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Harkness RW, Zhao H, Toyama Y, Schuck P, Kay LE. Exploring Host-Guest Interactions within a 600 kDa DegP Protease Cage Complex Using Hydrodynamics Measurements and Methyl-TROSY NMR. J Am Chem Soc 2024; 146:8242-8259. [PMID: 38477967 DOI: 10.1021/jacs.3c13247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The DegP protease-chaperone operates within the periplasm of Gram-negative bacteria, where it assists in the regulation of protein homeostasis, promotes virulence, and is essential to survival under stress. To carry out these tasks, DegP forms a network of preorganized apo oligomers that facilitate the capture of substrates within distributions of cage-like complexes which expand to encapsulate clients of various sizes. Although the architectures of DegP cage complexes are well understood, little is known about the structures, dynamics, and interactions of client proteins within DegP cages and the relationship between client structural dynamics and function. Here, we probe host-guest interactions within a 600 kDa DegP cage complex throughout the DegP activation cycle using a model α-helical client protein through a combination of hydrodynamics measurements, methyl-transverse relaxation optimized spectroscopy-based solution nuclear magnetic resonance studies, and proteolytic activity assays. We find that in the presence of the client, DegP cages assemble cooperatively with few intermediates. Our data further show that the N-terminal half of the bound client, which projects into the interior of the cages, is predominantly unfolded and flexible, and exchanges between multiple conformational states over a wide range of time scales. Finally, we show that a concerted structural transition of the protease domains of DegP occurs upon client engagement, leading to activation. Together, our findings support a model of DegP as a highly cooperative and dynamic molecular machine that stabilizes unfolded states of clients, primarily via interactions with their C-termini, giving rise to efficient cleavage.
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Affiliation(s)
- Robert W Harkness
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto M5G 0A4, Canada
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuki Toyama
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto M5G 0A4, Canada
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto M5G 0A4, Canada
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2
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. PLoS Comput Biol 2023; 19:e1011454. [PMID: 37669309 PMCID: PMC10503714 DOI: 10.1371/journal.pcbi.1011454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/15/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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3
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.14.540690. [PMID: 37425873 PMCID: PMC10327192 DOI: 10.1101/2023.05.14.540690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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Ma Y, Ding L, Li Z, Zhou C. Structural basis for TRIM72 oligomerization during membrane damage repair. Nat Commun 2023; 14:1555. [PMID: 36944613 PMCID: PMC10030467 DOI: 10.1038/s41467-023-37198-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Tripartite Motif Protein 72 (TRIM72, also named MG53) mediates membrane damage repair through membrane fusion and exocytosis. During injury, TRIM72 molecules form intermolecular disulfide bonds in response to the oxidative environment and TRIM72 oligomers are proposed to connect vesicles to the plasma membrane and promote membrane fusion in conjunction with other partners like dysferlin and caveolin. However, the detailed mechanism of TRIM72 oligomerization and action remains unclear. Here we present the crystal structure of TRIM72 B-box-coiled-coil-SPRY domains (BCC-SPRY), revealing the molecular basis of TRIM72 oligomerization, which is closely linked to disulfide bond formation. Through structure-guided mutagenesis, we have identified and characterized key residues that are important for the membrane repair function of TRIM72. Our results also demonstrate that TRIM72 interacts with several kinds of negatively charged lipids in addition to phosphatidylserine. Our work provides a structural foundation for further mechanistic studies as well as the clinical application of TRIM72.
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Affiliation(s)
- Yuemin Ma
- School of Public Health, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Lei Ding
- School of Public Health, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Zhenhai Li
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai, 200072, China
| | - Chun Zhou
- School of Public Health, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.
