1
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Wolf E, Herasymenko O, Kutera M, Lento C, Arrowsmith C, Ackloo S, Wilson D. Quantitative Hydrogen-Deuterium Exchange Mass Spectrometry for Simultaneous Structural Characterization and Affinity Indexing of Single Target Drug Candidate Libraries. Anal Chem 2024. [PMID: 39074309 DOI: 10.1021/acs.analchem.4c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Hydrogen-deuterium eXchange mass spectrometry (HDX-MS) is increasingly used in drug development to locate binding sites and to identify allosteric effects in drug/target interactions. However, the potential of this technique to quantitatively analyze drug candidate libraries remains largely unexplored. Here, a collection of 13 WDR5-targeting small molecules with surface plasmon resonance (SPR) dissociation coefficients (KD) ranging from 20 nM to ∼116 μM were characterized using differential HDX-MS (ΔHDX-MS). Conventional qualitative analysis of the ΔHDX-MS data set revealed the binding interfaces for all compounds and allosteric effects where present. We then demonstrated that ΔHDX-MS signal-to-noise (S/N) not only can rank library-relative affinity but also can accurately predict KD from a calibration curve constructed from high-quality SPR data. Three methods for S/N calculation are explored, each suitable for libraries with different characteristics. Our results demonstrate the potential for ΔHDX-MS use in drug candidate library affinity validation and/or determination while simultaneously characterizing structure.
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Affiliation(s)
- Esther Wolf
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | | | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Derek Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
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2
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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring Residue-Level Interactions between the Biofilm-Driving R2ab Protein and Polystyrene Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1213-1222. [PMID: 38174900 PMCID: PMC10843815 DOI: 10.1021/acs.langmuir.3c02609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of significant interest because it impacts an organism's response to a nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. A residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Lysine methylation experiments reveal subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX rates become slower overall in the presence of PSNPs. However, some regions of the R2ab protein exhibit faster than average exchange rates in the presence of PSNPs, while others are slower than the average behavior, suggesting conformational changes upon binding. HDX rates and methylation ratios support a recently proposed "adsorbotope" model for PSNPs, wherein adsorbed proteins consist of unfolded anchor points interspersed with partially structured regions. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how R2ab adsorbs onto PSNP surfaces, this research emphasizes the need for advanced methods to comprehend residue-level interactions in the nanoparticle corona.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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3
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Pirrone GF, Munsell EV, Ferguson HM, Al-Sayah MA, Luthra SA, Makarov AA. Automated High-Throughput Matrix Assisted Laser Desorption Ionization Mass Spectrometry Methodology for Formulation Assessment of Polyethylene-Glycol-Conjugated Cytokine Proteins. J Pharm Sci 2023; 112:2778-2782. [PMID: 37478972 DOI: 10.1016/j.xphs.2023.07.013] [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: 02/07/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Biological therapeutics are major contributors to the pharmaceutical pipeline and continue to grow in sales and scope. Additionally, the field's understanding of cancer biology has advanced such that biopharmaceuticals can harness the power of the immune system for oncology treatments. Several of these novel therapeutics are engineered versions of naturally occurring proteins designed to improve therapeutic properties including potency, target engagement and half-life extension. Cytokines, such as interferons and interleukins, are a broad class of signaling proteins which modulate the body's immune response; engineered cytokines have entered the clinic as promising new immuno-oncology therapies. While these therapies hold great promise, their additional structural complexity introduces analytical challenges, and traditional analytical platforms may be ill-suited to effectively assess product development risks. Further, the pharmaceutical industry relies on streamlining approaches for high-throughput experimentation to achieve speed and efficiency for the discovery and development of new modalities. These demands necessitate the use of state-of-the-art techniques to rapidly characterize these new modalities and guide process development and optimization. Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) is a rapid, sensitive and automatable technique amenable for high-throughput analysis of proteins. In this work, we have developed an automated MALDI-MS platform to prepare, acquire and analyze molecular degradation in engineered PEGylated cytokines formulation samples. This orthogonal technique integrated seamlessly with current developability risk assessment workflows, ultimately enabling selection of a final formulation strategy for clinical development.
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Affiliation(s)
- Gregory F Pirrone
- Merck & Co., Inc., Analytical Research & Development, 33 Avenue Louis Pasteur, Boston, MA, USA.
| | - Erik V Munsell
- Merck & Co., Inc., Discovery Pharmaceutical Sciences, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Heidi M Ferguson
- Merck & Co., Inc., Discovery Pharmaceutical Sciences, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Mohammad A Al-Sayah
- Merck & Co., Inc., Analytical Research & Development, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Suman A Luthra
- Merck & Co., Inc., Discovery Pharmaceutical Sciences, 33 Avenue Louis Pasteur, Boston, MA, USA
| | - Alexey A Makarov
- Merck & Co., Inc., Analytical Research & Development, 33 Avenue Louis Pasteur, Boston, MA, USA.
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4
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Somarathne RP, Misra SK, Kariyawasam CS, Kessl JJ, Sharp JS, Fitzkee NC. Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.554951. [PMID: 37693402 PMCID: PMC10491123 DOI: 10.1101/2023.08.28.554951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of high interest because it impacts the organism's response to the nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. Ultimately, a residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Through lysine methylation, we observe subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX measurements reveal that certain regions of the R2ab protein undergo faster exchange rates in the presence of PSNPs, suggesting conformational changes upon binding. Both results support a recently proposed "adsorbotope" model, wherein adsorbed proteins consist of unfolded anchor points interspersed with regions of partial structure. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how proteins respond to nanoparticle surfaces, this research emphasizes the need for advanced methods to comprehend these intricate interactions fully at the residue level.
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Affiliation(s)
- Radha P. Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
| | - Sandeep K. Misra
- Department of BioMolecular Sciences, University of Mississippi, University, MS 38677
| | | | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS 38677
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762
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5
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Komives EA. Dynamic allostery in thrombin-a review. Front Mol Biosci 2023; 10:1200465. [PMID: 37457835 PMCID: PMC10339233 DOI: 10.3389/fmolb.2023.1200465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Thrombin is a serine protease that catalyzes a large number of different reactions including proteolytic cleave of fibrinogen to make the fibrin clot (procoagulant activity), of the protease activated receptors (for cell signaling) and of protein C generating activated protein C (anticoagulant activity). Thrombin has an effector binding site called the anion binding exosite 1 that is allosterically coupled to the active site. In this review, we survey results from thermodynamic characterization of the allosteric coupling as well as hydrogen-deuterium exchange mass spectrometry to reveal which parts of the thrombin structure are changed upon effector binding and/or mutagenesis, and finally NMR spectroscopy to characterize the different timescales of motions elicited by the effectors. We also relate the experimental work to computational network analysis of the thrombin-thrombomodulin complex.
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6
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Shin G, Lim SI. Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods. Proteins 2022; 91:593-607. [PMID: 36573681 DOI: 10.1002/prot.26459] [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: 07/16/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing, and involves the recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy remain the gold standard for structural elucidation of protein complexes, their artificial and static analytic nature often produces a non-native interface that otherwise might be negligible or non-existent in a biological environment. Recently, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS) have become valuable analytic complements to the traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, especially when the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here, we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. Additionally, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and the related biological processes, to increase the probability of structure-based drug design.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
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7
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Grønnemose AL, Østerlund EC, Otzen DE, Jørgensen TJD. EGCG has Dual and Opposing Effects on the N-terminal Region of Self-associating α-synuclein Oligomers. J Mol Biol 2022; 434:167855. [PMID: 36240861 DOI: 10.1016/j.jmb.2022.167855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/11/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Oligomers of the protein α-synuclein (α-syn) are thought to be a major toxic species in Parkinson's disease, particularly through their ability to permeabilize cell membranes. The green tea polyphenol epigallocatechin gallate (EGCG) has been found to reduce this ability. We have analyzed α-syn oligomer dynamics and interconversion by H/D exchange monitored by mass spectrometry (HDX-MS). Our results show that the two oligomers OI and OII co-exist in equilibrium; OI is a multimer of OII and its dissociation can be followed by HDX-MS by virtue of the correlated exchange of the N-terminal region. Urea destabilizes the α-syn oligomers, dissociating OI to OII and monomers. Oligomers exposed to EGCG undergo Met oxidation. Intriguingly, EGCG induces an oxidation-dependent effect on the structure of the N-terminal region. For the non-oxidized N-terminal region, EGCG increases the stability of the folded structure as measured by a higher level of protection against H/D exchange. In contrast, protection is clearly abrogated in the Met oxidized N-terminal region. Having a non-oxidized and disordered N-terminal region is known to be essential for efficient membrane binding. Therefore, our results suggest that the combined effect of a structural stabilization of the non-oxidized N-terminal region and the presence of a disordered oxidized N-terminal region renders the oligomers less cytotoxic by decreasing the ability of the N-terminal region to bind to cell membranes and facilitate their permeabilization.
