1
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Dall NR, Mendonça CATF, Torres Vera HL, Marqusee S. The importance of the location of the N-terminus in successful protein folding in vivo and in vitro. Proc Natl Acad Sci U S A 2024; 121:e2321999121. [PMID: 39145938 DOI: 10.1073/pnas.2321999121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 07/16/2024] [Indexed: 08/16/2024] Open
Abstract
Protein folding in the cell often begins during translation. Many proteins fold more efficiently cotranslationally than when refolding from a denatured state. Changing the vectorial synthesis of the polypeptide chain through circular permutation could impact functional, soluble protein expression and interactions with cellular proteostasis factors. Here, we measure the solubility and function of every possible circular permutant (CP) of HaloTag in Escherichia coli cell lysate using a gel-based assay, and in living E. coli cells via FACS-seq. We find that 78% of HaloTag CPs retain protein function, though a subset of these proteins are also highly aggregation-prone. We examine the function of each CP in E. coli cells lacking the cotranslational chaperone trigger factor and the intracellular protease Lon and find no significant changes in function as a result of modifying the cellular proteostasis network. Finally, we biophysically characterize two topologically interesting CPs in vitro via circular dichroism and hydrogen-deuterium exchange coupled with mass spectrometry to reveal changes in global stability and folding kinetics with circular permutation. For CP33, we identify a change in the refolding intermediate as compared to wild-type (WT) HaloTag. Finally, we show that the strongest predictor of aggregation-prone expression in cells is the introduction of termini within the refolding intermediate. These results, in addition to our finding that termini insertion within the conformationally restrained core is most disruptive to protein function, indicate that successful folding of circular permutants may depend more on changes in folding pathway and termini insertion in flexible regions than on the availability of proteostasis factors.
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Affiliation(s)
- Natalie R Dall
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Carolina A T F Mendonça
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Héctor L Torres Vera
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
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2
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Karamitros CS, Murray K, Kumada Y, Johnson KA, D'Arcy S, Georgiou G. Mechanistic conformational and substrate selectivity profiles emerging in the evolution of enzymes via parallel trajectories. Nat Commun 2024; 15:7068. [PMID: 39152129 PMCID: PMC11329768 DOI: 10.1038/s41467-024-51133-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
Laboratory evolution studies have demonstrated that parallel evolutionary trajectories can lead to genetically distinct enzymes with high activity towards a non-preferred substrate. However, it is unknown whether such enzymes have convergent conformational dynamics and mechanistic features. To address this question, we use as a model the wild-type Homo sapiens kynureninase (HsKYNase), which is of great interest for cancer immunotherapy. Earlier, we isolated HsKYNase_66 through an unusual evolutionary trajectory, having a 410-fold increase in the kcat/KM for kynurenine (KYN) and reverse substrate selectivity relative to HsKYNase. Here, by following a different evolutionary trajectory we generate a genetically distinct variant, HsKYNase_93D9, that exhibits KYN catalytic activity comparable to that of HsKYNase_66, but instead it is a "generalist" that accepts 3'-hydroxykynurenine (OH-KYN) with the same proficiency. Pre-steady-state kinetic analysis reveals that while the evolution of HsKYNase_66 is accompanied by a change in the rate-determining step of the reactions, HsKYNase_93D9 retains the same catalytic mechanism as HsKYNase. HDX-MS shows that the conformational dynamics of the two enzymes are markedly different and distinct from ortholog prokaryotic enzymes with high KYN activity. Our work provides a mechanistic framework for understanding the relationship between evolutionary mechanisms and phenotypic traits of evolved generalist and specialist enzyme species.
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Affiliation(s)
- Christos S Karamitros
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA
- Research and Clinical Development, Nestlé Health Science, Lausanne, 1000, Switzerland
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
- Trajan Scientific America's, Inc. Boston, Massachusetts, MA, USA
| | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, TX, USA
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin (UT Austin), Austin, TX, USA.
- Department of Biomedical Engineering, University of Texas at Austin (UT Austin), Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin (UT Austin), Austin, TX, USA.
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3
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Ye X, Hu Y, Qiu H, Li N. Probe capsid structure stability and dynamics of adeno-associated virus as an important viral vector for gene therapy by hydrogen-deuterium exchange-mass spectrometry. Protein Sci 2024; 33:e5074. [PMID: 38888268 PMCID: PMC11184576 DOI: 10.1002/pro.5074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/14/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
Adeno-associated virus (AAV), a widely used gene therapy vector, is a small, nonenveloped virus that contains a single-stranded DNA genome with a maximum length of 4.7 kb. Despite extensive biophysical and structural characterization, many aspects of AAV functions remain elusive. This knowledge gap is primarily due to a lack of structurally resolved dynamic information and the absence of structural coverage of functionally critical segments on the AAV capsid. Here, we developed a protocol to study AAV structural dynamics by hydrogen-deuterium exchange mass spectrometry (HDX-MS), a powerful method for monitoring protein structure stability and dynamics in solution. We performed HDX-MS measurements on AAVs without or with different DNA payloads of different sizes, and obtained detailed dynamic information on the entire AAV sequence including the two functionally important segments not previously structurally characterized. The unique N terminus of the capsid protein VP1 (VP1u) was found to adopt a highly dynamic and unstable conformation with low HDX protection across the entire region, whereas the presence of a DNA payload increased its protection. The VP1 and VP2 shared region (VP1/2) showed no measurable protection, with or without DNA. Differential HDX between empty and full capsid samples allowed us to identify potential new DNA-capsid interaction sites located primarily around the five-fold channel, which differ from the three-fold pocket binding site previously identified. Our HDX-MS method for characterizing AAV structural dynamics opens a new way for future efforts to understand AAV structure-function relationships and engineer next-generation AAV vectors with improved gene delivery properties.
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Affiliation(s)
- Xiang Ye
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Yunli Hu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Haibo Qiu
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
| | - Ning Li
- Regeneron Pharmaceuticals, Inc.TarrytownNew YorkUSA
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4
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Jagielnicki M, Kucharska I, Bennett BC, Harris AL, Yeager M. Connexin Gap Junction Channels and Hemichannels: Insights from High-Resolution Structures. BIOLOGY 2024; 13:298. [PMID: 38785780 PMCID: PMC11117596 DOI: 10.3390/biology13050298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024]
Abstract
Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper functioning is crucial for many processes, including development, physiology, and response to disease and trauma. Abnormal GJC and HC communication can lead to numerous pathological states including inflammation, skin diseases, deafness, nervous system disorders, and cardiac arrhythmias. Over the last 15 years, high-resolution X-ray and electron cryomicroscopy (cryoEM) structures for seven Cx isoforms have revealed conservation in the four-helix transmembrane (TM) bundle of each subunit; an αβ fold in the disulfide-bonded extracellular loops and inter-subunit hydrogen bonding across the extracellular gap that mediates end-to-end docking to form a tight seal between hexamers in the GJC. Tissue injury is associated with cellular Ca2+ overload. Surprisingly, the binding of 12 Ca2+ ions in the Cx26 GJC results in a novel electrostatic gating mechanism that blocks cation permeation. In contrast, acidic pH during tissue injury elicits association of the N-terminal (NT) domains that sterically blocks the pore in a "ball-and-chain" fashion. The NT domains under physiologic conditions display multiple conformational states, stabilized by protein-protein and protein-lipid interactions, which may relate to gating mechanisms. The cryoEM maps also revealed putative lipid densities within the pore, intercalated among transmembrane α-helices and between protomers, the functions of which are unknown. For the future, time-resolved cryoEM of isolated Cx channels as well as cryotomography of GJCs and HCs in cells and tissues will yield a deeper insight into the mechanisms for channel regulation. The cytoplasmic loop (CL) and C-terminal (CT) domains are divergent in sequence and length, are likely involved in channel regulation, but are not visualized in the high-resolution X-ray and cryoEM maps presumably due to conformational flexibility. We expect that the integrated use of synergistic physicochemical, spectroscopic, biophysical, and computational methods will reveal conformational dynamics relevant to functional states. We anticipate that such a wealth of results under different pathologic conditions will accelerate drug discovery related to Cx channel modulation.