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5
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Uttinger MJ, Hundschell CS, Lautenbach V, Pusara S, Bäther S, Heyn TR, Keppler JK, Wenzel W, Walter J, Kozlowska M, Wagemans AM, Peukert W. Determination of specific and non-specific protein-protein interactions for beta-lactoglobulin by analytical ultracentrifugation and membrane osmometry experiments. SOFT MATTER 2022; 18:6739-6756. [PMID: 36040122 DOI: 10.1039/d2sm00908k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Protein-protein interactions are essential for the understanding of biological processes. Specific protein aggregation is an important aspect for many biological systems. In particular, electrostatic interactions play the key role for protein-protein interactions, as many amino acids have pH-dependent charge states. Moreover, protein dissociation is directly related to the solution pH, ionic strength, temperature and protein concentration. The subtle interplay between different specific and non-specific interactions is demonstrated for beta-lactoglobulin (BLG) with a focus on low salt concentrations, thus mimicking technically relevant processing conditions. BLG is a well-characterized model system, proven to attain its monomer-dimer equilibrium strongly dependent upon the pH of the solution. In this manuscript, we present a unique combination of analytical ultracentrifugation and membrane osmometry experiments, which quantifies specific and non-specific interactions, i.e. in terms of the dimer dissociation constants and the second osmotic virial coefficient, at pH 3 and 7 and sodium chloride concentrations of 10 mM and 100 mM. This provides direct insight to protein-protein interactions for a system with a concentration-dependent monomer-dimer equilibrium. Moreover, using a coarse-grained extended DLVO model in combination with molecular dynamics simulations, we quantify non-specific monomer-monomer, monomer-dimer and dimer-dimer interactions as well as the binding free energy of BLG dimerization from theoretical calculations. The experimentally determined interactions are shown to be mainly governed by electrostatic interactions and further agree with free energy calculations. Our experimental protocol aims to determine non-specific and specific interactions for a dynamically interacting system and provides an understanding of protein-protein interactions for BLG at low salt concentrations.
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Affiliation(s)
- M J Uttinger
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
| | - C S Hundschell
- Institute of Food Technology and Food Chemistry, Department of Food Colloids, Technical University Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - V Lautenbach
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
| | - S Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - S Bäther
- Institute of Food Technology and Food Chemistry, Department of Food Colloids, Technical University Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - T R Heyn
- Institute of Human Nutrition and Food Science, Division of Food Technology, Kiel University, 24118 Kiel, Germany
| | - J K Keppler
- Laboratory of Food Process Engineering, Wageningen University, Wageningen, The Netherlands
| | - W Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - J Walter
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
| | - M Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - A M Wagemans
- Institute of Food Technology and Food Chemistry, Department of Food Colloids, Technical University Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - W Peukert
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Haberstraße 9a, 91058 Erlangen, Germany.
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6
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Soltermann F, Struwe WB, Kukura P. Label-free methods for optical in vitro characterization of protein-protein interactions. Phys Chem Chem Phys 2021; 23:16488-16500. [PMID: 34342317 PMCID: PMC8359934 DOI: 10.1039/d1cp01072g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Philipp Kukura
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
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7
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Martin EW, Harmon TS, Hopkins JB, Chakravarthy S, Incicco JJ, Schuck P, Soranno A, Mittag T. A multi-step nucleation process determines the kinetics of prion-like domain phase separation. Nat Commun 2021; 12:4513. [PMID: 34301955 PMCID: PMC8302766 DOI: 10.1038/s41467-021-24727-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/30/2021] [Indexed: 11/08/2022] Open
Abstract
Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.
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Affiliation(s)
- Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Tyler S Harmon
- The Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Cells (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Cells (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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8
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Zhao H, Nguyen A, To SC, Schuck P. Calibrating analytical ultracentrifuges. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:353-362. [PMID: 33398460 PMCID: PMC8192337 DOI: 10.1007/s00249-020-01485-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022]
Abstract
Analytical ultracentrifugation (AUC) is based on the concept of recording and analyzing macroscopic macromolecular redistribution that results from a centrifugal force acting on the mass of suspended macromolecules in solution. Since AUC rests on first principles, it can provide an absolute measurement of macromolecular mass, sedimentation and diffusion coefficients, and many other quantities, provided that the solvent density and viscosity are known, and provided that the instrument is properly calibrated. Unfortunately, a large benchmark study revealed that many instruments exhibit very significant systematic errors. This includes the magnification of the optical detection system used to determine migration distance, the measurement of sedimentation time, and the measurement of the solution temperature governing viscosity. We have previously developed reference materials, tools, and protocols to detect and correct for systematic measurement errors in the AUC by comparison with independently calibrated standards. This 'external calibration' resulted in greatly improved precision and consistency of parameters across laboratories. Here we detail the steps required for calibration of the different data dimensions in the AUC. We demonstrate the calibration of three different instruments with absorbance and interference optical detection, and use measurements of the sedimentation coefficient of NISTmAb monomer as a test of consistency. Whereas the measured uncorrected sedimentation coefficients span a wide range from 6.22 to 6.61 S, proper calibration resulted in a tenfold reduced standard deviation of sedimentation coefficients. The calibrated relative standard deviation and mean error of 0.2% and 0.07%, respectively, is comparable with statistical errors and side-by-side repeatability in a single instrument.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Ai Nguyen
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Samuel C To
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
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