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Affiliation(s)
- Anne Louise Grønnemose
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Eva Christina Østerlund
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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8
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Rapid label-free cell-based Approach Membrane Permeability Assay using MALDI-hydrogen-deuterium exchange mass spectrometry for peptides. Anal Chim Acta 2022; 1225:340234. [DOI: 10.1016/j.aca.2022.340234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/14/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022]
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9
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Bibel B, Elkayam E, Silletti S, Komives EA, Joshua-Tor L. Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. eLife 2022; 11:76908. [PMID: 35638597 PMCID: PMC9154749 DOI: 10.7554/elife.76908] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
Argonaute (Ago) proteins play a central role in post-transcriptional gene regulation through RNA interference (RNAi). Agos bind small RNAs (sRNAs) including small interfering RNAs (siRNAs) and microRNAs (miRNAs) to form the functional core of the RNA-induced silencing complex (RISC). The sRNA is used as a guide to target mRNAs containing either partially or fully complementary sequences, ultimately leading to downregulation of the corresponding proteins. It was previously shown that the kinase CK1α phosphorylates a cluster of residues in the eukaryotic insertion (EI) of Ago, leading to the alleviation of miRNA-mediated repression through an undetermined mechanism. We show that binding of miRNA-loaded human Ago2 to target RNA with complementarity to the seed and 3’ supplementary regions of the miRNA primes the EI for hierarchical phosphorylation by CK1α. The added negative charges electrostatically promote target release, freeing Ago to seek out additional targets once it is dephosphorylated. The high conservation of potential phosphosites in the EI suggests that such a regulatory strategy may be a shared mechanism for regulating miRNA-mediated repression. Proteins are the chemical ‘workhorses’ of the cell: some help maintain a cell’s shape or structure, while others carry out the chemical reactions necessary for life. Organisms therefore need to keep tight control over the production of proteins in their cells, so that the right amount of each protein is made at the right time, in the right place. Instructions for making new proteins are encoded in a type of molecule called messenger RNA. Each messenger RNA contains the instructions for one protein, which are then ‘read’ and carried out by special cellular machinery called ribosomes. The cell can control how much protein it produces by regulating both the levels of different messenger RNA and the amount of protein ribosomes are allowed to make from those instructions. The main way to regulate the levels of messenger RNA is through their transcription from the genome. However, this needs fine tuning. Cells can do this in a highly specific way using molecules called microRNAs. A microRNA works by directing a protein called Argonaute to the messenger RNA that it targets. Once Argonaute arrives, it can call in additional ‘helper proteins’ to shut down, or reduce, protein production from that messenger RNA, or alternatively to break down the messenger RNA altogether. Cells can use an enzyme called CK1α to attach bulky chemical groups onto a specific part of the Argonaute protein, in a reaction termed phosphorylation. The ability to carry out this reaction (and to reverse it) also seems to be important for microRNAs to do their job properly, but why has remained unknown. Bibel et al. wanted to determine what triggers CK1α to phosphorylate Argonaute, and how this affects interactions between microRNAs, Argonaute and their target messenger RNAs. A series of ‘test tube’ experiments looked at the interaction between purified CK1α and Argonaute under different conditions. These demonstrated that CK1α could only carry out its phosphorylation reaction when Argonaute was already interacting with a microRNA and its corresponding messenger RNA. Further measurements revealed that phosphorylation of Argonaute made it detach from the messenger RNA more quickly. This suggests that phosphorylation might be a way to let Argonaute seek out new messenger RNAs after blocking protein production at its first ‘target’. These results shed new light on a fundamental mechanism that cells use to control protein production. Bibel et al. propose that this mechanism may be shared across many different species and could one day help guide the development of new medical therapies based on microRNAs.
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Affiliation(s)
- Brianna Bibel
- Cold Spring Harbor Laboratory School of Biological Sciences
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
| | - Elad Elkayam
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory School of Biological Sciences
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
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10
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Hamuro Y, Coales SJ. Hydrogen/Deuterium Exchange Mass Spectrometry for Weak Binders. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:735-739. [PMID: 35230104 DOI: 10.1021/jasms.1c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This note describes theoretical and experimental considerations to observe perturbation of a protein upon binding to a ligand with weak affinity by hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most popular application of HDX-MS is to determine the binding site of a drug or drug lead in a protein target. However, when the affinity of a ligand is weak, driving the equilibrium to the formation of a complex is difficult, and thus, observing the perturbation upon binding is also challenging. Theoretical consideration indicates that the original concentration of a ligand over the dissociation constant ([L0]/KD) is roughly equal to the maximum protection factor expected for the experiment when the original concentration of a ligand is significantly larger than the original concentration of a protein and the dissociation constant ([L0] ≫ [P0] and [L0] ≫ KD). When HDX-MS analysis of a protein with a ligand of low affinity and low solubility is carried out, it may be challenging to achieve high enough ligand concentration to drive the equilibrium in favor of the complex due to the low solubility. There are two methods to alleviate this issue: (i) spiking a low affinity/low solubility ligand to exchange buffer to lower the required ligand concentration in aqueous protein stock solution and (ii) mixing a 1:1 ratio of aqueous protein-ligand stock solution and deuterated buffer to initiate the exchange reaction instead of the commonly used 1:9 ratio.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
| | - Stephen J Coales
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
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11
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Balasubramaniam D, Schroeder O, Russell AM, Fitchett JR, Austin AK, Beyer TP, Chen YQ, Day JW, Ehsani M, Heng AR, Zhen EY, Davies J, Glaesner W, Jones BE, Siegel RW, Qian YW, Konrad RJ. An anti-ANGPTL3/8 antibody decreases circulating triglycerides by binding to a LPL-inhibitory leucine zipper-like motif. J Lipid Res 2022; 63:100198. [PMID: 35307397 PMCID: PMC9036128 DOI: 10.1016/j.jlr.2022.100198] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
Triglycerides (TG) are required for fatty acid transport and storage and are essential for human health. Angiopoietin-like-protein 8 (ANGPTL8) has previously been shown to form a complex with ANGPTL3 that increases circulating TG by potently inhibiting LPL. We also recently showed that the TG-lowering apolipoprotein A5 (ApoA5) decreases TG levels by suppressing ANGPTL3/8-mediated LPL inhibition. To understand how LPL binds ANGPTL3/8 and ApoA5 blocks this interaction, we used hydrogen-deuterium exchange mass-spectrometry and molecular modeling to map binding sites of LPL and ApoA5 on ANGPTL3/8. Remarkably, we found that LPL and ApoA5 both bound a unique ANGPTL3/8 epitope consisting of N-terminal regions of ANGPTL3 and ANGPTL8 that are unmasked upon formation of the ANGPTL3/8 complex. We further used ANGPTL3/8 as an immunogen to develop an antibody targeting this same epitope. After refocusing on antibodies that bound ANGPTL3/8, as opposed to ANGPTL3 or ANGPTL8 alone, we utilized bio-layer interferometry to select an antibody exhibiting high-affinity binding to the desired epitope. We revealed an ANGPTL3/8 leucine zipper-like motif within the anti-ANGPTL3/8 epitope, the LPL-inhibitory region, and the ApoA5-interacting region, suggesting the mechanism by which ApoA5 lowers TG is via competition with LPL for the same ANGPTL3/8-binding site. Supporting this hypothesis, we demonstrate that the anti-ANGPTL3/8 antibody potently blocked ANGPTL3/8-mediated LPL inhibition in vitro and dramatically lowered TG levels in vivo. Together, these data show that an anti-ANGPTL3/8 antibody targeting the same leucine zipper-containing epitope recognized by LPL and ApoA5 markedly decreases TG by suppressing ANGPTL3/8-mediated LPL inhibition.