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Affiliation(s)
- Maciej Jagielnicki
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Chemistry, University of Miami, 1201 Memorial Drive, Miami, FL 33146, USA; (M.J.); (I.K.)
| | - Iga Kucharska
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Chemistry, University of Miami, 1201 Memorial Drive, Miami, FL 33146, USA; (M.J.); (I.K.)
| | - Brad C. Bennett
- Department of Biological and Environmental Sciences, Howard College of Arts and Sciences, Samford University, Birmingham, AL 35229, USA;
| | - Andrew L. Harris
- Rutgers New Jersey Medical School, Department of Pharmacology, Physiology and Neuroscience, Newark, NJ 07103, USA;
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Chemistry, University of Miami, 1201 Memorial Drive, Miami, FL 33146, USA; (M.J.); (I.K.)
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL 33146, USA
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5
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. eLife 2024; 12:RP92462. [PMID: 38381130 PMCID: PMC10942615 DOI: 10.7554/elife.92462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Yuqi Shi
- Thermo Fisher ScientificSan JoseUnited States
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Katleen Willibal
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Nathan D Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - H Ronald Kaback
- Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech UniversityLubbockUnited States
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
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6
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Largy E, Ranz M, Gabelica V. A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA. J Am Chem Soc 2023; 145:26843-26857. [PMID: 38044563 DOI: 10.1021/jacs.3c09365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging, because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize the G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in the inner and outer tetrads. We also established relationships among exchange rates, numbers of tetrads and bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.
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Affiliation(s)
- Eric Largy
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Matthieu Ranz
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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7
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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8
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558283. [PMID: 37790566 PMCID: PMC10542114 DOI: 10.1101/2023.09.18.558283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of the Na+-coupled major facilitator superfamily transporters. With a conformational nanobody (Nb), we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. Collectively with the available outward-facing sugar-bound structures, both the outer and inner barriers were localized. The N- and C-terminal residues of the inner barrier contribute to the sugar selectivity pocket. When the inner barrier is broken as shown in the inward-open conformation, the sugar selectivity pocket is also broken. The binding assays by isothermal titration calorimetry revealed that this inward-facing conformation trapped by the conformation-selective Nb exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for the substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is also supported by molecular dynamics simulations. Furthermore, the use of this Nb in combination with the hydron/deuterium exchange mass spectrometry allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | | | - Nathan D. Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Els Pardon
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - H. Ronald Kaback
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
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9
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Ortner M, Guschtschin-Schmidt N, Stelzer W, Muhle-Goll C, Langosch D. Permissive Conformations of a Transmembrane Helix Allow Intramembrane Proteolysis by γ-Secretase. J Mol Biol 2023; 435:168218. [PMID: 37536392 DOI: 10.1016/j.jmb.2023.168218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
The intramembrane protease γ-secretase activates important signaling molecules, such as Notch receptors. It is still unclear, however, how different elements within the primary structure of substrate transmembrane domains (TMDs) contribute to their cleavability. Using a newly developed yeast-based cleavage assay, we identified three crucial regions within the TMDs of the paralogs Notch1 and Notch3 by mutational and gain-of-function approaches. The AAAA or AGAV motifs within the N-terminal half of the TMDs were found to confer strong conformational flexibility to these TMD helices, as determined by mutagenesis coupled to deuterium/hydrogen exchange. Crucial amino acids within the C-terminal half may support substrate docking into the catalytic cleft of presenilin, the enzymatic subunit of γ-secretase. Further, residues close to the C-termini of the TMDs may stabilize a tripartite β-sheet in the substrate/enzyme complex. NMR structures reveal different extents of helix bending as well as an ability to adopt widely differing conformational substates, depending on the sequence of the N-terminal half. The difference in cleavability between Notch1 and Notch3 TMDs is jointly determined by the conformational repertoires of the TMD helices and the sequences of the C-terminal half, as suggested by mutagenesis and building molecular models. In sum, cleavability of a γ-secretase substrate is enabled by different functions of cooperating TMD regions, which deepens our mechanistic understanding of substrate/non-substrate discrimination in intramembrane proteolysis.
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Affiliation(s)
- Martin Ortner
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Nadja Guschtschin-Schmidt
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Walter Stelzer
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Dieter Langosch
- Chair of Biopolymer Chemistry, Technical University of Munich, Freising, Germany.
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10
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Salmas R, Harris MJ, Borysik AJ. Mapping HDX-MS Data to Protein Conformations through Training Ensemble-Based Models. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1989-1997. [PMID: 37550799 PMCID: PMC10485923 DOI: 10.1021/jasms.3c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
An original approach that adopts machine learning inference to predict protein structural information using hydrogen-deuterium exchange mass spectrometry (HDX-MS) is described. The method exploits an in-house optimization program that increases the resolution of HDX-MS data from peptides to amino acids. A system is trained using Gradient Tree Boosting as a type of machine learning ensemble technique to assign a protein secondary structure. Using limited training data we generate a discriminative model that uses optimized HDX-MS data to predict protein secondary structure with an accuracy of 75%. This research could form the basis for new methods exploiting artificial intelligence to model protein conformations by HDX-MS.
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Affiliation(s)
| | | | - Antoni J. Borysik
- Department of Chemistry,
Britannia House, King’s College London, London SE1 1DB, U.K.
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11
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Mathew A, Giskes F, Lekkas A, Greisch JF, Eijkel GB, Anthony IGM, Fort K, Heck AJR, Papanastasiou D, Makarov AA, Ellis SR, Heeren RMA. An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319176 DOI: 10.1021/jasms.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase.
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Affiliation(s)
- Anjusha Mathew
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Frans Giskes
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Alexandros Lekkas
- Fasmatech Science and Technology, Demokritos NCSR, 15310 Agia Paraskevi, Athens, Greece
| | - Jean-François Greisch
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gert B Eijkel
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ian G M Anthony
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Kyle Fort
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Alexander A Makarov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
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12
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Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape. iScience 2023; 26:106282. [PMID: 36910327 PMCID: PMC9968663 DOI: 10.1016/j.isci.2023.106282] [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: 10/20/2022] [Revised: 01/10/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Three-dimensional structure and dynamics are essential for protein function. Advancements in hydrogen-deuterium exchange (HDX) techniques enable probing protein dynamic information in physiologically relevant conditions. HDX-coupled mass spectrometry (HDX-MS) has been broadly applied in pharmaceutical industries. However, it is challenging to obtain dynamics information at the single amino acid resolution and time consuming to perform the experiments and process the data. Here, we demonstrate the first deep learning model, artificial intelligence-based HDX (AI-HDX), that predicts intrinsic protein dynamics based on the protein sequence. It uncovers the protein structural dynamics by combining deep learning, experimental HDX, sequence alignment, and protein structure prediction. AI-HDX can be broadly applied to drug discovery, protein engineering, and biomedical studies. As a demonstration, we elucidated receptor-binding domain structural dynamics as a potential mechanism of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody efficacy and immune escape. AI-HDX fundamentally differs from the current AI tools for protein analysis and may transform protein design for various applications.
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13
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Sabo KA, Albekioni E, Caliger D, Coleman NJ, Thornberg E, Avellaneda Matteo D, Komives EA, Silletti S, Sohl CD. Capturing the Dynamic Conformational Changes of Human Isocitrate Dehydrogenase 1 (IDH1) upon Ligand and Metal Binding Using Hydrogen-Deuterium Exchange Mass Spectrometry. Biochemistry 2023; 62:1145-1159. [PMID: 36854124 PMCID: PMC10089636 DOI: 10.1021/acs.biochem.2c00636] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Human isocitrate dehydrogenase 1 (IDH1) is a highly conserved metabolic enzyme that catalyzes the interconversion of isocitrate and α-ketoglutarate. Kinetic and structural studies with IDH1 have revealed evidence of striking conformational changes that occur upon binding of its substrates, isocitrate and NADP+, and its catalytic metal cation. Here, we used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to build a comprehensive map of the dynamic conformational changes experienced by IDH1 upon ligand binding. IDH1 proved well-suited for HDX-MS analysis, allowing us to capture profound changes in solvent accessibility at substrate binding sites and at a known regulatory region, as well as at more distant local subdomains that appear to support closure of this protein into its active conformation. HDX-MS analysis suggested that IDH1 is primarily purified with NADP(H) bound in the absence of its metal cation. Subsequent metal cation binding, even in the absence of isocitrate, was critical for driving large conformational changes. WT IDH1 folded into its fully closed conformation only when the full complement of substrates and metal was present. Finally, we show evidence supporting a previously hypothesized partially open conformation that forms prior to the catalytically active state, and we propose this conformation is driven by isocitrate binding in the absence of metal.
