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Barclay A, Kragelund BB, Arleth L, Pedersen MC. Modeling of flexible membrane-bound biomolecular complexes for solution small-angle scattering. J Colloid Interface Sci 2023; 635:611-621. [PMID: 36634513 DOI: 10.1016/j.jcis.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/18/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Recent advances in protein expression protocols, sample handling, and experimental set up of small-angle scattering experiments have allowed users of the technique to structurally investigate biomolecules of growing complexity and structural disorder. Notable examples include intrinsically disordered proteins, multi-domain proteins and membrane proteins in suitable carrier systems. Here, we outline a modeling scheme for calculating the scattering profiles from such complex samples. This kind of modeling is necessary for structural information to be refined from the corresponding data. The scheme bases itself on a hybrid of classical form factor based modeling and the well-known spherical harmonics-based formulation of small-angle scattering amplitudes. Our framework can account for flexible domains alongside other structurally elaborate components of the molecular system in question. We demonstrate the utility of this modeling scheme through a recent example of a structural model of the growth hormone receptor membrane protein in a phospholipid bilayer nanodisc which is refined against experimental SAXS data. Additionally we investigate how the scattering profiles from the complex would appear under different scattering contrasts. For each contrast situation we discuss what structural information is contained and the related consequences for modeling of the data.
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Affiliation(s)
- Abigail Barclay
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark.
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
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2
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Anisotropic Protein-Protein Interactions in Dilute and Concentrated Solutions. J Colloid Interface Sci 2022; 629:794-804. [DOI: 10.1016/j.jcis.2022.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022]
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3
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Gao R, Pan H, Lian J. Recent advances in the discovery, characterization, and engineering of poly(ethylene terephthalate) (PET) hydrolases. Enzyme Microb Technol 2021; 150:109868. [PMID: 34489027 DOI: 10.1016/j.enzmictec.2021.109868] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/28/2022]
Abstract
Poly(ethylene terephthalate) (PET) is a class of polyester plastic composed of terephthalic acid (TPA) and ethylene glycol (EG). The accumulation of large amount of PET waste has resulted in severe environmental and health problems. Microbial polyester hydrolases with the ability to degrade PET provide an economy- and environment-friendly approach for the treatment of PET waste. In recent years, many PET hydrolases have been discovered and characterized from various microorganisms and engineered for better performance under practical application conditions. Here, recent progress in the discovery, characterization, and enzymatic mechanism elucidation of PET hydrolases is firstly reviewed. Then, structure-guided protein engineering of PET hydrolases with increased enzymatic activities, expanded substrate specificity, as well as improved protein stability is summarized. In addition, strategies for efficient expression of recombinant PET hydrolases, including secretory expression and cell-surface display, are briefly introduced. This review is concluded with future perspectives in biodegradation and subsequent biotransformation of PET wastes to produce value-added compounds.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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4
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Jensen GV, Rosenmejer KR, Huda P, Arleth L. Oligomerization of Pharmaceutically Relevant Insulin Analogues for Varying Concentration and Salinity Revealed by Small-Angle X-ray Scattering. Mol Pharm 2021; 18:3272-3280. [PMID: 34351780 DOI: 10.1021/acs.molpharmaceut.1c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two different insulin analogues, insulin degludec and lithocholyl insulin, were studied by small-angle X-ray scattering with respect to their self-assembly and interactions in solution at different concentrations of insulin and salt, NaCl. Very different behavior was observed for the two. Insulin degludec, linked to a hexadecanedioic acid, consistently formed di-hexamers, without any further oligomeric growth upon screening of electrostatic repulsions, indicating a stable di-hexamer unit without further oligomerization, as expected in the presence of phenol. The other insulin analogue, linked to the sterol lithocholic acid, formed n-hexamers with n ranging from 1 to 15, increasing with NaCl concentration and insulin concentration, indicating attractive forces in competition with the electrostatic repulsion and solution entropy. At the highest concentration of insulin and NaCl, a liquid crystal phase was observed, which has not previously been identified, featuring a quadratic structure organized into layers, which might hold interesting properties for pharmaceutical applications.