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Affiliation(s)
| | - Oliver Schroeder
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Anna M Russell
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | | | - Aaron K Austin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Thomas P Beyer
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Yan Q Chen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Jonathan W Day
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Mariam Ehsani
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Aik Roy Heng
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Eugene Y Zhen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Julian Davies
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Wolfgang Glaesner
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Bryan E Jones
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Robert W Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Yue-Wei Qian
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Robert J Konrad
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA.
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12
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Trainor K, Doyle CM, Metcalfe-Roach A, Steckner J, Lipovšek D, Malakian H, Langley D, Krystek SR, Meiering EM. Design for Solubility May Reveal Induction of Amide Hydrogen/Deuterium Exchange by Protein Self-Association. J Mol Biol 2021; 434:167398. [PMID: 34902431 DOI: 10.1016/j.jmb.2021.167398] [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: 07/29/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
Structural heterogeneity often constrains the characterization of aggregating proteins to indirect or low-resolution methods, obscuring mechanistic details of association. Here, we report progress in understanding the aggregation of Adnectins, engineered binding proteins with an immunoglobulin-like fold. We rationally design Adnectin solubility and measure amide hydrogen/deuterium exchange (HDX) under conditions that permit transient protein self-association. Protein-protein binding commonly slows rates of HDX; in contrast, we find that Adnectin association may induce faster HDX for certain amides, particularly in the C-terminal β-strand. In aggregation-prone proteins, we identify a pattern of very different rates of amide HDX for residues linked by reciprocal hydrogen bonds in the native structure. These results may be explained by local loss of native structure and formation of an inter-protein interface. Amide HDX induced by self-association, detected here by deliberate modulation of propensity for such interactions, may be a general phenomenon with the potential to expose mechanisms of aggregation by diverse proteins.
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Affiliation(s)
- Kyle Trainor
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Colleen M Doyle
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.
| | - Avril Metcalfe-Roach
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.
| | - Julia Steckner
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Daša Lipovšek
- Bristol Myers Squibb, Cambridge, MA 02140, United States.
| | | | - David Langley
- Bristol Myers Squibb, Cambridge, MA 02140, United States
| | | | - Elizabeth M Meiering
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada.
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13
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Lim XX, Shu B, Zhang S, Tan AWK, Ng TS, Lim XN, Chew VSY, Shi J, Screaton GR, Lok SM, Anand GS. Human antibody C10 neutralizes by diminishing Zika but enhancing dengue virus dynamics. Cell 2021; 184:6067-6080.e13. [PMID: 34852238 DOI: 10.1016/j.cell.2021.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 02/04/2023]
Abstract
The human monoclonal antibody (HmAb) C10 potently cross-neutralizes Zika virus (ZIKV) and dengue virus. Analysis of antibody fragment (Fab) C10 interactions with ZIKV and dengue virus serotype 2 (DENV2) particles by cryoelectron microscopy (cryo-EM) and amide hydrogen/deuterium exchange mass spectrometry (HDXMS) shows that Fab C10 binding decreases overall ZIKV particle dynamics, whereas with DENV2, the same Fab causes increased dynamics. Testing of different Fab C10:DENV2 E protein molar ratios revealed that, at higher Fab ratios, especially at saturated concentrations, the Fab enhanced viral dynamics (detected by HDXMS), and observation under cryo-EM showed increased numbers of distorted particles. Our results suggest that Fab C10 stabilizes ZIKV but that with DENV2 particles, high Fab C10 occupancy promotes E protein dimer conformational changes leading to overall increased particle dynamics and distortion of the viral surface. This is the first instance of a broadly neutralizing antibody eliciting virus-specific increases in whole virus particle dynamics.
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Affiliation(s)
- Xin-Xiang Lim
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Bo Shu
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Shuijun Zhang
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Aaron W K Tan
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Thiam-Seng Ng
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Xin-Ni Lim
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Valerie S-Y Chew
- Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jian Shi
- Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Gavin R Screaton
- Medical Sciences Division, University of Oxford, Oxford OX3 9DU, UK
| | - Shee-Mei Lok
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Duke-National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, Huck Institutes of the Life Sciences, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA.
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14
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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15
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Peacock RB, Komives EA. Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin. Biochemistry 2021; 60:3441-3448. [PMID: 34159782 DOI: 10.1021/acs.biochem.1c00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A deeper understanding of how hydrogen/deuterium exchange mass spectrometry (HDX-MS) reveals allostery is important because HDX-MS can reveal allostery in systems that are not amenable to nuclear magnetic resonance (NMR) spectroscopy. We were able to study thrombin and its complex with thrombomodulin, an allosteric regulator, by both HDX-MS and NMR. In this Perspective, we compare and contrast the results from both experiments and from molecular dynamics simulations. NMR detects changes in the chemical environment around the protein backbone N-H bond vectors, providing residue-level information about the conformational exchange between distinct states. HDX-MS detects changes in amide proton solvent accessibility and H-bonding. Taking advantage of NMR relaxation dispersion measurements of the time scale of motions, we draw conclusions about the motions reflected in HDX-MS experiments. Both experiments detect allostery, but they reveal different components of the allosteric transition. The insights gained from integrating NMR and HDX-MS into thrombin dynamics enable a clearer interpretation of the evidence for allostery revealed by HDX-MS in larger protein complexes and assemblies that are not amenable to NMR.
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Affiliation(s)
- Riley B Peacock
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
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16
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Gerak CAN, Cho SY, Kolesnikov M, Okon M, Murphy MEP, Sessions RB, Roberge M, McIntosh LP. Biophysical characterization of the ETV6 PNT domain polymerization interfaces. J Biol Chem 2021; 296:100284. [PMID: 33450226 PMCID: PMC7949025 DOI: 10.1016/j.jbc.2021.100284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 11/21/2022] Open
Abstract
ETV6 is an E26 transformation specific family transcriptional repressor that self-associates by its PNT domain to facilitate cooperative DNA binding. Chromosomal translocations frequently generate constitutively active oncoproteins with the ETV6 PNT domain fused to the kinase domain of one of many protein tyrosine kinases. Although an attractive target for therapeutic intervention, the propensity of the ETV6 PNT domain to polymerize via the tight head-to-tail association of two relatively flat interfaces makes it challenging to identify suitable small molecule inhibitors of this protein-protein interaction. Herein, we provide a comprehensive biophysical characterization of the ETV6 PNT domain interaction interfaces to aid future drug discovery efforts and help define the mechanisms by which its self-association mediates transcriptional repression. Using NMR spectroscopy, X-ray crystallography, and molecular dynamics simulations, along with amide hydrogen exchange measurements, we demonstrate that monomeric PNT domain variants adopt very stable helical bundle folds that do not change in conformation upon self-association into heterodimer models of the ETV6 polymer. Surface plasmon resonance-monitored alanine scanning mutagenesis studies identified hot spot regions within the self-association interfaces. These regions include both central hydrophobic residues and flanking salt-bridging residues. Collectively, these studies indicate that small molecules targeted to these hydrophobic or charged regions within the relatively rigid interfaces could potentially serve as orthosteric inhibitors of ETV6 PNT domain polymerization.
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Affiliation(s)
- Chloe A N Gerak
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sophia Y Cho
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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17
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Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
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Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
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18
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Makarov AA, Pirrone GF, Shchurik V, Regalado EL, Mangion I. Liposome Artificial Membrane Permeability Assay by MALDI-hydrogen-deuterium exchange mass spectrometry for peptides and small proteins. Anal Chim Acta 2020; 1099:111-118. [PMID: 31986267 DOI: 10.1016/j.aca.2019.09.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/30/2019] [Accepted: 09/23/2019] [Indexed: 02/07/2023]
Abstract
The pharmaceutical industry's focus has expanded to include peptide and protein-based therapeutics; however, some analytical challenges have arisen along the way, including the urgent need for fast and robust measurement of the membrane permeability of peptides and small proteins. In this study, a simple and efficient approach that utilizes MALDI-TOF-MS to study peptide and protein permeability through an artificial liposome membrane in conjunction with a differential hydrogen-deuterium exchange (HDX) methodology is described. A non-aqueous (aprotic) matrix was evaluated for use with MALDI sample preparation in order to eliminate undesirable hydrogen-deuterium back-exchange. Peptides and proteins were incubated with liposomes and their penetration into the liposome membrane over time was measured by MALDI-MS. A differential HDX approach was used to distinguish the peptides outside of the liposome from those inside. In this regard, the peptides on the outside of the liposomes were labeled using short exposure to deuterium oxide, while the peptides inside of the liposomes were protected from labeling. Subsequently, the unlabeled versus labeled peak area ratios for peptide and protein samples were compared using MALDI-TOF-MS. In this proof-of-concept study, we developed the Liposome Artificial Membrane Permeability Assay (LAMPA) workflow to study three well-known membrane-active model peptides (melittin, alamethicin, and gramicidin) and two model proteins (aprotinin and ubiquitin). The permeability results obtained from this were corroborated by previously reported data for studied peptides and proteins. The proposed LAMPA by MALDI-HDX-MS can be applied in an ultra-high-throughput manner for studying and rank-ordering membrane permeability of peptides and small proteins.