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Affiliation(s)
- Kaitlyn A Sabo
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
| | - Elene Albekioni
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
| | - Danielle Caliger
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
| | - Nalani J Coleman
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
| | - Ella Thornberg
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
| | - Diego Avellaneda Matteo
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
| | - Elizabeth A Komives
- University of California, San Diego, Department of Chemistry and Biochemistry, La Jolla, California 92093, United States
| | - Steve Silletti
- University of California, San Diego, Department of Chemistry and Biochemistry, La Jolla, California 92093, United States
| | - Christal D Sohl
- San Diego State University, Department of Chemistry and Biochemistry, San Diego, California 92182, United States
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14
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McKinnon TAJ. 2B or not 2B: art thou autoinhibitory? Blood 2023; 141:1102-1103. [PMID: 36893008 DOI: 10.1182/blood.2022019577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
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15
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Legan ER, Liu Y, Arce NA, Parker ET, Lollar P, Zhang XF, Li R. Type 2B von Willebrand disease mutations differentially perturb autoinhibition of the A1 domain. Blood 2023; 141:1221-1232. [PMID: 36580664 PMCID: PMC10023833 DOI: 10.1182/blood.2022017239] [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] [Received: 05/31/2022] [Revised: 12/05/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Type 2B von Willebrand disease (VWD) is an inherited bleeding disorder in which a subset of point mutations in the von Willebrand factor (VWF) A1 domain and recently identified autoinhibitory module (AIM) cause spontaneous binding to glycoprotein Ibα (GPIbα) on the platelet surface. All reported type 2B VWD mutations share this enhanced binding; however, type 2B VWD manifests as variable bleeding complications and platelet levels in patients, depending on the underlying mutation. Understanding how these mutations localizing to a similar region can result in such disparate patient outcomes is essential for detailing our understanding of VWF regulatory and activation mechanisms. In this study, we produced recombinant glycosylated AIM-A1 fragments bearing type 2B VWD mutations and examined how each mutation affects the A1 domain's thermodynamic stability, conformational dynamics, and biomechanical regulation of the AIM. We found that the A1 domain with mutations associated with severe bleeding occupy a higher affinity state correlating with enhanced flexibility in the secondary GPIbα-binding sites. Conversely, mutation P1266L, associated with normal platelet levels, has similar proportions of high-affinity molecules to wild-type (WT) but shares regions of solvent accessibility with both WT and other type 2B VWD mutations. V1316M exhibited exceptional instability and solvent exposure compared with all variants. Lastly, examination of the mechanical stability of each variant revealed variable AIM unfolding. Together, these studies illustrate that the heterogeneity among type 2B VWD mutations is evident in AIM-A1 fragments.
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Affiliation(s)
- Emily R. Legan
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, Bethlehem, PA
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA
| | - Nicholas A. Arce
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Ernest T. Parker
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Pete Lollar
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - X. Frank Zhang
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
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16
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Cooperation of N- and C-terminal substrate transmembrane domain segments in intramembrane proteolysis by γ-secretase. Commun Biol 2023; 6:177. [PMID: 36792683 PMCID: PMC9931712 DOI: 10.1038/s42003-023-04470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 01/11/2023] [Indexed: 02/17/2023] Open
Abstract
Intramembrane proteases play a pivotal role in biology and medicine, but how these proteases decode cleavability of a substrate transmembrane (TM) domain remains unclear. Here, we study the role of conformational flexibility of a TM domain, as determined by deuterium/hydrogen exchange, on substrate cleavability by γ-secretase in vitro and in cellulo. By comparing hybrid TMDs based on the natural amyloid precursor protein TM domain and an artificial poly-Leu non-substrate, we find that substrate cleavage requires conformational flexibility within the N-terminal half of the TMD helix (TM-N). Robust cleavability also requires the C-terminal TM sequence (TM-C) containing substrate cleavage sites. Since flexibility of TM-C does not correlate with cleavage efficiency, the role of the TM-C may be defined mainly by its ability to form a cleavage-competent state near the active site, together with parts of presenilin, the enzymatic component of γ-secretase. In sum, cleavability of a γ-secretase substrate appears to depend on cooperating TM domain segments, which deepens our mechanistic understanding of intramembrane proteolysis.
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17
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Abstract
GPR21 is a class-A orphan G protein-coupled receptor (GPCR) and a potential therapeutic target for type 2 diabetes and other metabolic disorders. This receptor shows high basal activity in coupling to multiple G proteins in the absence of any known endogenous agonist or synthetic ligand. Here, we present the structures of ligand-free human GPR21 bound to heterotrimeric miniGs and miniG15 proteins, respectively. We identified an agonist-like motif in extracellular loop 2 (ECL2) that occupies the orthosteric pocket and promotes receptor activation. A side pocket that may be employed as a new ligand binding site was also uncovered. Remarkably, G protein binding is accommodated by a flexible cytoplasmic portion of transmembrane helix 6 (TM6) which adopts little or undetectable outward movement. These findings will enable the design of modulators for GPR21 for understanding its signal transduction and exploring opportunity for deorphanization.
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18
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Papadopoulou AA, Stelzer W, Silber M, Schlosser C, Spitz C, Haug-Kröper M, Straub T, Müller SA, Lichtenthaler SF, Muhle-Goll C, Langosch D, Fluhrer R. Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage. Sci Rep 2022; 12:20987. [PMID: 36470941 PMCID: PMC9722940 DOI: 10.1038/s41598-022-24772-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Signal-Peptide Peptidase Like-3 (SPPL3) is an intramembrane cleaving aspartyl protease that causes secretion of extracellular domains from type-II transmembrane proteins. Numerous Golgi-localized glycosidases and glucosyltransferases have been identified as physiological SPPL3 substrates. By SPPL3 dependent processing, glycan-transferring enzymes are deactivated inside the cell, as their active site-containing domain is cleaved and secreted. Thus, SPPL3 impacts on glycan patterns of many cellular and secreted proteins and can regulate protein glycosylation. However, the characteristics that make a substrate a favourable candidate for SPPL3-dependent cleavage remain unknown. To gain insights into substrate requirements, we investigated the function of a GxxxG motif located in the transmembrane domain of N-acetylglucosaminyltransferase V (GnTV), a well-known SPPL3 substrate. SPPL3-dependent secretion of the substrate's ectodomain was affected by mutations disrupting the GxxxG motif. Using deuterium/hydrogen exchange and NMR spectroscopy, we studied the effect of these mutations on the helix flexibility of the GnTV transmembrane domain and observed that increased flexibility facilitates SPPL3-dependent shedding and vice versa. This study provides first insights into the characteristics of SPPL3 substrates, combining molecular biology, biochemistry, and biophysical techniques and its results will provide the basis for better understanding the characteristics of SPPL3 substrates with implications for the substrates of other intramembrane proteases.
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Affiliation(s)
- Alkmini A. Papadopoulou
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Walter Stelzer
- grid.6936.a0000000123222966Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Mara Silber
- grid.7892.40000 0001 0075 5874Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany ,grid.7892.40000 0001 0075 5874Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Christine Schlosser
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Charlotte Spitz
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Martina Haug-Kröper
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
| | - Tobias Straub
- grid.5252.00000 0004 1936 973XCore Facility Bioinformatics, Biomedical Center, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Stephan A. Müller
- grid.424247.30000 0004 0438 0426DZNE – German Center for Neurodegenerative Diseases, Munich, Germany
| | - Stefan F. Lichtenthaler
- grid.424247.30000 0004 0438 0426DZNE – German Center for Neurodegenerative Diseases, Munich, Germany ,grid.15474.330000 0004 0477 2438Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Claudia Muhle-Goll
- grid.7892.40000 0001 0075 5874Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany ,grid.7892.40000 0001 0075 5874Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Dieter Langosch
- grid.6936.a0000000123222966Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Regina Fluhrer
- grid.7307.30000 0001 2108 9006Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Universitätstrasse 2, 86159 Augsburg, Germany
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19
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Harman JL, Reardon PN, Costello SM, Warren GD, Phillips SR, Connor PJ, Marqusee S, Harms MJ. Evolution avoids a pathological stabilizing interaction in the immune protein S100A9. Proc Natl Acad Sci U S A 2022; 119:e2208029119. [PMID: 36194634 PMCID: PMC9565474 DOI: 10.1073/pnas.2208029119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/07/2022] [Indexed: 01/03/2023] Open
Abstract
Stability constrains evolution. While much is known about constraints on destabilizing mutations, less is known about the constraints on stabilizing mutations. We recently identified a mutation in the innate immune protein S100A9 that provides insight into such constraints. When introduced into human S100A9, M63F simultaneously increases the stability of the protein and disrupts its natural ability to activate Toll-like receptor 4. Using chemical denaturation, we found that M63F stabilizes a calcium-bound conformation of hS100A9. We then used NMR to solve the structure of the mutant protein, revealing that the mutation distorts the hydrophobic binding surface of hS100A9, explaining its deleterious effect on function. Hydrogen-deuterium exchange (HDX) experiments revealed stabilization of the region around M63F in the structure, notably Phe37. In the structure of the M63F mutant, the Phe37 and Phe63 sidechains are in contact, plausibly forming an edge-face π-stack. Mutating Phe37 to Leu abolished the stabilizing effect of M63F as probed by both chemical denaturation and HDX. It also restored the biological activity of S100A9 disrupted by M63F. These findings reveal that Phe63 creates a molecular staple with Phe37 that stabilizes a nonfunctional conformation of the protein, thus disrupting function. Using a bioinformatic analysis, we found that S100A9 proteins from different organisms rarely have Phe at both positions 37 and 63, suggesting that avoiding a pathological stabilizing interaction indeed constrains S100A9 evolution. This work highlights an important evolutionary constraint on stabilizing mutations, namely, that they must avoid inappropriately stabilizing nonfunctional protein conformations.