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Affiliation(s)
- Grethe V Jensen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Katrine R Rosenmejer
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Pie Huda
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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5
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Larsen AH, Pedersen JS, Arleth L. Assessment of structure factors for analysis of small-angle scattering data from desired or undesired aggregates. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720006500] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aggregation processes are central features of many systems ranging from colloids and polymers to inorganic nanoparticles and biological systems. Some aggregated structures are controlled and desirable, e.g. in the design of size-controlled clustered nanoparticles or some protein-based drugs. In other cases, the aggregates are undesirable, e.g. protein aggregation involved in neurodegenerative diseases or in vitro studies of single protein structures. In either case, experimental and analytical tools are needed to cast light on the aggregation processes. Aggregation processes can be studied with small-angle scattering, but analytical descriptions of the aggregates are needed for detailed structural analysis. This paper presents a list of useful small-angle scattering structure factors, including a novel structure factor for a spherical cluster with local correlations between the constituent particles. Several of the structure factors were renormalized to get correct limit values in both the high-q and low-q limit, where q is the modulus of the scattering vector. The structure factors were critically evaluated against simulated data. Structure factors describing fractal aggregates provided approximate descriptions of the simulated data for all tested structures, from linear to globular aggregates. The addition of a correlation hole for the constituent particles in the fractal structure factors significantly improved the fits in all cases. Linear aggregates were best described by a linear structure factor and globular aggregates by the newly derived spherical cluster structure factor. As a central point, it is shown that the structure factors could be used to take aggregation contributions into account for samples of monomeric protein containing a minor fraction of aggregated protein. After applying structure factors in the analysis, the correct structure and oligomeric state of the protein were determined. Thus, by careful use of the presented structure factors, important structural information can be retrieved from small-angle scattering data, both when aggregates are desired and when they are undesired.
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6
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Xu Z, Cen YK, Zou SP, Xue YP, Zheng YG. Recent advances in the improvement of enzyme thermostability by structure modification. Crit Rev Biotechnol 2019; 40:83-98. [DOI: 10.1080/07388551.2019.1682963] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Zhe Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Ping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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7
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Pekarsky A, Veiter L, Rajamanickam V, Herwig C, Grünwald-Gruber C, Altmann F, Spadiut O. Production of a recombinant peroxidase in different glyco-engineered Pichia pastoris strains: a morphological and physiological comparison. Microb Cell Fact 2018; 17:183. [PMID: 30474550 PMCID: PMC6260843 DOI: 10.1186/s12934-018-1032-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/16/2018] [Indexed: 02/07/2023] Open
Abstract
Background The methylotrophic yeast Pichia pastoris is a common host for the production of recombinant proteins. However, hypermannosylation hinders the use of recombinant proteins from yeast in most biopharmaceutical applications. Glyco-engineered yeast strains produce more homogeneously glycosylated proteins, but can be physiologically impaired and show tendencies for cellular agglomeration, hence are hard to cultivate. Further, comprehensive data regarding growth, physiology and recombinant protein production in the controlled environment of a bioreactor are scarce. Results A Man5GlcNAc2 glycosylating and a Man8–10GlcNAc2 glycosylating strain showed similar morphological traits during methanol induced shake-flask cultivations to produce the recombinant model protein HRP C1A. Both glyco-engineered strains displayed larger single and budding cells than a wild type strain as well as strong cellular agglomeration. The cores of these agglomerates appeared to be less viable. Despite agglomeration, the Man5GlcNAc2 glycosylating strain showed superior growth, physiology and HRP C1A productivity compared to the Man8–10GlcNAc2 glycosylating strain in shake-flasks and in the bioreactor. Conducting dynamic methanol pulsing revealed that HRP C1A productivity of the Man5GlcNAc2 glycosylating strain is best at a temperature of 30 °C. Conclusion This study provides the first comprehensive evaluation of growth, physiology and recombinant protein production of a Man5GlcNAc2 glycosylating strain in the controlled environment of a bioreactor. Furthermore, it is evident that cellular agglomeration is likely triggered by a reduced glycan length of cell surface glycans, but does not necessarily lead to lower metabolic activity and recombinant protein production. Man5GlcNAc2 glycosylated HRP C1A production is feasible, yields active protein similar to the wild type strain, but thermal stability of HRP C1A is negatively affected by reduced glycosylation. Electronic supplementary material The online version of this article (10.1186/s12934-018-1032-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Pekarsky
