1
|
Sokratous K, Cooper-Shepherd DA, Ujma J, Qu F, Giles K, Ben-Younis A, Hensen M, Langridge JI, Gault J, Jazayeri A, Liko I, Hopper JTS. Enhanced Declustering Enables Native Top-Down Analysis of Membrane Protein Complexes using Ion-Mobility Time-Aligned Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1891-1901. [PMID: 39007842 DOI: 10.1021/jasms.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Native mass spectrometry (MS) is proving to be a disruptive technique for studying the interactions of proteins, necessary for understanding the functional roles of these biomolecules. Recent research is expanding the application of native MS towards membrane proteins directly from isolated membrane preparations or from purified detergent micelles. The former results in complex spectra comprising several heterogeneous protein complexes; the latter enables therapeutic protein targets to be screened against multiplexed preparations of compound libraries. In both cases, the resulting spectra are increasingly complex to assign/interpret, and the key to these new directions of native MS research is the ability to perform native top-down analysis, which allows unambiguous peak assignment. To achieve this, detergent removal is necessary prior to MS analyzers, which allow selection of specific m/z values, representing the parent ion for downstream activation. Here, we describe a novel, enhanced declustering (ED) device installed into the first pumping region of a cyclic IMS-enabled mass spectrometry platform. The device enables declustering of ions prior to the quadrupole by imparting collisional activation through an oscillating electric field applied between two parallel plates. The positioning of the device enables liberation of membrane protein ions from detergent micelles. Quadrupole selection can now be utilized to isolate protein-ligand complexes, and downstream collision cells enable the dissociation and identification of binding partners. We demonstrate that ion mobility (IM) significantly aids in the assignment of top-down spectra, aligning fragments to their corresponding parent ions by means of IM drift time. Using this approach, we were able to confidently assign and identify a novel hit compound against PfMATE, obtained from multiplexed ligand libraries.
Collapse
Affiliation(s)
- Kleitos Sokratous
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | | | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Feng Qu
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Aisha Ben-Younis
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Mario Hensen
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Joseph Gault
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Ali Jazayeri
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Idlir Liko
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Jonathan T S Hopper
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| |
Collapse
|
2
|
Masson MAC, Karpfenstein R, de Oliveira-Silva D, Teuler JM, Archirel P, Maître P, Correra TC. Evaluation of Ca2+ Binding Sites in Tacrolimus by Infrared Multiple Photon Dissociation Spectroscopy. J Phys Chem B 2018; 122:9860-9868. [DOI: 10.1021/acs.jpcb.8b06523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Maria Angélica C. Masson
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, São Paulo, Brazil
| | - Renan Karpfenstein
- Department of Chemistry, Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, St. Prof. Arthur Riedel 275, 09972-270 Diadema, São Paulo, Brazil
| | - Diogo de Oliveira-Silva
- Department of Chemistry, Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, St. Prof. Arthur Riedel 275, 09972-270 Diadema, São Paulo, Brazil
| | - Jean-Marie Teuler
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Pierre Archirel
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Philippe Maître
- Laboratoire de Chimie Physique, URM8000, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Thiago C. Correra
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, São Paulo, Brazil
| |
Collapse
|
3
|
Eschweiler JD, Kerr R, Rabuck-Gibbons J, Ruotolo BT. Sizing Up Protein-Ligand Complexes: The Rise of Structural Mass Spectrometry Approaches in the Pharmaceutical Sciences. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:25-44. [PMID: 28301749 DOI: 10.1146/annurev-anchem-061516-045414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies.
Collapse
Affiliation(s)
| | - Richard Kerr
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| | | | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| |
Collapse
|
4
|
Cesa LC, Mapp AK, Gestwicki JE. Direct and Propagated Effects of Small Molecules on Protein-Protein Interaction Networks. Front Bioeng Biotechnol 2015; 3:119. [PMID: 26380257 PMCID: PMC4547496 DOI: 10.3389/fbioe.2015.00119] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/05/2015] [Indexed: 12/15/2022] Open
Abstract
Networks of protein–protein interactions (PPIs) link all aspects of cellular biology. Dysfunction in the assembly or dynamics of PPI networks is a hallmark of human disease, and as such, there is growing interest in the discovery of small molecules that either promote or inhibit PPIs. PPIs were once considered undruggable because of their relatively large buried surface areas and difficult topologies. Despite these challenges, recent advances in chemical screening methodologies, combined with improvements in structural and computational biology have made some of these targets more tractable. In this review, we highlight developments that have opened the door to potent chemical modulators. We focus on how allostery is being used to produce surprisingly robust changes in PPIs, even for the most challenging targets. We also discuss how interfering with one PPI can propagate changes through the broader web of interactions. Through this analysis, it is becoming clear that a combination of direct and propagated effects on PPI networks is ultimately how small molecules re-shape biology.