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Affiliation(s)
- Joseph L Harman
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick N Reardon
- College of Science, NMR Facility, Oregon State University, Corvallis, OR 97331
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720
| | - Gus D Warren
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Sophia R Phillips
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick J Connor
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
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20
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Huang J, Chu X, Luo Y, Wang Y, Zhang Y, Zhang Y, Li H. Insights into Phosphorylation-Induced Protein Allostery and Conformational Dynamics of Glycogen Phosphorylase via Integrative Structural Mass Spectrometry and In Silico Modeling. ACS Chem Biol 2022; 17:1951-1962. [PMID: 35675581 DOI: 10.1021/acschembio.2c00393] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric regulation plays a fundamental role in innumerable biological processes. Understanding its dynamic mechanism and impact at the molecular level is of great importance in disease diagnosis and drug discovery. Glycogen phosphorylase (GP) is a phosphoprotein responding to allosteric regulation and has significant biological importance to glycogen metabolism. Although the atomic structures of GP have been previously solved, the conformational dynamics of GP related to allostery regulation remain largely elusive due to its macromolecular size (∼196 kDa). Here, we integrated native top-down mass spectrometry (nTD-MS), hydrogen-deuterium exchange MS (HDX-MS), protection factor (PF) analysis, molecular dynamics (MD) simulations, and allostery signaling analysis to examine the structural basis and dynamics for the allosteric regulation of GP by phosphorylation. nTD-MS reveals differences in structural stability as well as oligomeric state between the unphosphorylated (GPb) and phosphorylated (GPa) forms. HDX-MS, PF analysis, and MD simulations further pinpoint the structural differences between GPb and GPa involving the binding interfaces (the N-terminal and tower-tower helices), catalytic site, and PLP-binding region. More importantly, it also allowed us to complete the missing link of the long-range communication process from the N-terminal tail to the catalytic site caused by phosphorylation. This integrative MS and in silico-based platform is highly complementary to biophysical approaches and yields valuable insights into protein structures and dynamic regulation.
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Affiliation(s)
- Jing Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China
| | - Xiakun Chu
- Advanced Materials Thrust, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong 511400, China
| | - Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China
| | - Yong Wang
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, College of Life Sciences, Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Haining 314400, China
| | - Ying Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China
| | - Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou Higher Education Mega Center, No. 132 Wai Huan Dong Lu, Guangzhou 510006, China.,Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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21
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Lei Y, Fei P, Song B, Shi W, Luo C, Luo D, Li D, Chen W, Zheng J. A loosened gating mechanism of RIG-I leads to autoimmune disorders. Nucleic Acids Res 2022; 50:5850-5863. [PMID: 35580046 PMCID: PMC9177982 DOI: 10.1093/nar/gkac361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 11/12/2022] Open
Abstract
DDX58 encodes RIG-I, a cytosolic RNA sensor that ensures immune surveillance of nonself RNAs. Individuals with RIG-IE510V and RIG-IQ517H mutations have increased susceptibility to Singleton-Merten syndrome (SMS) defects, resulting in tissue-specific (mild) and classic (severe) phenotypes. The coupling between RNA recognition and conformational changes is central to RIG-I RNA proofreading, but the molecular determinants leading to dissociated disease phenotypes remain unknown. Herein, we employed hydrogen/deuterium exchange mass spectrometry (HDX-MS) and single molecule magnetic tweezers (MT) to precisely examine how subtle conformational changes in the helicase insertion domain (HEL2i) promote impaired ATPase and erroneous RNA proofreading activities. We showed that the mutations cause a loosened latch-gate engagement in apo RIG-I, which in turn gradually dampens its self RNA (Cap2 moiety:m7G cap and N1-2-2′-O-methylation RNA) proofreading ability, leading to increased immunopathy. These results reveal HEL2i as a unique checkpoint directing two specialized functions, i.e. stabilizing the CARD2-HEL2i interface and gating the helicase from incoming self RNAs; thus, these findings add new insights into the role of HEL2i in the control of antiviral innate immunity and autoimmunity diseases.
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Affiliation(s)
- Yixuan Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Panyu Fei
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Bin Song
- The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjia Shi
- The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Cheng Luo
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,The Chemical Biology Center, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, Zhejiang, China
| | - Dahai Luo
- Lee Kong Chian School of Medicine, NTU Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, 636921, Singapore
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-Machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jie Zheng
- The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, Zhejiang, China
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22
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Schweibenz BD, Devarkar SC, Solotchi M, Craig C, Zheng J, Pascal BD, Gokhale S, Xie P, Griffin PR, Patel SS. The intrinsically disordered CARDs-Helicase linker in RIG-I is a molecular gate for RNA proofreading. EMBO J 2022; 41:e109782. [PMID: 35437807 PMCID: PMC9108607 DOI: 10.15252/embj.2021109782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 01/22/2023] Open
Abstract
The innate immune receptor RIG-I provides a first line of defense against viral infections. Viral RNAs are recognized by RIG-I's C-terminal domain (CTD), but the RNA must engage the helicase domain to release the signaling CARD (Caspase Activation and Recruitment Domain) domains from their autoinhibitory CARD2:Hel2i interactions. Because the helicase itself lacks RNA specificity, mechanisms to proofread RNAs entering the helicase domain must exist. Although such mechanisms would be crucial in preventing aberrant immune responses by non-specific RNAs, they remain largely uncharacterized to date. This study reveals a previously unknown proofreading mechanism through which RIG-I ensures that the helicase engages RNAs explicitly recognized by the CTD. A crucial part of this mechanism involves the intrinsically disordered CARDs-Helicase Linker (CHL), which connects the CARDs to the helicase subdomain Hel1. CHL uses its negatively charged regions to antagonize incoming RNAs electrostatically. In addition to this RNA gating function, CHL is essential for stabilization of the CARD2:Hel2i interface. Overall, we uncover that the CHL and CARD2:Hel2i interface work together to establish a tunable gating mechanism that allows CTD-chosen RNAs to bind the helicase domain, while at the same time blocking non-specific RNAs. These findings also indicate that CHL could represent a novel target for RIG-I-based therapeutics.