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Lukas Veiter
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Vignesh Rajamanickam
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Christoph Herwig
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, TU Wien, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
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8
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Larsen AH, Dorosz J, Thorsen TS, Johansen NT, Darwish T, Midtgaard SR, Arleth L, Kastrup JS. Small-angle neutron scattering studies on the AMPA receptor GluA2 in the resting, AMPA-bound and GYKI-53655-bound states. IUCRJ 2018; 5:780-793. [PMID: 30443361 PMCID: PMC6211538 DOI: 10.1107/s2052252518012186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/28/2018] [Indexed: 06/09/2023]
Abstract
The AMPA receptor GluA2 belongs to the family of ionotropic glutamate receptors, which are responsible for most of the fast excitatory neuronal signalling in the central nervous system. These receptors are important for memory and learning, but have also been associated with brain diseases such as Alzheimer's disease and epilepsy. Today, one drug is on the market for the treatment of epilepsy targeting AMPA receptors, i.e. a negative allosteric modulator of these receptors. Recently, crystal structures and cryo-electron microscopy (cryo-EM) structures of full-length GluA2 in the resting (apo), activated and desensitized states have been reported. Here, solution structures of full-length GluA2 are reported using small-angle neutron scattering (SANS) with a novel, fully matched-out detergent. The GluA2 solution structure was investigated in the resting state as well as in the presence of AMPA and of the negative allosteric modulator GYKI-53655. In solution and at neutral pH, the SANS data clearly indicate that GluA2 is in a compact form in the resting state. The solution structure resembles the crystal structure of GluA2 in the resting state, with an estimated maximum distance (D max) of 179 ± 11 Å and a radius of gyration (R g) of 61.9 ± 0.4 Å. An ab initio model of GluA2 in solution generated using DAMMIF clearly showed the individual domains, i.e. the extracellular N-terminal domains and ligand-binding domains as well as the transmembrane domain. Solution structures revealed that GluA2 remained in a compact form in the presence of AMPA or GYKI-53655. At acidic pH only, GluA2 in the presence of AMPA adopted a more open conformation of the extracellular part (estimated D max of 189 ± 5 Å and R g of 65.2 ± 0.5 Å), resembling the most open, desensitized class 3 cryo-EM structure of GluA2 in the presence of quisqualate. In conclusion, this methodological study may serve as an example for future SANS studies on membrane proteins.
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Affiliation(s)
- Andreas Haahr Larsen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thor Seneca Thorsen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Nicolai Tidemand Johansen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Tamim Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Australia
| | - Søren Roi Midtgaard
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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9
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Shirke AN, White C, Englaender JA, Zwarycz A, Butterfoss GL, Linhardt RJ, Gross RA. Stabilizing Leaf and Branch Compost Cutinase (LCC) with Glycosylation: Mechanism and Effect on PET Hydrolysis. Biochemistry 2018; 57:1190-1200. [PMID: 29328676 DOI: 10.1021/acs.biochem.7b01189] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cutinases are polyester hydrolases that show a remarkable capability to hydrolyze polyethylene terephthalate (PET) to its monomeric units. This revelation has stimulated research aimed at developing sustainable and green cutinase-catalyzed PET recycling methods. Leaf and branch compost cutinase (LCC) is particularly suited toward these ends given its relatively high PET hydrolysis activity and thermostability. Any practical enzymatic PET recycling application will require that the protein have kinetic stability at or above the PET glass transition temperature (Tg, i.e., 70 °C). This paper elucidates the thermodynamics and kinetics of LCC conformational and colloidal stability. Aggregation emerged as a major contributor that reduces LCC kinetic stability. In its native state, LCC is prone to aggregation owing to electrostatic interactions. Further, with increasing temperature, perturbation of LCC's tertiary structure and corresponding exposure of hydrophobic domains leads to rapid aggregation. Glycosylation was employed in an attempt to impede LCC aggregation. Owing to the presence of three putative N-glycosylation sites, expression of native LCC in Pichia pastoris resulted in the production of glycosylated LCC (LCC-G). LCC-G showed improved stability to native state aggregation while increasing the temperature for thermal induced aggregation by 10 °C. Furthermore, stabilization against thermal aggregation resulted in improved catalytic PET hydrolysis both at its optimum temperature and concentration.