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Affiliation(s)
- Alexey A Makarov
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA.
| | - Gregory F Pirrone
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Vladimir Shchurik
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Erik L Regalado
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Ian Mangion
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
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19
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Eggertson MJ, Fadgen K, Engen JR, Wales TE. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data. Methods Mol Biol 2020; 2051:407-435. [PMID: 31552640 DOI: 10.1007/978-1-4939-9744-2_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A major component of a hydrogen exchange mass spectrometry experiment is the analysis of protein and peptide mass spectra to yield information about deuterium incorporation. The processing of data that are produced includes the identification of each peptic peptide to create a master table/array of peptide identity that typically includes sequence, retention time and retention time range, mass range, and undeuterated mass. The amount of deuterium incorporated into each of the peptides in this array must then be determined. Various software platforms have been developed in order to perform this specific type of data analysis. We describe the fundamental parameters to be considered at each step along the way and how data processing, either by an individual or by software, must approach the analysis.
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Affiliation(s)
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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20
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Lumpkin RJ, Komives EA. DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data. Mol Cell Proteomics 2019; 18:2516-2523. [PMID: 31594786 PMCID: PMC6885705 DOI: 10.1074/mcp.tir119.001731] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/17/2019] [Indexed: 11/06/2022] Open
Abstract
Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) has become widely popular for mapping protein-ligand interfaces, for understanding protein-protein interactions, and for discovering dynamic allostery. Several platforms are now available which provide large data sets of amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data. Although many of these platforms provide some down-stream processing, a comprehensive software that provides the most commonly used down-stream processing tools such as automatic back-exchange correction options, analysis of overlapping peptides, calculations of relative deuterium uptake into regions of the protein after such corrections, rigorous statistical analysis of the significance of uptake differences, and generation of high quality figures for data presentation is not yet available. Here we describe the Deuterium Exchange Correction and Analysis (DECA) software package, which provides all these downstream processing options for data from the most popular mass spectrometry platforms. The major functions of the software are demonstrated on sample data.
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Affiliation(s)
- Ryan J Lumpkin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378.
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21
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Mohammadiarani H, Shaw VS, Neubig RR, Vashisth H. Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins. J Phys Chem B 2018; 122:9314-9323. [PMID: 30222348 PMCID: PMC6430106 DOI: 10.1021/acs.jpcb.8b07494] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hydrogen-deuterium exchange (HDX) experiments are widely used in studies of protein dynamics. To predict the propensity of amide hydrogens for exchange with deuterium, several models have been reported in which computations of amide-hydrogen protection factors are carried out using molecular dynamics (MD) simulations. Given significant variation in the criteria used in different models, the robustness and broader applicability of these models to other proteins, especially homologous proteins showing distinct amide-exchange patterns, remains unknown. The sensitivity of the predictions when MD simulations are conducted with different force-fields is yet to tested and quantified. Using MD simulations and experimental HDX data on three homologous signaling proteins, we report detailed studies quantifying the performance of seven previously reported models (M1-M7) of two general types: empirical and fractional-population models. We find that the empirical models show inconsistent predictions but predictions of the fractional population models are robust. Contrary to previously reported work, we find that the solvent-accessible surface area of amide hydrogens is a useful metric when combined with a new metric defining the distances of amide hydrogens from the first polar atoms in proteins. On the basis of this, we report two new models, one empirical (M8) and one population-based (M9). We find strong protection of amide hydrogens from solvent exchange both within the stable helical motifs and also in the interhelical loops. We further observe that the exchange-competent states of amide hydrogens occur on the sub 100 ps time-scale via localized fluctuations, and such states among amides of a given protein do not appear to show any cooperativity or allosteric coupling.
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Affiliation(s)
- Hossein Mohammadiarani
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
| | - Vincent S Shaw
- Department of Pharmacology and Toxicology , Michigan State University , East Lansing , Michigan 48825 , United States
| | - Richard R Neubig
- Department of Pharmacology and Toxicology , Michigan State University , East Lansing , Michigan 48825 , United States
| | - Harish Vashisth
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
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22
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Ramirez-Sarmiento CA, Komives EA. Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions. Methods 2018; 144:43-52. [PMID: 29627358 DOI: 10.1016/j.ymeth.2018.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 11/29/2022] Open
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDXMS) has emerged as a powerful approach for revealing folding and allostery in protein-protein interactions. The advent of higher resolution mass spectrometers combined with ion mobility separation and ultra performance liquid chromatographic separations have allowed the complete coverage of large protein sequences and multi-protein complexes. Liquid-handling robots have improved the reproducibility and accurate temperature control of the sample preparation. Many researchers are also appreciating the power of combining biophysical approaches such as stopped-flow fluorescence, single molecule FRET, and molecular dynamics simulations with HDXMS. In this review, we focus on studies that have used a combination of approaches to reveal (re)folding of proteins as well as on long-distance allosteric changes upon interaction.
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Affiliation(s)
- Cesar A Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, United States.
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23
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Hamuro Y, Coales SJ. Optimization of Feasibility Stage for Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:623-629. [PMID: 29299838 DOI: 10.1007/s13361-017-1860-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 05/12/2023]
Abstract
The practice of HDX-MS remains somewhat difficult, not only for newcomers but also for veterans, despite its increasing popularity. While a typical HDX-MS project starts with a feasibility stage where the experimental conditions are optimized and the peptide map is generated prior to the HDX study stage, the literature usually reports only the HDX study stage. In this protocol, we describe a few considerations for the initial feasibility stage, more specifically, how to optimize quench conditions, how to tackle the carryover issue, and how to apply the pepsin specificity rule. Two sets of quench conditions are described depending on the presence of disulfide bonds to facilitate the quench condition optimization process. Four protocols are outlined to minimize carryover during the feasibility stage: (1) addition of a detergent to the quench buffer, (2) injection of a detergent or chaotrope to the protease column after each sample injection, (3) back-flushing of the trap column and the analytical column with a new plumbing configuration, and (4) use of PEEK (or PEEK coated) frits instead of stainless steel frits for the columns. The application of the pepsin specificity rule after peptide map generation and not before peptide map generation is suggested. The rule can be used not only to remove falsely identified peptides, but also to check the sample purity. A well-optimized HDX-MS feasibility stage makes subsequent HDX study stage smoother and the resulting HDX data more reliable. Graphical Abstract ᅟ.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation (scientifically co-founded by Professor Virgil Woods and now dissolved), Monmouth Junction, NJ, USA.
