96
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Pastor I, Pitulice L, Balcells C, Vilaseca E, Madurga S, Isvoran A, Cascante M, Mas F. Effect of crowding by Dextrans in enzymatic reactions. Biophys Chem 2014; 185:8-13. [DOI: 10.1016/j.bpc.2013.10.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/23/2013] [Accepted: 10/26/2013] [Indexed: 11/29/2022]
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97
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Mandal SS, Cristiglio V, Lindner P, Bhattacharyya AJ. Small-angle neutron scattering studies of hemoglobin confined inside silica tubes of varying sizes. Chemphyschem 2013; 15:302-9. [PMID: 24339406 DOI: 10.1002/cphc.201300863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/14/2013] [Indexed: 11/08/2022]
Abstract
In addition to the chemical nature of the surface, the dimensions of the confining host exert a significant influence on confined protein structures; this results in immense biological implications, especially those concerning the enzymatic activities of the protein. This study probes the structure of hemoglobin (Hb), a model protein, confined inside silica tubes with pore diameters that vary by one order of magnitude (≈20-200 nm). The effect of confinement on the protein structure is probed by comparison with the structure of the protein in solution. Small-angle neutron scattering (SANS), which provides information on protein tertiary and quaternary structures, is employed to study the influence of the tube pore diameter on the structure and configuration of the confined protein in detail. Confinement significantly influences the structural stability of Hb and the structure depends on the Si-tube pore diameter. The high radius of gyration (Rg) and polydispersity of Hb in the 20 nm diameter Si-tube indicates that Hb undergoes a significant amount of aggregation. However, for Si-tube diameters greater or equal to 100 nm, the Rg of Hb is found to be in very close proximity to that obtained from the protein data bank (PDB) reported structure (Rg of native Hb=23.8 Å). This strongly indicates that the protein has a preference for the more native-like non-aggregated state if confined inside tubes of diameter greater or equal to 100 nm. Further insight into the Hb structure is obtained from the distance distribution function, p(r), and ab initio models calculated from the SANS patterns. These also suggest that the Si-tube size is a key parameter for protein stability and structure.
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Affiliation(s)
- Soumit S Mandal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012 (India), Fax: (+91) 80-23601310
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98
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Pawar MG, Srivatsan SG. Environment-responsive fluorescent nucleoside analogue probe for studying oligonucleotide dynamics in a model cell-like compartment. J Phys Chem B 2013; 117:14273-82. [PMID: 24161106 DOI: 10.1021/jp4071168] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of fluorescent nucleoside analogue probes that have been used in the in vitro study of nucleic acids are not suitable for cell-based biophysical assays because they exhibit excitation maxima in the UV region and low quantum yields within oligonucleotides. Therefore, we propose that the photophysical characterization of oligonucleotides labeled with a fluorescent nucleoside analogue in reverse micelles (RM), which are good biological membrane models and UV-transparent, could provide an alternative approach to studying the properties of nucleic acids in a cell-like confined environment. In this context, we describe the photophysical properties of an environment-sensitive fluorescent uridine analogue (1), based on the 5-(benzo[b]thiophen-2-yl)pyrimidine core, in micelles and RM. The emissive nucleoside, which is polarity- and viscosity-sensitive, reports the environment of the surfactant assemblies via changes in its fluorescence properties. The nucleoside analogue, incorporated into an RNA oligonucleotide and hybridized to its complementary DNA and RNA oligonucleotides, exhibits a significantly higher fluorescence intensity, lifetime, and anisotropy in RM than in aqueous buffer, which is consistent with the environment of RM. Collectively, our results demonstrate that nucleoside 1 could be utilized as a fluorescent label to study the function of nucleic acids in a model cellular milieu.
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Affiliation(s)
- Maroti G Pawar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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99
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Murphy RM, Roberts CJ. Protein misfolding and aggregation research: Some thoughts on improving quality and utility. Biotechnol Prog 2013; 29:1109-15. [DOI: 10.1002/btpr.1812] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/11/2013] [Indexed: 01/19/2023]
Affiliation(s)
- Regina M. Murphy
- Dept. of Chemical and Biological Engineering; University of Wisconsin; Madison WI
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100
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Reversible and non-reversible thermal denaturation of lysozyme with varying pH at low ionic strength. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2064-70. [DOI: 10.1016/j.bbapap.2013.06.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 05/29/2013] [Accepted: 06/04/2013] [Indexed: 12/23/2022]
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