Collapse
Affiliation(s)
- Laura C Cesa
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA
| | - Anna K Mapp
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Chemistry, University of Michigan , Ann Arbor, MI , USA
| | - Jason E Gestwicki
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, University of California San Francisco , San Francisco, CA , USA
| |
Collapse
|
5
|
Maurer MM, Donohoe GC, Valentine SJ. Advances in ion mobility-mass spectrometry instrumentation and techniques for characterizing structural heterogeneity. Analyst 2015; 140:6782-98. [PMID: 26114255 DOI: 10.1039/c5an00922g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Enabling IM-MS instrumentation and techniques for characterizing sample structural heterogeneity have developed rapidly over the last five years.
Collapse
Affiliation(s)
- Megan M. Maurer
- C. Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | - Gregory C. Donohoe
- C. Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | | |
Collapse
|
6
|
Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
| | | |
Collapse
|
7
|
Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
8
|
Li L, Li C, Alexov E. On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014; 13. [PMID: 25018579 DOI: 10.1142/s0219633614400021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute-water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.
Collapse
Affiliation(s)
- Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| | - Chuan Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
9
|
Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein. Proc Natl Acad Sci U S A 2013; 110:E2782-91. [PMID: 23824290 DOI: 10.1073/pnas.1308846110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
HBc, the capsid-forming "core protein" of human hepatitis B virus (HBV), is a multidomain, α-helical homodimer that aggressively forms human HBV capsids. Structural plasticity has been proposed to be important to the myriad functions HBc mediates during viral replication. Here, we report detailed thermodynamic analyses of the folding of the dimeric HBc protomer under conditions that prevented capsid formation. Central to our success was the use of ion mobility spectrometry-mass spectrometry and microscale thermophoresis, which allowed folding mechanisms to be characterized using just micrograms of protein. HBc folds in a three-state transition with a stable, dimeric, α-helical intermediate. Extensive protein engineering showed thermodynamic linkage between different structural domains. Unusual effects associated with mutating some residues suggest structural strain, arising from frustrated contacts, is present in the native dimer. We found evidence of structural gatekeepers that, when mutated, alleviated native strain and prevented (or significantly attenuated) capsid formation by tuning the population of alternative native conformations. This strain is likely an evolved feature that helps HBc access the different structures associated with its diverse essential functions. The subtle balance between native and strained contacts may provide the means to tune conformational properties of HBc by molecular interactions or mutations, thereby conferring allosteric regulation of structure and function. The ability to trap HBc conformers thermodynamically by mutation, and thereby ablate HBV capsid formation, provides proof of principle for designing antivirals that elicit similar effects.
Collapse
|
10
|
Deng L, Kitova EN, Klassen JS. Mapping protein-ligand interactions in the gas phase using a functional group replacement strategy. Comparison of CID and BIRD activation methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:988-996. [PMID: 23702709 DOI: 10.1007/s13361-013-0651-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
Intermolecular interactions in the gaseous ions of two protein-ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH3, L1) and streptavidin homotetramer (S4) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. CID was performed on protonated ions of a series of structurally related complexes based on the (scFv + L1) and (S4 + 4B) complexes, at the +10 and +13 charge states, respectively. Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50% of the reactant ion (Ec50) upon modification of protein residues or ligand functional groups. For the (scFv + L1)(10+) ion, it was found that deoxygenation of L1 (at Gal C3 and C6 and Man C4 and C6) or mutation of His101 (to Ala) resulted in a decrease in Ec50 values. These results suggest that the four hydroxyl groups and His101 participate in intermolecular H-bonds. These findings agree with those obtained using the blackbody infrared radiative dissociation (BIRD)-FGR method. However, the CID-FGR method failed to reveal the relative strengths of the intermolecular interactions or establish Man C4 OH and His101 as an H-bond donor/acceptor pair. The CID-FGR method correctly identified Tyr43, but not Ser27, Trp79, and Trp120, as a stabilizing contact in the (S4 + 4B)(13+) ion. In fact, mutation of Trp79 and Trp120 led to an increase in the Ec50 value. Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein-ligand complexes.
Collapse
Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | | | | |
Collapse
|
11
|
Coupling electrospray corona discharge, charge reduction and ion mobility mass spectrometry: From peptides to large macromolecular protein complexes. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0120-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|