- SGS Life North America, 606 Brandywine Parkway, West Chester, PA, 19380, USA.
| | - Stephen J Coales
- ExSAR Corporation (scientifically co-founded by Professor Virgil Woods and now dissolved), Monmouth Junction, NJ, USA
- LEAP Technologies, 1015 Aviation Parkway, Suite 1000, Morrisville, NC, 27560, USA
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24
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Pirrone GF, Wang H, Canfield N, Chin AS, Rhodes TA, Makarov AA. Use of MALDI-MS Combined with Differential Hydrogen–Deuterium Exchange for Semiautomated Protein Global Conformational Screening. Anal Chem 2017; 89:8351-8357. [DOI: 10.1021/acs.analchem.7b01590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gregory F. Pirrone
- Merck & Co., Inc., MRL, †Process Research & Development and ‡Pharmaceutical Sciences, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Heather Wang
- Merck & Co., Inc., MRL, †Process Research & Development and ‡Pharmaceutical Sciences, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Nicole Canfield
- Merck & Co., Inc., MRL, †Process Research & Development and ‡Pharmaceutical Sciences, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Alexander S. Chin
- Merck & Co., Inc., MRL, †Process Research & Development and ‡Pharmaceutical Sciences, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Timothy A. Rhodes
- Merck & Co., Inc., MRL, †Process Research & Development and ‡Pharmaceutical Sciences, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Alexey A. Makarov
- Merck & Co., Inc., MRL, †Process Research & Development and ‡Pharmaceutical Sciences, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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25
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Wang L, Chance MR. Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment. Mol Cell Proteomics 2017; 16:706-716. [PMID: 28275051 DOI: 10.1074/mcp.o116.064386] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/06/2017] [Indexed: 12/17/2022] Open
Abstract
Protein footprinting mediated by mass spectrometry has evolved over the last 30 years from proof of concept to commonplace biophysics tool, with unique capabilities for assessing structure and dynamics of purified proteins in physiological states in solution. This review outlines the history and current capabilities of two major methods of protein footprinting: reversible hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (HRF), an irreversible covalent labeling approach. Technological advances in both approaches now permit high-resolution assessments of protein structure including secondary and tertiary structure stability mediated by backbone interactions (measured via HDX) and solvent accessibility of side chains (measured via HRF). Applications across many academic fields and in biotechnology drug development are illustrated including: detection of protein interfaces, identification of ligand/drug binding sites, and monitoring dynamics of protein conformational changes along with future prospects for advancement of protein footprinting in structural biology and biophysics research.
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Affiliation(s)
- Liwen Wang
- From the ‡Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mark R Chance
- From the ‡Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio
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26
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Chandramohan A, Krishnamurthy S, Larsson A, Nordlund P, Jansson A, Anand GS. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design. PLoS Comput Biol 2016; 12:e1004840. [PMID: 27253209 PMCID: PMC4890749 DOI: 10.1371/journal.pcbi.1004840] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/01/2016] [Indexed: 12/24/2022] Open
Abstract
A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites. This assumes a greater challenge when considering the interactions of low affinity ligands (dissociation constants, KD, in the μM range or lower). Amide hydrogen deuterium Exchange mass spectrometry (HDXMS) is a robust method that can provide both structural insights and dynamics information on both high affinity and transient protein-ligand interactions. In this study, an application of HDXMS for probing the dynamics of low affinity ligands to proteins is described using the N-terminal ATPase domain of Hsp90. Comparison of Hsp90 dynamics between high affinity natural inhibitors (KD ~ nM) and fragment compounds reveal that HDXMS is highly sensitive in mapping the interactions of both high and low affinity ligands. HDXMS reports on changes that reflect both orthosteric effects and allosteric changes accompanying binding. Orthosteric sites can be identified by overlaying HDXMS onto structural information of protein-ligand complexes. Regions distal to orthosteric sites indicate long range conformational changes with implications for allostery. HDXMS, thus finds powerful utility as a high throughput method for compound library screening to identify binding sites and describe allostery with important implications for fragment-based ligand discovery (FBLD). Ligand interactions with proteins result in broad changes that are propagated throughout the target proteins, across space and time. These changes can be broadly classified into: orthosteric effects at the ligand binding site and allosteric changes at distal sites. These allosteric changes are difficult to localize and distinguish from binding interactions. In this study, we describe the application of amide hydrogen/deuterium exchange mass-spectrometry (HDXMS) to differentiate between changes occurring at the binding site and at distal allosteric sites by combining HDXMS with X-ray crystallography. Every ligand or a fragment mediates distinct contacts and results in changes in deuterium uptake across the protein. By comparing with orthosteric structural information, it is possible to identify long-range changes (action at a distance) due to the ligands. An important application of HDXMS is that it can identify subtle changes in protein dynamics that cannot be picked up by quantitative screens of protein-ligand interactions or crystal structures. This gives us the ability to describe ligand binding based on the response from different regions in the proteins. Thus it provides us with the potential to accurately measure and compare changes in dynamics upon binding different ligands and fragments, which is greatly valuable in fragment-based ligand design.
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Affiliation(s)
- Arun Chandramohan
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Paer Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Anna Jansson
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Ganesh S. Anand
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail:
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Arora J, Hickey JM, Majumdar R, Esfandiary R, Bishop SM, Samra HS, Middaugh CR, Weis DD, Volkin DB. Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody. MAbs 2016; 7:525-39. [PMID: 25875351 PMCID: PMC4622866 DOI: 10.1080/19420862.2015.1029217] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is a need for new analytical approaches to better characterize the nature of the concentration-dependent, reversible self-association (RSA) of monoclonal antibodies (mAbs) directly, and with high resolution, when these proteins are formulated as highly concentrated solutions. In the work reported here, hydrogen exchange mass spectrometry (HX-MS) was used to define the concentration-dependent RSA interface, and to characterize the effects of association on the backbone dynamics of an IgG1 mAb (mAb-C). Dynamic light scattering, chemical cross-linking, and solution viscosity measurements were used to determine conditions that caused the RSA of mAb-C. A novel HX-MS experimental approach was then applied to directly monitor differences in local flexibility of mAb-C due to RSA at different protein concentrations in deuterated buffers. First, a stable formulation containing lyoprotectants that permitted freeze-drying of mAb-C at both 5 and 60 mg/mL was identified. Upon reconstitution with RSA-promoting deuterated solutions, the low vs. high protein concentration samples displayed different levels of solution viscosity (i.e., approx. 1 to 75 mPa.s). The reconstituted mAb-C samples were then analyzed by HX-MS. Two specific sequences covering complementarity-determining regions CDR2H and CDR2L (in the variable heavy and light chains, respectively) showed significant protection against deuterium uptake (i.e., decreased hydrogen exchange). These results define the major protein-protein interfaces associated with the concentration-dependent RSA of mAb-C. Surprisingly, certain peptide segments in the VH domain, the constant domain (CH2), and the hinge region (CH1-CH2 interface) concomitantly showed significant increases in local flexibility at high vs. low protein concentrations. These results indicate the presence of longer-range, distant dynamic coupling effects within mAb-C occurring upon RSA.
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Key Words
- ADCs, antibody-drug conjugates
- BS2G, bis (sulfosuccinimidyl) 2,2,4,4 glutarate
- BsAbs, bispecific antibodies
- CD, circular dichroism
- CDR, complementarity-determining regions
- CH1-CH3, constant domains 1–3 respectively of the heavy chain
- DLS, dynamic light scattering
- Fab, antigen binding fragment
- Fc, crystallizable fragment
- HC, heavy chain
- HPLC, high-performance liquid chromatography
- HX-MS, hydrogen exchange mass spectrometry
- IgG1, immunoglobulin G1
- LC, light chain
- RSA, reversible self-association
- SC, subcutaneous
- SEC, size-exclusion chromatography
- VH/VL, variable domain of the heavy/light chain
- aggregation
- flexibility
- high protein concentration
- hydrogen exchange
- immunoglobulin G1
- mAb, monoclonal antibody
- mass spectrometry
- monoclonal antibody
- protein-protein interactions
- reversible self-association
- stability
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Affiliation(s)
- Jayant Arora
- a Department of Pharmaceutical Chemistry; Macromolecule and Vaccine Stabilization Center; University of Kansas ; Lawrence , KS , USA
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Gallagher ES, Hudgens JW. Mapping Protein–Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry. Methods Enzymol 2016; 566:357-404. [DOI: 10.1016/bs.mie.2015.08.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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Yang SW, Ting HC, Lo YT, Wu TY, Huang HW, Yang CJ, Chan JFR, Chuang MC, Hsu YHH. Guanine nucleotide induced conformational change of Cdc42 revealed by hydrogen/deuterium exchange mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:42-51. [PMID: 26542736 DOI: 10.1016/j.bbapap.2015.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 10/26/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
Abstract
Cdc42 regulates pathways related to cell division. Dysregulation of Cdc42 can lead to cancer, cardiovascular diseases and neurodegenerative diseases. GTP induced activation mechanism plays an important role in the activity and biological functions of Cdc42. P-loop, Switch I and Switch II are critical regions modulating the enzymatic activity of Cdc42. We applied amide hydrogen/deuterium exchange coupled with liquid chromatography mass spectrometry (HDXMS) to investigate the dynamic changes of apo-Cdc42 after GDP, GTP and GMP-PCP binding. The natural substrate GTP induced significant decreases of deuteration in P-loop and Switch II, moderate changes of deuteration in Switch I and significant changes of deuteration in the α7 helix, a region far away from the active site. GTP binding induced similar effects on H/D exchange to its non-hydrolysable analog, GMP-PCP. HDXMS results indicate that GTP binding blocked the solvent accessibility in the active site leading to the decrease of H/D exchange rate surrounding the active site, and further triggered a conformational change resulting in the drastic decrease of H/D exchange rate at the remote α7 helix. Comparing the deuteration levels in three activation states of apo-Cdc42, Cdc42-GDP and Cdc42-GMP-PCP, the apo-Cdc42 has the most flexible structure, which can be stabilized by guanine nucleotide binding. The rates of H/D exchange of Cdc42-GDP are between the GMP-PCP-bound and the apo form, but more closely to the GMP-PCP-bound form. Our results show that the activation of Cdc42 is a process of conformational changes involved with P-loop, Switch II and α7 helix for structural stabilization.