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Affiliation(s)
- Abhijit N Shirke
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Christine White
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jacob A Englaender
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Allison Zwarycz
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi , Abu Dhabi, UAE
| | - Robert J Linhardt
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Richard A Gross
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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10
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Shirke AN, Su A, Jones JA, Butterfoss GL, Koffas MA, Kim JR, Gross RA. Comparative thermal inactivation analysis ofAspergillus oryzaeandThiellavia terrestriscutinase: Role of glycosylation. Biotechnol Bioeng 2016; 114:63-73. [DOI: 10.1002/bit.26052] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 07/01/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Abhijit N. Shirke
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; Troy New York
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York
| | - An Su
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; Troy New York
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York
| | - J. Andrew Jones
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Troy New York
| | - Glenn L. Butterfoss
- Center for Genomics and Systems Biology; New York University Abu Dhabi; Abu Dhabi UAE
| | - Mattheos A.G. Koffas
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York
- Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; Troy New York
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering; New York University Tandon School of Engineering; Brooklyn New York
| | - Richard A. Gross
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; Troy New York
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York
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11
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Hartel AJW, Glogger M, Jones NG, Abuillan W, Batram C, Hermann A, Fenz SF, Tanaka M, Engstler M. N-glycosylation enables high lateral mobility of GPI-anchored proteins at a molecular crowding threshold. Nat Commun 2016; 7:12870. [PMID: 27641538 PMCID: PMC5031801 DOI: 10.1038/ncomms12870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/09/2016] [Indexed: 01/17/2023] Open
Abstract
The protein density in biological membranes can be extraordinarily high, but the impact of molecular crowding on the diffusion of membrane proteins has not been studied systematically in a natural system. The diversity of the membrane proteome of most cells may preclude systematic studies. African trypanosomes, however, feature a uniform surface coat that is dominated by a single type of variant surface glycoprotein (VSG). Here we study the density-dependence of the diffusion of different glycosylphosphatidylinositol-anchored VSG-types on living cells and in artificial membranes. Our results suggest that a specific molecular crowding threshold (MCT) limits diffusion and hence affects protein function. Obstacles in the form of heterologous proteins compromise the diffusion coefficient and the MCT. The trypanosome VSG-coat operates very close to its MCT. Importantly, our experiments show that N-linked glycans act as molecular insulators that reduce retarding intermolecular interactions allowing membrane proteins to function correctly even when densely packed.
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Affiliation(s)
- Andreas J. W. Hartel
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Marius Glogger
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Nicola G. Jones
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
| | - Christopher Batram
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Anne Hermann
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Susanne F. Fenz
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
- Institute for Integrated Cell-Material Science (WPI iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Markus Engstler
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
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12
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Heterologous expression of Hordeum vulgare protein Z4 in Pichia pastoris shows increased structural stability. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Biswas S, Chowdhury PK. Correlated and Anticorrelated Domain Movement of Human Serum Albumin: A Peek into the Complexity of the Crowded Milieu. J Phys Chem B 2016; 120:4897-911. [DOI: 10.1021/acs.jpcb.6b01671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Biswas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit Kumar Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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14
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Munch HK, Nygaard J, Christensen NJ, Engelbrekt C, Østergaard M, Porsgaard T, Hoeg-Jensen T, Zhang J, Arleth L, Thulstrup PW, Jensen KJ. Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites. Angew Chem Int Ed Engl 2016; 55:2378-81. [DOI: 10.1002/anie.201509088] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/01/2015] [Indexed: 11/06/2022]
Affiliation(s)
| | - Jesper Nygaard
- MAX-lab; Lund University; Sweden
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | | | | | | | | | - Jingdong Zhang
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby Denmark
| | - Lise Arleth
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Denmark
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15
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Munch HK, Nygaard J, Christensen NJ, Engelbrekt C, Østergaard M, Porsgaard T, Hoeg-Jensen T, Zhang J, Arleth L, Thulstrup PW, Jensen KJ. Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Jesper Nygaard
- MAX-lab; Lund University; Sweden
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | | | | | | | | | - Jingdong Zhang