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Affiliation(s)
- Brandon D Schweibenz
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Graduate Program in Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Swapnil C Devarkar
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Graduate Program in Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Mihai Solotchi
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Cell and Development Biology, Rutgers University, Piscataway, NJ, USA
| | - Candice Craig
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Graduate Program in Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.,Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ, USA
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA.,Department of Integrative Structural and Computational Biology, Jupiter, FL, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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23
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Costello SM, Shoemaker SR, Hobbs HT, Nguyen AW, Hsieh CL, Maynard JA, McLellan JS, Pak JE, Marqusee S. The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes. Nat Struct Mol Biol 2022; 29:229-238. [PMID: 35236990 PMCID: PMC9007726 DOI: 10.1038/s41594-022-00735-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen-deuterium exchange monitored by mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-electron microscopy, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation-an open trimer-contains easily accessible receptor-binding domains. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Shawn M Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Helen T Hobbs
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
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24
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Ahrens CH, Wade JT, Champion MM, Langer JD. A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry. J Bacteriol 2022; 204:e0035321. [PMID: 34748388 PMCID: PMC8765459 DOI: 10.1128/jb.00353-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
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Affiliation(s)
- Christian H. Ahrens
- Agroscope, Method Development and Analytics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Julian D. Langer
- Mass Spectrometry and Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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25
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Healey RD, Saied EM, Cong X, Karsai G, Gabellier L, Saint-Paul J, Del Nero E, Jeannot S, Drapeau M, Fontanel S, Maurel D, Basu S, Leyrat C, Golebiowski J, Bossis G, Bechara C, Hornemann T, Arenz C, Granier S. Discovery and Mechanism of Action of Small Molecule Inhibitors of Ceramidases. Angew Chem Int Ed Engl 2022; 61:e202109967. [PMID: 34668624 DOI: 10.1002/anie.202109967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/21/2021] [Indexed: 01/09/2023]
Abstract
Sphingolipid metabolism is tightly controlled by enzymes to regulate essential processes in human physiology. The central metabolite is ceramide, a pro-apoptotic lipid catabolized by ceramidase enzymes to produce pro-proliferative sphingosine-1-phosphate. Alkaline ceramidases are transmembrane enzymes that recently attracted attention for drug development in fatty liver diseases. However, due to their hydrophobic nature, no specific small molecule inhibitors have been reported. We present the discovery and mechanism of action of the first drug-like inhibitors of alkaline ceramidase 3 (ACER3). In particular, we chemically engineered novel fluorescent ceramide substrates enabling screening of large compound libraries and characterized enzyme:inhibitor interactions using mass spectrometry and MD simulations. In addition to revealing a new paradigm for inhibition of lipid metabolising enzymes with non-lipidic small molecules, our data lay the ground for targeting ACER3 in drug discovery efforts.
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Affiliation(s)
- Robert D Healey
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Essa M Saied
- Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
- Chemistry Department, Faculty of Science, Suez Canal University, 41522, Ismailia, Egypt
| | - Xiaojing Cong
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Gergely Karsai
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | | | - Julie Saint-Paul
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Elise Del Nero
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Sylvain Jeannot
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Marion Drapeau
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Simon Fontanel
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Damien Maurel
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Shibom Basu
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, France
| | - Cedric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, South Korea
| | | | - Cherine Bechara
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
- Institut Universitaire de France (IUF), Paris, France
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | - Christoph Arenz
- Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Sebastien Granier
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
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26
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Ounoughene Y, Fourgous E, Boublik Y, Saland E, Guiraud N, Recher C, Urbach S, Fort P, Sarry JE, Fesquet D, Roche S. SHED-Dependent Oncogenic Signaling of the PEAK3 Pseudo-Kinase. Cancers (Basel) 2021; 13:cancers13246344. [PMID: 34944965 PMCID: PMC8699254 DOI: 10.3390/cancers13246344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023] Open
Abstract
Simple Summary The human kinome is composed of about 50 pseudo-kinases with unclear function, because they are predicted to be catalytically inactive; however, they are shown to play an important role in cancer, similar to active kinases. Understanding how these pseudo-kinases promote tumor formation despite their catalytic inactivity is a great challenge, which may lead to innovative anti-cancer therapies. The PEAK1 and 2 pseudo-kinases have emerged as important components of the protein tyrosine kinase pathway implicated in cancer progression. They can signal using a scaffolding mechanism via a conserved split helical dimerization (SHED) module. In this study, we uncovered a similar SHED-dependent oncogenic activity for PEAK3, a recently discovered new member of this family. We also show that this new signaling mechanism may be implicated in acute myeloid leukemia. Abstract The PEAK1 and Pragmin/PEAK2 pseudo-kinases have emerged as important components of the protein tyrosine kinase pathway implicated in cancer progression. They can signal using a scaffolding mechanism that involves a conserved split helical dimerization (SHED) module. We recently identified PEAK3 as a novel member of this family based on structural homology; however, its signaling mechanism remains unclear. In this study, we found that, although it can self-associate, PEAK3 shows higher evolutionary divergence than PEAK1/2. Moreover, the PEAK3 protein is strongly expressed in human hematopoietic cells and is upregulated in acute myeloid leukemia. Functionally, PEAK3 overexpression in U2OS sarcoma cells enhanced their growth and migratory properties, while its silencing in THP1 leukemic cells reduced these effects. Importantly, an intact SHED module was required for these PEAK3 oncogenic activities. Mechanistically, through a phosphokinase survey, we identified PEAK3 as a novel inducer of AKT signaling, independent of growth-factor stimulation. Then, proteomic analyses revealed that PEAK3 interacts with the signaling proteins GRB2 and ASAP1/2 and the protein kinase PYK2, and that these interactions require the SHED domain. Moreover, PEAK3 activated PYK2, which promoted PEAK3 tyrosine phosphorylation, its association with GRB2 and ASAP1, and AKT signaling. Thus, the PEAK1-3 pseudo-kinases may use a conserved SHED-dependent mechanism to activate specific signaling proteins to promote oncogenesis.
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Affiliation(s)
- Youcef Ounoughene
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Elise Fourgous
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Yvan Boublik
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Estelle Saland
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Nathan Guiraud
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Christian Recher
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Serge Urbach
- IGF, CNRS, INSERM, University Montpellier, F-34000 Montpellier, France;
| | - Philippe Fort
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
| | - Jean-Emmanuel Sarry
- CRCT, INSERM, CNRS, University of Toulouse, Equipe Labellisée Ligue Contre le Cancer, F-31037 Toulouse, France; (E.S.); (N.G.); (C.R.); (J.-E.S.)
| | - Didier Fesquet
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
- Correspondence: (D.F.); (S.R.)
| | - Serge Roche
- CRBM, University Montpellier, CNRS, Equipe Labellisée Ligue Contre le Cancer, F-34000 Montpellier, France; (Y.O.); (E.F.); (Y.B.); (P.F.)
- Correspondence: (D.F.); (S.R.)
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27
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Salmas RE, Borysik AJ. Exploiting the Propagation of Constrained Variables for Enhanced HDX-MS Data Optimization. Anal Chem 2021; 93:16417-16424. [PMID: 34860510 DOI: 10.1021/acs.analchem.1c03082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nonlinear programming has found useful applications in protein biophysics to help understand the microscopic exchange kinetics of data obtained using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finding a microscopic kinetic solution for HDX-MS data provides a window into local protein stability and energetics allowing them to be quantified and understood. Optimization of HDX-MS data is a significant challenge, however, due to the requirement to solve a large number of variables simultaneously with exceptionally large variable bounds. Modeled rates are frequently uncertain with an explicate dependency on the initial guess values. In order to enhance the search for a minimum solution in HDX-MS optimization, the ability of selected constrained variables to propagate throughout the data is considered. We reveal that locally bound constrained optimization induces a global effect on all variables. The global response to local constraints is large and surprisingly long-range, but the outcome is unpredictable, unexpectedly decreasing the overall accuracy of certain data sets depending on the stringency of the constraints. Utilizing previously described in-house validation criteria based on covariance matrices, a method is described that is able to accurately determine whether constraints benefit or impair the optimization of HDX-MS data. From this, we establish a new two-stage method for our online optimizer HDXmodeller that can effectively leverage locally bound variables to enhance HDX-MS data modeling.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Department of Chemistry, Britannia House, King's College London, London SE1 1DB, United Kingdom
| | - Antoni James Borysik
- Department of Chemistry, Britannia House, King's College London, London SE1 1DB, United Kingdom
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28
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Structural dynamics in the evolution of a bilobed protein scaffold. Proc Natl Acad Sci U S A 2021; 118:2026165118. [PMID: 34845009 PMCID: PMC8694067 DOI: 10.1073/pnas.2026165118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Proteins conduct numerous complex biological functions by use of tailored structural dynamics. The molecular details of how these emerged from ancestral peptides remains mysterious. How does nature utilize the same repertoire of folds to diversify function? To shed light on this, we analyzed bilobed proteins with a common structural core, which is spread throughout the tree of life and is involved in diverse biological functions such as transcription, enzymatic catalysis, membrane transport, and signaling. We show here that the structural dynamics of the structural core differentiate predominantly via terminal additions during a long-period evolution. This diversifies substrate specificity and, ultimately, biological function. Novel biophysical tools allow the structural dynamics of proteins and the regulation of such dynamics by binding partners to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remain poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the periplasmic-binding protein–like II domain family, have undergone divergent evolution, leading to adaptation of their structural dynamics. We performed a structural analysis on ∼600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Förster resonance energy transfer and Hydrogen–Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enable distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extracytoplasmic transport-related proteins. Structural embellishments of the core created interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately altered substrate specificity. Our findings reveal an as-yet-unrecognized mechanism for the emergence of functional promiscuity during long periods of evolution and are applicable to a large number of domain architectures.