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Affiliation(s)
- Sheng-Wei Yang
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Hsiu-Chi Ting
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Yi-Ting Lo
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Ting-Yuan Wu
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Hung-Wei Huang
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Chia-Jung Yang
- Department of Materials Engineering, National Chung Hsing University, Taichung, Taiwan
| | | | | | - Yuan-Hao Howard Hsu
- Department of Chemistry, Tunghai University, Taichung, Taiwan; Life Science Research Center, Tunghai University, Taichung, Taiwan.
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30
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Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry. Methods 2015; 89:45-53. [DOI: 10.1016/j.ymeth.2015.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 12/22/2022] Open
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31
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Dailing A, Luchini A, Liotta L. Unlocking the secrets to protein-protein interface drug targets using structural mass spectrometry techniques. Expert Rev Proteomics 2015; 12:457-67. [PMID: 26400464 DOI: 10.1586/14789450.2015.1079487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-protein interactions (PPIs) drive all biologic systems at the subcellular and extracellular level. Changes in the specificity and affinity of these interactions can lead to cellular malfunctions and disease. Consequently, the binding interfaces between interacting protein partners are important drug targets for the next generation of therapies that block such interactions. Unfortunately, protein-protein contact points have proven to be very difficult pharmacological targets because they are hidden within complex 3D interfaces. For the vast majority of characterized binary PPIs, the specific amino acid sequence of their close contact regions remains unknown. There has been an important need for an experimental technology that can rapidly reveal the functionally important contact points of native protein complexes in solution. In this review, experimental techniques employing mass spectrometry to explore protein interaction binding sites are discussed. Hydrogen-deuterium exchange, hydroxyl radical footprinting, crosslinking and the newest technology protein painting are compared and contrasted.
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Affiliation(s)
| | - Alessandra Luchini
- a Center for Applied Proteomics and Molecular Medicine, Life Sciences Lab Building, George Mason University, 10920 University Boulevard, Manassas, Virginia 20110, USA
| | - Lance Liotta
- a Center for Applied Proteomics and Molecular Medicine, Life Sciences Lab Building, George Mason University, 10920 University Boulevard, Manassas, Virginia 20110, USA
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32
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Abstract
Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.
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33
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Tamò GE, Abriata LA, Dal Peraro M. The importance of dynamics in integrative modeling of supramolecular assemblies. Curr Opin Struct Biol 2015; 31:28-34. [PMID: 25795087 DOI: 10.1016/j.sbi.2015.02.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/10/2015] [Accepted: 02/26/2015] [Indexed: 11/16/2022]
Abstract
Revealing the atomistic architecture of supramolecular complexes is a fundamental step toward a deeper understanding of cellular functioning. To date, this formidable task is facilitated by an emerging array of integrative modeling approaches that combine experimental data from different sources. One major challenge these methods have to face is the treatment of the dynamic rearrangements of the individual subunits upon assembly. While this flexibility can be sampled at different levels, integrating native dynamic determinants with available experimental inputs can provide an effective way to reveal the molecular recognition mechanisms at the basis of supramolecular assembly.
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Affiliation(s)
- Giorgio E Tamò
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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Balasubramaniam D, Schiffer J, Parnell J, Mir SP, Amaro RE, Komives EA. How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry 2015; 54:1673-80. [PMID: 25654263 DOI: 10.1021/bi501420n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ankyrin repeat and SOCS box (ASB) family is composed of 18 proteins and belongs to the suppressor of cytokine signaling (SOCS) box protein superfamily. The ASB proteins function as the substrate-recognition subunits of ECS-type (ElonginBC-Cullin-SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that specifically transfer ubiquitin to cellular proteins targeting them for degradation by the proteasome. ASB9 binds to creatine kinase (CK) and targets it for degradation; however, the way in which ASB9 interacts with CK is not yet known. We present a complete characterization of the binding of ASB9 to CK. One ASB9 molecule binds to a dimer of CK. The binding affinity of ASB9(1-252) was extremely tight, and no dissociation could be observed. Deletion of the 34 N-terminal amino acids forming ASB9(35-252) resulted in weakening of the binding, so that a binding affinity of 2.6 nM could be measured. Amide hydrogen-deuterium exchange (HDXMS) experiments showed that both ASB9(1-252) and ASB9(35-252) protected the same region of CK, residues 182-203, which forms one side of the active site. The HDXMS experiments indicated that the N-terminal disordered region and first ankyrin repeat of ASB9 are protected from exchange in the complex. Molecular docking yielded a structural model consistent with all of the data that suggested the N-terminal residues of ASB9(1-252) may lie in one CK active site. This model was corroborated by enzymatic activity assays and mutational analysis.
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Affiliation(s)
- Deepa Balasubramaniam
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0378, United States
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35
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Yan ECY, Wang Z, Fu L. Proteins at Interfaces Probed by Chiral Vibrational Sum Frequency Generation Spectroscopy. J Phys Chem B 2015; 119:2769-85. [DOI: 10.1021/jp508926e] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, CT 06511, United States
| | - Zhuguang Wang
- Department of Chemistry, Yale University, New Haven, CT 06511, United States
| | - Li Fu
- Department of Chemistry, Yale University, New Haven, CT 06511, United States
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36
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Sheff JG, Schriemer DC. Toward Standardizing Deuterium Content Reporting in Hydrogen Exchange-MS. Anal Chem 2014; 86:11962-5. [DOI: 10.1021/ac5034424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joey G. Sheff
- Department
of Chemistry, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - David C. Schriemer
- Department
of Chemistry, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Department
of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1,Canada
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37
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Wang W, Iacob RE, Luoh RP, Engen JR, Lippard SJ. Electron transfer control in soluble methane monooxygenase. J Am Chem Soc 2014; 136:9754-62. [PMID: 24937475 PMCID: PMC4105053 DOI: 10.1021/ja504688z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The
hydroxylation or epoxidation of hydrocarbons by bacterial multicomponent
monooxygenases (BMMs) requires the interplay of three or four protein
components. How component protein interactions control catalysis,
however, is not well understood. In particular, the binding sites
of the reductase components on the surface of their cognate hydroxylases
and the role(s) that the regulatory proteins play during intermolecular
electron transfer leading to the hydroxylase reduction have been enigmatic.
Here we determine the reductase binding site on the hydroxylase of
a BMM enzyme, soluble methane monooxygenase (sMMO) from Methylococcus
capsulatus (Bath). We present evidence that the ferredoxin
domain of the reductase binds to the canyon region of the hydroxylase,
previously determined to be the regulatory protein binding site as
well. The latter thus inhibits reductase binding to the hydroxylase
and, consequently, intermolecular electron transfer from the reductase
to the hydroxylase diiron active site. The binding competition between
the regulatory protein and the reductase may serve as a control mechanism
for regulating electron transfer, and other BMM enzymes are likely
to adopt the same mechanism.
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Affiliation(s)
- Weixue Wang
- Departments of †Chemistry and §Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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38
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Li H, Lu L, Chen R, Quan L, Xia X, Lü Q. PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta. PLoS One 2014; 9:e94769. [PMID: 24801496 PMCID: PMC4011740 DOI: 10.1371/journal.pone.0094769] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 03/19/2014] [Indexed: 01/12/2023] Open
Abstract
Structural information related to protein–peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein–peptide interactions explored by experimental ways. Protein–peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein–peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein–peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.