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby Denmark
| | - Lise Arleth
- Niels Bohr Institute; University of Copenhagen; Denmark
| | | | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Denmark
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Nygaard J, Munch HK, Thulstrup PW, Christensen NJ, Hoeg-Jensen T, Jensen KJ, Arleth L. Metal ion controlled self-assembly of a chemically reengineered protein drug studied by small-angle X-ray scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12159-12170. [PMID: 22853842 DOI: 10.1021/la301291w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Precise control of the oligomeric state of proteins is of central importance for biological function and for the properties of biopharmaceutical drugs. Here, the self-assembly of 2,2'-bipyridine conjugated monomeric insulin analogues, induced through coordination to divalent metal ions, was studied. This protein drug system was designed to form non-native homo-oligomers through selective coordination of two divalent metal ions, Fe(II) and Zn(II), respectively. The insulin type chosen for this study is a variant designed for a reduced tendency toward native dimer formation at physiological concentrations. A small-angle X-ray scattering analysis of the bipyridine-modified insulin system confirmed an organization into a novel well-ordered structure based on insulin trimers, as induced by the addition of Fe(II). In contrast, unmodified monomeric insulin formed larger and more randomly structured assemblies upon addition of Fe(II). The addition of Zn(II), on the other hand, led to the formation of small quantities of insulin hexamers for both the bipyridine-modified and the unmodified monomeric insulin. Interestingly, the location of the bipyridine-modification significantly affects the tendency to hexamer formation as compared to the unmodified insulin. Our study shows how combining a structural study and chemical design can be used to obtain molecular understanding and control of the self-assembly of a protein drug. This knowledge may eventually be employed to develop an optimized in vivo drug release profile.
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Affiliation(s)
- Jesper Nygaard
- Niels Bohr Institute, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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17
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Malik L, Nygaard J, Hoiberg-Nielsen R, Arleth L, Hoeg-Jensen T, Jensen KJ. Perfluoroalkyl chains direct novel self-assembly of insulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:593-603. [PMID: 22129241 DOI: 10.1021/la203042c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The self-assembly of biopharmaceutical peptides into multimeric, nanoscale objects, as well as their disassembly to monomers, is central for their mode of action. Here, we describe a bioorthogonal strategy, using a non-native recognition principle, for control of protein self-assembly based on intermolecular fluorous interactions and demonstrate it for the small protein insulin. Perfluorinated alkyl chains of varying length were attached to desB30 human insulin by acylation of the ε-amine of the side-chain of LysB29. The insulin analogues were formulated with Zn(II) and phenol to form hexamers. The self-segregation of fluorous groups directed the insulin hexamers to self-assemble. The structures of the systems were investigated by circular dichroism (CD) spectroscopy and synchrotron small-angle X-ray scattering. Also, the binding affinity to the insulin receptor was measured. Interestingly, varying the length of the perfluoroalkyl chain provided three different scenarios for self-assembly; the short chains hardly affected the native hexameric structure, the medium-length chains induced fractal-like structures with the insulin hexamer as the fundamental building block, while the longest chains lead to the formation of structures with local cylindrical geometry. This hierarchical self-assembly system, which combines Zn(II) mediated hexamer formation with fluorous interactions, is a promising tool to control the formation of high molecular weight complexes of insulin and potentially other proteins.
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Affiliation(s)
- Leila Malik
- IGM, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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18
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Mertens HDT, Svergun DI. Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 2010; 172:128-41. [PMID: 20558299 DOI: 10.1016/j.jsb.2010.06.012] [Citation(s) in RCA: 389] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 06/08/2010] [Accepted: 06/10/2010] [Indexed: 01/27/2023]
Abstract
Small-angle scattering of X-rays (SAXS) is an established method for the low-resolution structural characterization of biological macromolecules in solution. The technique provides three-dimensional low-resolution structures, using ab initio and rigid body modeling, and allow one to assess the oligomeric state of proteins and protein complexes. In addition, SAXS is a powerful tool for structure validation and the quantitative analysis of flexible systems, and is highly complementary to the high resolution methods of X-ray crystallography and NMR. At present, SAXS analysis methods have reached an advanced state, allowing for automated and rapid characterization of protein solutions in terms of low-resolution models, quaternary structure and oligomeric composition. In this communication, main approaches to the characterization of proteins and protein complexes using SAXS are reviewed. The tools for the analysis of proteins in solution are presented, and the impact that these tools have made in modern structural biology is discussed.
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Affiliation(s)
- Haydyn D T Mertens
- European Molecular Biology Laboratory-Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, Germany
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