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29
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Gutkowska M, Kaus‐Drobek M, Hoffman‐Sommer M, Małgorzata Pamuła M, Daria Leja A, Perycz M, Lichocka M, Witek A, Wojtas M, Dadlez M, Swiezewska E, Surmacz L. Impact of C-terminal truncations in the Arabidopsis Rab escort protein (REP) on REP-Rab interaction and plant fertility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1400-1421. [PMID: 34592024 PMCID: PMC9293207 DOI: 10.1111/tpj.15519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Lipid anchors are common post-translational modifications for proteins engaged in signaling and vesicular transport in eukaryotic cells. Rab proteins are geranylgeranylated at their C-termini, a modification which is important for their stable binding to lipid bilayers. The Rab escort protein (REP) is an accessory protein of the Rab geranylgeranyl transferase (RGT) complex and it is obligatory for Rab prenylation. While REP-Rab interactions have been studied by biochemical, structural, and genetic methods in animals and yeast, data on the plant RGT complex are still limited. Here we use hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the structural basis of plant REP-Rab binding. The obtained results show that the interaction of REP with Rabs is highly dynamic and involves specific structural changes in both partners. In some cases the Rab and REP regions involved in the interaction are molecule-specific, and in other cases they are common for a subset of Rabs. In particular, the C-terminus of REP is not involved in binding of unprenylated Rab proteins in plants, in contrast to mammalian REP. In line with this, a C-terminal REP truncation does not have pronounced phenotypic effects in planta. On the contrary, a complete lack of functional REP leads to male sterility in Arabidopsis: pollen grains develop in the anthers, but they do not germinate efficiently and hence are unable to transmit the mutated allele. The presented data show that the mechanism of action of REP in the process of Rab geranylgeranylation is different in plants than in animals or yeast.
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Affiliation(s)
- Małgorzata Gutkowska
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Magdalena Kaus‐Drobek
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
- Mossakowski Medical Research CentrePolish Academy of Sciencesul. Pawinskiego 5, 02‐106WarsawPoland
| | - Marta Hoffman‐Sommer
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | | | - Anna Daria Leja
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Małgorzata Perycz
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
- Institute of Computer SciencePolish Academy of Sciencesul. Jana Kazimierza 501‐248WarsawPoland
| | - Małgorzata Lichocka
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Agnieszka Witek
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Magdalena Wojtas
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Michał Dadlez
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Ewa Swiezewska
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Liliana Surmacz
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
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30
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Healey RD, Saied EM, Cong X, Karsai G, Gabellier L, Saint‐Paul J, Del Nero E, Jeannot S, Drapeau M, Fontanel S, Maurel D, Basu S, Leyrat C, Golebiowski J, Bossis G, Bechara C, Hornemann T, Arenz C, Granier S. Discovery and Mechanism of Action of Small Molecule Inhibitors of Ceramidases**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Robert D. Healey
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Essa M. Saied
- Institute for chemistry Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 12489 Berlin Germany
- Chemistry Department Faculty of Science Suez Canal University 41522 Ismailia Egypt
| | - Xiaojing Cong
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Gergely Karsai
- Institute of Clinical Chemistry University Hospital Zurich University of Zurich Zurich 8091 Switzerland
| | | | - Julie Saint‐Paul
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Elise Del Nero
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Sylvain Jeannot
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Marion Drapeau
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Simon Fontanel
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Damien Maurel
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Shibom Basu
- EMBL Grenoble 71 Avenue des Martyrs, CS 90181 38042 Grenoble France
| | - Cedric Leyrat
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Jérôme Golebiowski
- Université Côte d'Azur CNRS Institut de Chimie de Nice UMR7272 Nice 06108 France
- Department of Brain and Cognitive Sciences Daegu Gyeongbuk Institute of Science and Technology Daegu 711-873 South Korea
| | | | - Cherine Bechara
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
- Institut Universitaire de France (IUF) Paris France
| | - Thorsten Hornemann
- Institute of Clinical Chemistry University Hospital Zurich University of Zurich Zurich 8091 Switzerland
| | - Christoph Arenz
- Institute for chemistry Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 12489 Berlin Germany
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31
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Zhdanova PV, Ishchenko AA, Chernonosov AA, Zharkov DO, Koval VV. Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry. J Mol Biol 2021; 434:167334. [PMID: 34757057 DOI: 10.1016/j.jmb.2021.167334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/31/2022]
Abstract
Base excision DNA repair (BER) is necessary for removal of damaged nucleobases from the genome and their replacement with normal nucleobases. BER is initiated by DNA glycosylases, the enzymes that cleave the N-glycosidic bonds of damaged deoxynucleotides. Human endonuclease VIII-like protein 2 (hNEIL2), belonging to the helix-two-turn-helix structural superfamily of DNA glycosylases, is an enzyme uniquely specific for oxidized pyrimidines in non-canonical DNA substrates such as bubbles and loops. The structure of hNEIL2 has not been solved; its closest homologs with known structures are NEIL2 from opossum and from giant mimivirus. Here we analyze the conformational dynamics of free hNEIL2 using a combination of hydrogen/deuterium exchange mass spectrometry, homology modeling and molecular dynamics simulations. We show that a prominent feature of vertebrate NEIL2 - a large insert in its N-terminal domain absent from other DNA glycosylases - is unstructured in solution. It was suggested that helix-two-turn-helix DNA glycosylases undergo open-close transition upon DNA binding, with the large movement of their N- and C-terminal domains, but the open conformation has been elusive to capture. Our data point to the open conformation as favorable for free hNEIL2 in solution. Overall, our results are consistent with the view of hNEIL2 as a conformationally flexible protein, which may be due to its participation in the repair of non-canonical DNA structures and/or to the involvement in functional and regulatory protein-protein interactions.
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Affiliation(s)
- Polina V Zhdanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia
| | - Alexander A Ishchenko
- Groupe "Réparation de lADN", Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif F-94805, France
| | | | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia.
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32
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Scrosati PM, Yin V, Konermann L. Hydrogen/Deuterium Exchange Measurements May Provide an Incomplete View of Protein Dynamics: a Case Study on Cytochrome c. Anal Chem 2021; 93:14121-14129. [PMID: 34644496 DOI: 10.1021/acs.analchem.1c02471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many aspects of protein function rely on conformational fluctuations. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) provides a window into these dynamics. Despite the widespread use of HDX-MS, it remains unclear whether this technique provides a truly comprehensive view of protein dynamics. HDX is mediated by H-bond-opening/closing events, implying that HDX methods provide an H-bond-centric view. This raises the question if there could be fluctuations that leave the H-bond network unaffected, thereby rendering them undetectable by HDX-MS. We explore this issue in experiments on cytochrome c (cyt c). Compared to the Fe(II) protein, Fe(III) cyt c shows enhanced deuteration on both the distal and proximal sides of the heme. Previous studies have attributed the enhanced dynamics of Fe(III) cyt c to the facile and reversible rupture of the distal M80-Fe(III) bond. Using molecular dynamics (MD) simulations, we conducted a detailed analysis of various cyt c conformers. Our MD data confirm that rupture of the M80-Fe(III) contact triggers major reorientation of the distal Ω loop. Surprisingly, this event takes place with only miniscule H-bonding alterations. In other words, the distal loop dynamics are almost "HDX-silent". Moreover, distal loop movements cannot account for enhanced dynamics on the opposite (proximal) side of the heme. Instead, enhanced deuteration of Fe(III) cyt c is attributed to sparsely populated conformers where both the distal (M80) and proximal (H18) coordination bonds have been ruptured, along with opening of numerous H-bonds on both sides of the heme. We conclude that there can be major structural fluctuations that are only weakly coupled to changes in H-bonding, making them virtually impossible to track by HDX-MS. In such cases, HDX-MS may provide an incomplete view of protein dynamics.