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Affiliation(s)
- Haiou Li
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Liyao Lu
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rong Chen
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Lijun Quan
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoyan Xia
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Provincial Key Lab for Information Processing Technologies, Suzhou, Jiangsu, China
| | - Qiang Lü
- School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China
- Jiangsu Provincial Key Lab for Information Processing Technologies, Suzhou, Jiangsu, China
- * E-mail:
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Abstract
B cell epitope mapping is widely applied to determine antibody-binding sites. Several methods exist to map B cell epitopes and here we describe three methods that are characterized by the simultaneous analysis of multiple peptides. In the first approach a microarray of overlapping synthetic peptides derived from an antigenic protein is used and the binding of the antibodies is analyzed by fluorescently labeled secondary antibodies. This method is particularly suited for the identification of linear epitopes of an established target protein. In the second approach the binding of antibodies to a random synthetic peptide library immobilized on microbeads is determined by enzyme-conjugated secondary antibodies and the selection of antibody-bound beads by a light microscope. This method can be applied when information on the identity of the antigenic protein is lacking. In the third method an antigen is proteolytically digested and antibody binding to the resulting peptides is analyzed by surface plasmon resonance imaging (iSPR). The latter method can be applied when the purified antigenic protein is available.
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Affiliation(s)
- Sanne M M Hensen
- Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences, Institute for Molecules and Materials and Netherlands Proteomics Centre, Radboud University Nijmegen, 9101, NL-6500 HB, Nijmegen, The Netherlands
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40
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Singh H, Dai Y, Outten FW, Busenlehner LS. Escherichia coli SufE sulfur transfer protein modulates the SufS cysteine desulfurase through allosteric conformational dynamics. J Biol Chem 2013; 288:36189-200. [PMID: 24196966 PMCID: PMC3868733 DOI: 10.1074/jbc.m113.525709] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/05/2013] [Indexed: 11/06/2022] Open
Abstract
Fe-S clusters are critical metallocofactors required for cell function. Fe-S cluster biogenesis is carried out by assembly machinery consisting of multiple proteins. Fe-S cluster biogenesis proteins work together to mobilize sulfide and iron, form the nascent cluster, traffic the cluster to target metalloproteins, and regulate the assembly machinery in response to cellular Fe-S cluster demand. A complex series of protein-protein interactions is required for the assembly machinery to function properly. Despite considerable progress in obtaining static three-dimensional structures of the assembly proteins, little is known about transient protein-protein interactions during cluster assembly or the role of protein dynamics in the cluster assembly process. The Escherichia coli cysteine desulfurase SufS (EC 2.8.1.7) and its accessory protein SufE work together to mobilize persulfide from L-cysteine, which is then donated to the SufB Fe-S cluster scaffold. Here we use amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize SufS-SufE interactions and protein dynamics in solution. HDX-MS analysis shows that SufE binds near the SufS active site to accept persulfide from Cys-364. Furthermore, SufE binding initiates allosteric changes in other parts of the SufS structure that likely affect SufS catalysis and alter SufS monomer-monomer interactions. SufE enhances the initial l-cysteine substrate binding to SufS and formation of the external aldimine with pyridoxal phosphate required for early steps in SufS catalysis. Together, these results provide a new picture of the SufS-SufE sulfur transferase pathway and suggest a more active role for SufE in promoting the SufS cysteine desulfurase reaction for Fe-S cluster assembly.
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Affiliation(s)
- Harsimran Singh
- From the Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487 and
| | - Yuyuan Dai
- the Department of Chemistry and Biochemistry, The University of South Carolina, Columbia, South Carolina 29208
| | - F. Wayne Outten
- the Department of Chemistry and Biochemistry, The University of South Carolina, Columbia, South Carolina 29208
| | - Laura S. Busenlehner
- From the Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487 and
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41
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Veesler D, Khayat R, Krishnamurthy S, Snijder J, Huang RK, Heck AJR, Anand GS, Johnson JE. Architecture of a dsDNA viral capsid in complex with its maturation protease. Structure 2013; 22:230-7. [PMID: 24361271 DOI: 10.1016/j.str.2013.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/30/2022]
Abstract
Most double-stranded DNA (dsDNA) viruses, including bacteriophages and herpesviruses, rely on a staged assembly process of capsid formation. A viral protease is required for many of them to disconnect scaffolding domains/proteins from the capsid shell, therefore priming the maturation process. We used the bacteriophage HK97 as a model system to decipher the molecular mechanisms underlying the recruitment of the maturation protease by the assembling procapsid and the influence exerted onto the latter. Comparisons of the procapsid with and without protease using single-particle cryoelectron microscopy reconstructions, hydrogen/deuterium exchange coupled to mass spectrometry, and native mass spectrometry demonstrated that the protease interacts with the scaffolding domains within the procapsid interior and stabilizes them as well as the whole particle. The results suggest that the thermodynamic consequences of protease packaging are to shift the equilibrium between isolated coat subunit capsomers and procapsid in favor of the latter by stabilizing the assembled particle before making the process irreversible through proteolysis of the scaffolding domains.
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Affiliation(s)
- David Veesler
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Reza Khayat
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Srinath Krishnamurthy
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Joost Snijder
- 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, 3584CH, Utrecht, The Netherlands
| | - Rick K Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Albert 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, 3584CH, Utrecht, The Netherlands
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Ramírez-Sarmiento CA, Baez M, Wilson CAM, Babul J, Komives EA, Guixé V. Observation of solvent penetration during cold denaturation of E. coli phosphofructokinase-2. Biophys J 2013; 104:2254-63. [PMID: 23708365 DOI: 10.1016/j.bpj.2013.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/07/2013] [Accepted: 04/12/2013] [Indexed: 11/16/2022] Open
Abstract
Phosphofructokinase-2 is a dimeric enzyme that undergoes cold denaturation following a highly cooperative N2 2I mechanism with dimer dissociation and formation of an expanded monomeric intermediate. Here, we use intrinsic fluorescence of a tryptophan located at the dimer interface to show that dimer dissociation occurs slowly, over several hours. We then use hydrogen-deuterium exchange mass spectrometry experiments, performed by taking time points over the cold denaturation process, to measure amide exchange throughout the protein during approach to the cold denatured state. As expected, a peptide corresponding to the dimer interface became more solvent exposed over time at 3°C; unexpectedly, amide exchange increased throughout the protein over time at 3°C. The rate of increase in amide exchange over time at 3°C was the same for each region and equaled the rate of dimer dissociation measured by tryptophan fluorescence, suggesting that dimer dissociation and formation of the cold denatured intermediate occur without appreciable buildup of folded monomer. The observation that throughout the protein amide exchange increases as phosphofructokinase-2 cold denatures provides experimental evidence for theoretical predictions that cold denaturation primarily occurs by solvent penetration into the hydrophobic core of proteins in a sequence-independent manner.
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London N, Raveh B, Schueler-Furman O. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr Opin Struct Biol 2013; 23:894-902. [PMID: 24138780 DOI: 10.1016/j.sbi.2013.07.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/25/2022]
Abstract
Peptide-mediated interactions are gaining increased attention due to their predominant roles in the many regulatory processes that involve dynamic interactions between proteins. The structures of such interactions provide an excellent starting point for their characterization and manipulation, and can provide leads for targeted inhibitor design. The relatively few experimentally determined structures of peptide-protein complexes can be complemented with an outburst of modeling approaches that have been introduced in recent years, with increasing accuracy and applicability to ever more systems. We review different methods to address the considerable challenges in modeling the binding of a short yet highly flexible peptide to its partner. These methods apply an array of sampling strategies and draw from a recent amassing of knowledge about the biophysical nature of peptide-protein interactions. We elaborate on applications of these structure-based approaches and in particular on the characterization of peptide binding specificity to different peptide-binding domains and enzymes. Such applications can identify new biological targets and thus complement our current view of protein-protein interactions in living organisms. Accurate peptide-protein docking is of particular importance in the light of increased appreciation of the crucial functional roles of disordered regions and the many linear binding motifs embedded within.