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Affiliation(s)
- Pablo M Scrosati
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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33
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Molecular insights into mechanisms of GPCR hijacking by Staphylococcus aureus. Proc Natl Acad Sci U S A 2021; 118:2108856118. [PMID: 34663701 DOI: 10.1073/pnas.2108856118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 11/18/2022] Open
Abstract
Atypical chemokine receptor 1 (ACKR1) is a G protein-coupled receptor (GPCR) targeted by Staphylococcus aureus bicomponent pore-forming leukotoxins to promote bacterial growth and immune evasion. Here, we have developed an integrative molecular pharmacology and structural biology approach in order to characterize the effect of leukotoxins HlgA and HlgB on ACKR1 structure and function. Interestingly, using cell-based assays and native mass spectrometry, we found that both components HlgA and HlgB compete with endogenous chemokines through a direct binding with the extracellular domain of ACKR1. Unexpectedly, hydrogen/deuterium exchange mass spectrometry analysis revealed that toxin binding allosterically modulates the intracellular G protein-binding domain of the receptor, resulting in dissociation and/or changes in the architecture of ACKR1-Gαi1 protein complexes observed in living cells. Altogether, our study brings important molecular insights into the initial steps of leukotoxins targeting a host GPCR.
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34
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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35
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Fenton-Chemistry-Based Oxidative Modification of Proteins Reflects Their Conformation. Int J Mol Sci 2021; 22:ijms22189927. [PMID: 34576105 PMCID: PMC8469487 DOI: 10.3390/ijms22189927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 11/25/2022] Open
Abstract
In order to understand protein structure to a sufficient extent for, e.g., drug discovery, no single technique can provide satisfactory information on both the lowest-energy conformation and on dynamic changes over time (the ‘four-dimensional’ protein structure). Instead, a combination of complementary techniques is required. Mass spectrometry methods have shown promise in addressing protein dynamics, but often rely on the use of high-end commercial or custom instruments. Here, we apply well-established chemistry to conformation-sensitive oxidative protein labelling on a timescale of a few seconds, followed by analysis through a routine protein analysis workflow. For a set of model proteins, we show that site selectivity of labelling can indeed be rationalised in terms of known structural information, and that conformational changes induced by ligand binding are reflected in the modification pattern. In addition to conventional bottom-up analysis, further insights are obtained from intact mass measurement and native mass spectrometry. We believe that this method will provide a valuable and robust addition to the ‘toolbox’ of mass spectrometry researchers studying higher-order protein structure.
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Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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37
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Stocks BB, Bird GH, Walensky LD, Melanson JE. Characterizing Native and Hydrocarbon-Stapled Enfuvirtide Conformations with Ion Mobility Mass Spectrometry and Hydrogen-Deuterium Exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:753-761. [PMID: 33534566 DOI: 10.1021/jasms.0c00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The number of approved peptide therapeutics, as well as those in development, has been increasing in recent years. Frequently, the biological activity of such peptides is elicited through the adoption of secondary structural elements upon interaction with their cellular target. However, many therapeutic peptides are unstructured in solution and accordingly exhibit a poor bioavailability due to rapid proteolysis in vivo. To combat this degradation, numerous naturally occurring peptides with therapeutic properties contain stabilizing features, such as N-to-C cyclization or disulfide bonds. Recently, hydrocarbon stapling via non-native amino acid substitution followed by ring-closing metathesis has been shown to induce a dramatic stabilization of α-helical peptides. Identifying the ideal staple location along the peptide backbone is a critical developmental step, and methods to streamline this optimization are needed. Mass spectrometry-based methods such as ion mobility (IM) and hydrogen-deuterium exchange (HDX) can detect multiple discrete peptide conformations, a significant advantage over bulk spectroscopic techniques. In this study we use IM-MS and HDX-MS to demonstrate that the native 36-residue enfuvirtide peptide is highly dynamic in solution and the conformational ensemble populated by stabilized constructs depends heavily on the staple location. Further, our measurements yielded results that correlate well with the average α-helical content measured by circular dichroism. The MS-based approaches described herein represent sensitive and potentially high-throughput methods for characterizing and identifying optimally stapled peptides.
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Affiliation(s)
- Bradley B Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Gregory H Bird
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Loren D Walensky
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Jeremy E Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
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38
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HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation. Commun Biol 2021; 4:199. [PMID: 33589746 PMCID: PMC7884430 DOI: 10.1038/s42003-021-01709-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
The extent to which proteins are protected from hydrogen deuterium exchange (HDX) provides valuable insight into their folding, dynamics and interactions. Characterised by mass spectrometry (MS), HDX benefits from negligible mass restrictions and exceptional throughput and sensitivity but at the expense of resolution. Exchange mechanisms which naturally transpire for individual residues cannot be accurately located or understood because amino acids are characterised in differently sized groups depending on the extent of proteolytic digestion. Here we report HDXmodeller, the world's first online webserver for high-resolution HDX-MS. HDXmodeller accepts low-resolution HDX-MS input data and returns high-resolution exchange rates quantified for each residue. Crucially, HDXmodeller also returns a set of unique statistics that can correctly validate exchange rate models to an accuracy of 99%. Remarkably, these statistics are derived without any prior knowledge of the individual exchange rates and facilitate unparallel user confidence and the capacity to evaluate different data optimisation strategies.
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39
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Hevler JF, Lukassen MV, Cabrera-Orefice A, Arnold S, Pronker MF, Franc V, Heck AJR. Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry. EMBO J 2021; 40:e106174. [PMID: 33459420 PMCID: PMC7883291 DOI: 10.15252/embj.2020106174] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Cross-linking mass spectrometry has developed into an important method to study protein structures and interactions. The in-solution cross-linking workflows involve time and sample consuming steps and do not provide sensible solutions for differentiating cross-links obtained from co-occurring protein oligomers, complexes, or conformers. Here we developed a cross-linking workflow combining blue native PAGE with in-gel cross-linking mass spectrometry (IGX-MS). This workflow circumvents steps, such as buffer exchange and cross-linker concentration optimization. Additionally, IGX-MS enables the parallel analysis of co-occurring protein complexes using only small amounts of sample. Another benefit of IGX-MS, demonstrated by experiments on GroEL and purified bovine heart mitochondria, is the substantial reduction of undesired over-length cross-links compared to in-solution cross-linking. We next used IGX-MS to investigate the complement components C5, C6, and their hetero-dimeric C5b6 complex. The obtained cross-links were used to generate a refined structural model of the complement component C6, resembling C6 in its inactivated state. This finding shows that IGX-MS can provide new insights into the initial stages of the terminal complement pathway.
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Affiliation(s)
- Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Marie V Lukassen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, Utrecht, The Netherlands
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40
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Karamitros CS, Murray K, Sugiyama Y, Kumada Y, Johnson KA, Georgiou G, D'Arcy S, Stone EM. Conformational Dynamics Contribute to Substrate Selectivity and Catalysis in Human Kynureninase. ACS Chem Biol 2020; 15:3159-3166. [PMID: 33275413 PMCID: PMC11104311 DOI: 10.1021/acschembio.0c00676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Kynureninases (KYNases) are enzymes that play a key role in tryptophan catabolism through the degradation of intermediate kynurenine and 3'-hydroxy-kynurenine metabolites (KYN and OH-KYN, respectively). Bacterial KYNases exhibit high catalytic efficiency toward KYN and moderate activity toward OH-KYN, whereas animal KYNases are highly selective for OH-KYN, exhibiting only minimal activity toward the smaller KYN substrate. These differences reflect divergent pathways for KYN and OH-KYN utilization in the respective kingdoms. We examined the Homo sapiens and Pseudomonas fluorescens KYNases (HsKYNase and PfKYNase respectively) using pre-steady-state and hydrogen-deuterium exchange mass spectrometry (HDX-MS) methodologies. We discovered that the activity of HsKYNase critically depends on formation of hydrogen bonds with the hydroxyl group of OH-KYN to stabilize the entire active site and allow productive substrate turnover. With the preferred OH-KYN substrate, stabilization is observed at the substrate-binding site and the region surrounding the PLP cofactor. With the nonpreferred KYN substrate, less stabilization occurs, revealing a direct correlation with activity. This correlation holds true for PfKYNases; however there is only a modest stabilization at the substrate-binding site, suggesting that substrate discrimination is simply achieved by steric hindrance. We speculate that eukaryotic KYNases use dynamic mobility as a mechanism of substrate specificity to commit OH-KYN to nicotinamide synthesis and avoid futile hydrolysis of KYN. These findings have important ramifications for the engineering of HsKynase with high KYN activity as required for clinical applications in cancer immunotherapy. Our study shows how homologous enzymes with conserved active sites can use dynamics to discriminate between two highly similar substrates.
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Affiliation(s)
- Christos S Karamitros
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle Murray
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Yusuke Sugiyama
- Department of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Yoichi Kumada
- Department of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas 78712, United States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Everett M Stone
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Oncology, University of Texas Dell Medical School, LiveSTRONG Cancer Institutes, Austin, Texas 78712, United States
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41
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Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020; 93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Botzanowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Florian Georgescauld
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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42
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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43
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Zheng J, Strutzenberg TS, Reich A, Dharmarajan V, Pascal BD, Crynen GC, Novick SJ, Garcia-Ordonez RD, Griffin PR. Comparative Analysis of Cleavage Specificities of Immobilized Porcine Pepsin and Nepenthesin II under Hydrogen/Deuterium Exchange Conditions. Anal Chem 2020; 92:11018-11028. [PMID: 32658454 DOI: 10.1021/acs.analchem.9b05694] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen/Deuterium Exchange (HDX) coupled with Mass Spectrometry (HDX-MS) is a sensitive and robust method to probe protein conformational changes and protein-ligand interactions. HDX-MS relies on successful proteolytic digestion of target proteins under acidic conditions to localize perturbations in exchange behavior to protein structure. The ability of the protease to produce small peptides and overlapping fragments and provide sufficient coverage of the protein sequence is essential for localizing regions of interest. While the acid protease pepsin has been the enzyme of choice for HDX-MS studies, recently, it was shown that aspartic proteases from carnivorous pitcher plants of the genus Nepenthes are active under low-pH conditions and cleave at basic residues that are "forbidden" in peptic digests. In this report, we describe the utility of one of these enzymes, Nepenthesin II (NepII), in a HDX-MS workflow. A systematic and statistical analysis of data from 11 proteins (6391 amino acid residues) digested with immobilized porcine pepsin or NepII under conditions compatible with HDX-MS was performed to examine protease cleavage specificities. The cleavage of pepsin was most influenced by the amino acid residue at position P1. Phe, Leu, and Met are favored residues, each with a cleavage probability of greater than 40%. His, Lys, Arg, or Pro residues prohibit cleavage when found at the P1 position. In contrast, NepII offers advantageous cleavage to all basic residues and produces shortened peptides that could improve the spatial resolution in HDX-MS studies.
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Affiliation(s)
- Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Timothy S Strutzenberg
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Adrian Reich
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | | | - Bruce D Pascal
- Omics Informatics LLC, Honolulu, Hawaii 96813, United States
| | - Gogce C Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, United States
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44
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Engen JR, Komives EA. Complementarity of Hydrogen/Deuterium Exchange Mass Spectrometry and Cryo-Electron Microscopy. Trends Biochem Sci 2020; 45:906-918. [PMID: 32487353 DOI: 10.1016/j.tibs.2020.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/23/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022]
Abstract
Methodological improvements in both single particle cryo-electron microscopy (cryo-EM) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) mean that the two methods are being more frequently used together to tackle complex problems in structural biology. There are many benefits to this combination, including for the analysis of low-resolution density, for structural validation, in the analysis of individual proteins versus the same proteins in large complexes, studies of allostery, protein quality control during cryo-EM construct optimization, and in the study of protein movements/dynamics during function. As will be highlighted in this review, through careful considerations of potential sample and conformational heterogeneity, many joint studies have recently been demonstrated, and many future studies using this combination are anticipated.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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45
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Chance MR, Farquhar ER, Yang S, Lodowski DT, Kiselar J. Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution. J Mol Biol 2020; 432:2973-2984. [PMID: 32088185 PMCID: PMC7245549 DOI: 10.1016/j.jmb.2020.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/25/2022]
Abstract
Structural biology is entering an exciting time where many new high-resolution structures of large complexes and membrane proteins are determined regularly. These advances have been driven by over fifteen years of technology advancements, first in macromolecular crystallography, and recently in Cryo-electron microscopy. These structures are allowing detailed questions about functional mechanisms of the structures, and the biology enabled by these structures, to be addressed for the first time. At the same time, mass spectrometry technologies for protein structure analysis, "footprinting" studies, have improved their sensitivity and resolution dramatically and can provide detailed sub-peptide and residue level information for validating structures and interactions or understanding the dynamics of structures in the context of ligand binding or assembly. In this perspective, we review the use of protein footprinting to extend our understanding of macromolecular systems, particularly for systems challenging for analysis by other techniques, such as intrinsically disordered proteins, amyloidogenic proteins, and other proteins/complexes so far recalcitrant to existing methods. We also illustrate how the availability of high-resolution structural information can be a foundation for a suite of hybrid approaches to divine structure-function relationships beyond what individual techniques can deliver.
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Affiliation(s)
- Mark R Chance
- Case Center for Proteomics and Bioinformatics, USA; Case Center for Synchrotron Biosciences, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
| | | | - Sichun Yang
- Case Center for Proteomics and Bioinformatics, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - David T Lodowski
- Case Center for Proteomics and Bioinformatics, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Janna Kiselar
- Case Center for Proteomics and Bioinformatics, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
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46
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Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020; 432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
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47
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Hansen K, Politis A. Improving Peptide Fragmentation for Hydrogen-Deuterium Exchange Mass Spectrometry Using a Time-Dependent Collision Energy Calculator. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:996-999. [PMID: 32141743 DOI: 10.1021/jasms.9b00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is becoming a popular technique for interrogating biological systems. In recent years, advancements have been made to increase peptide coverage for proteins that resist digestion such as antibodies and membrane proteins. These methods commonly include using alternative digestion enzymes or longer chromatographic gradients, which may be expensive or time-consuming to implement. Here, we recommend an efficient proteomics-based approach to increase peptide confidence and coverage. A major filtering parameter for peptides in HDX is the number of product ions detected; this is a result of the collision energy (CE) applied within the MS. A traditional linear ramp achieves optimal CE for only short periods of time. More product ions will be created and detected if optimal CE can be achieved for a longer period of time. As a result, the coverage, redundancy, and data confidence are all increased. We achieved this by implementing a mobility-dependent CE look up table (LUT) which increases the CE as a function of mobility. We developed a program to calculate the optimal CE for a set of peptides and MS settings based on initial reference samples. We demonstrated the utility of the CE LUT on three protein samples including the soluble phosphorylase B, IgG2, and the membrane-stabilized AcrB. We showed that applying a CE LUT provided 8.5-50% more peptides compared to a linear CE ramp. The results demonstrate that a time-dependent CE LUT is a quick and inexpensive method to increase data confidence and peptide abundance for HDX-MS experiments.
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Affiliation(s)
- Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
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48
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Steigenberger B, Albanese P, Heck AJR, Scheltema RA. To Cleave or Not To Cleave in XL-MS? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:196-206. [PMID: 32031400 DOI: 10.1021/jasms.9b00085] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is an efficient technique for uncovering structural features and interactions of the in-solution state of the proteins under investigation. Distance constraints obtained by this technique are highly complementary to classical structural biology approaches like X-ray crystallography and cryo-EM and have successfully been leveraged to shed light on protein structures of increasing size and complexity. To accomplish this, small reagents are used that typically incorporate two amine reactive moieties connected by a spacer arm and that can be applied in solution to protein structures of any size. Over the years, many reagents initially developed for different applications were adopted, and others were specifically developed for XL-MS. This has resulted in a vast array of options, making it difficult to make the right choice for specific experiments. Here, we delve into the previous decade of published XL-MS literature to uncover which workflows have been predominantly applied. We focus on application papers as these represent proof that biologically valid results can be extracted. This ignores some more recent approaches that did not have sufficient time to become more widely applied, for which we supply a separate discussion. From our selection, we extract information on the types of samples, cross-linking reagent, prefractionation, instruments, and data analysis, to highlight widely used workflows. All of the results are summarized in an easy-to-use flow chart defined by selection points resulting from our analysis. Although potentially biased by our own experiences, we expect this overview to be useful for novices stepping into this rapidly expanding field.
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Affiliation(s)
- B Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - P Albanese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - A J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - R A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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