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Affiliation(s)
- Nir London
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
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Lemaire P, Debois D, Smargiasso N, Quinton L, Gabelica V, De Pauw EA. Use of 1,5-diaminonaphthalene to combine matrix-assisted laser desorption/ionization in-source decay fragmentation with hydrogen/deuterium exchange. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1837-1846. [PMID: 23857929 DOI: 10.1002/rcm.6627] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/12/2013] [Accepted: 05/13/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE In-Source Decay (ISD) in Matrix-Assisted Laser Desorption/Ionization (MALDI) mass spectrometry is a fast and easy top-down activation method. Our objective is to find a suitable matrix to locate the deuterons following in-solution hydrogen/deuterium exchange (HDX). This matrix must circumvent the commonly encountered undesired back-exchange reactions, in order to preserve the regioselective deuteration pattern. METHODS The 1,5-diaminonaphthalene (1,5-DAN) matrix is known to be suitable for MALDI-ISD fragmentation. MALDI Mass Spectrometry Imaging (MSI) was employed to compare 1,5-DAN and other commonly used MALDI matrices with respect to the extent of back-exchange and the uniformity of the H/D exchange profiles within the MALDI spots. We tested the back-exchange on the highly sensitive amyloid-beta peptide (1-40), and proved the regioselectivity on ubiquitin and β-endorphin. RESULTS MALDI-MSI results show that 1,5-DAN leads to the least back-exchange over all the spot. MALDI-ISD fragmentation combined with H/D exchange using 1,5-DAN matrix was validated by localizing deuterons in native ubiquitin. Results agree with previous data obtained by Nuclear Magnetic Resonance (NMR) and Electron Transfer Dissociation (ETD). Moreover, 1,5-DAN matrix was used to study the H/D exchange profile of the methanol-induced helical structure of β-endorphin, and the relative protection can be explained by the polarity of residues involved in hydrogen bond formation. CONCLUSIONS We found that controlling crystallization is the most important parameter when combining H/D exchange with MALDI. The 1,5-DAN matrix is characterized by a fast crystallization kinetics, and therefore gives robust and reliable H/D exchange profiles using MALDI-ISD.
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Affiliation(s)
- Pascale Lemaire
- GIGA-R, Mass Spectrometry Laboratory, Department of Chemistry, Chemistry Building B6c, University of Liège, B-4000 Liège, Belgium
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Balasubramaniam D, Komives EA. Hydrogen-exchange mass spectrometry for the study of intrinsic disorder in proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1202-9. [PMID: 23099262 PMCID: PMC3600394 DOI: 10.1016/j.bbapap.2012.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/11/2012] [Accepted: 10/15/2012] [Indexed: 12/14/2022]
Abstract
Amide hydrogen/deuterium exchange detected by mass spectrometry (HXMS) is seeing wider use for the identification of intrinsically disordered parts of proteins. In this review, we discuss examples of how discovery of intrinsically disordered regions and their removal can aid in structure determination, biopharmaceutical quality control, the characterization of how post-translational modifications affect weak structuring of disordered regions, the study of coupled folding and binding, and the characterization of amyloid formation. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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Affiliation(s)
- Deepa Balasubramaniam
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378
| | - Elizabeth A. Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378
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Bereszczak JZ, Rose RJ, van Duijn E, Watts NR, Wingfield PT, Steven AC, Heck AJR. Epitope-distal effects accompany the binding of two distinct antibodies to hepatitis B virus capsids. J Am Chem Soc 2013; 135:6504-12. [PMID: 23597076 PMCID: PMC3658141 DOI: 10.1021/ja402023x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Infection of humans by hepatitis B virus (HBV) induces the copious production of antibodies directed against the capsid protein (Cp). A large variety of anticapsid antibodies have been identified that differ in their epitopes. These data, and the status of the capsid as a major clinical antigen, motivate studies to achieve a more detailed understanding of their interactions. In this study, we focused on the Fab fragments of two monoclonal antibodies, E1 and 3120. E1 has been shown to bind to the side of outward-protruding spikes whereas 3120 binds to the "floor" region of the capsid, between spikes. We used hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) to investigate the effects on HBV capsids of binding these antibodies. Conventionally, capsids loaded with saturating amounts of Fabs would be too massive to be readily amenable to HDX-MS. However, by focusing on the Cp protein, we were able to acquire deuterium uptake profiles covering the entire 149-residue sequence and reveal, in localized detail, changes in H/D exchange rates accompanying antibody binding. We find increased protection of the known E1 and 3120 epitopes on the capsid upon binding and show that regions distant from the epitopes are also affected. In particular, the α2a helix (residues 24-34) and the mobile C-terminus (residues 141-149) become substantially less solvent-exposed. Our data indicate that even at substoichiometric antibody binding an overall increase in the rigidity of the capsid is elicited, as well as a general dampening of its breathing motions.
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Affiliation(s)
- Jessica Z. Bereszczak
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
| | - Rebecca J. Rose
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
| | - Esther van Duijn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
| | - Norman R. Watts
- Protein Expression Laboratory, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Alasdair C. Steven
- Laboratory of Structural Biology, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- The Netherlands Proteomics Centre, The Netherlands
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Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes. Methods 2013; 59:372-81. [DOI: 10.1016/j.ymeth.2012.12.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/30/2012] [Accepted: 12/14/2012] [Indexed: 11/25/2022] Open
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Engen JR, Wales TE, Chen S, Marzluff EM, Hassell KM, Weis DD, Smithgall TE. Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. INT REV PHYS CHEM 2013; 32:96-127. [PMID: 23682200 DOI: 10.1080/0144235x.2012.751175] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Many proteins do not exist in a single rigid conformation. Protein motions, or dynamics, exist and in many cases are important for protein function. The analysis of protein dynamics relies on biophysical techniques that can distinguish simultaneously existing populations of molecules and their rates of interconversion. Hydrogen exchange (HX) detected by mass spectrometry (MS) is contributing to our understanding of protein motions by revealing unfolding and dynamics on a wide timescale, ranging from seconds to hours to days. In this review we discuss HX MS-based analyses of protein dynamics, using our studies of multi-domain kinases as examples. Using HX MS, we have successfully probed protein dynamics and unfolding in the isolated SH3, SH2 and kinase domains of the c-Src and Abl kinase families, as well as the role of inter- and intra-molecular interactions in the global control of kinase function. Coupled with high-resolution structural information, HX MS has proved to be a powerful and versatile tool for the analysis of the conformational dynamics in these kinase systems, and has provided fresh insight regarding the regulatory control of these important signaling proteins. HX MS studies of dynamics are applicable not only to the proteins we illustrate here, but to a very wide range of proteins and protein systems, and should play a role in both classification of and greater understanding of the prevalence of protein motion.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
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Malovichko MV, Sabo TM, Maurer MC. Ligand binding to anion-binding exosites regulates conformational properties of thrombin. J Biol Chem 2013; 288:8667-8678. [PMID: 23378535 DOI: 10.1074/jbc.m112.410829] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thrombin participates in coagulation, anticoagulation, and initiation of platelet activation. To fulfill its diverse roles and maintain hemostasis, this serine protease is regulated via the extended active site region and anion-binding exosites (ABEs) I and II. For the current project, amide proton hydrogen-deuterium exchange coupled with MALDI-TOF mass spectrometry was used to characterize ligand binding to individual exosites and to investigate the presence of exosite-active site and exosite-exosite interactions. PAR3(44-56) and PAR1(49-62) were observed to bind to thrombin ABE I and then to exhibit long range effects over to ABE II. By contrast, Hirudin(54-65) focused more on ABE I and did not transmit influences over to ABE II. Although these three ligands were each directed to ABE I, they did not promote the same conformational consequences. D-Phe-Pro-Arg-chloromethyl ketone inhibition at the thrombin active site led to further local and long range consequences to thrombin-ABE I ligand complexes with the autolysis loop often most affected. When Hirudin(54-65) was bound to ABE I, it was still possible to bind GpIbα(269-286) or fibrinogen γ'(410-427) to ABE II. Each ligand exerted its predominant influences on thrombin and also allowed interexosite communication. The results obtained support the proposal that thrombin is a highly dynamic protein. The transmission of ligand-specific local and long range conformational events is proposed to help regulate this multifunctional enzyme.
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Affiliation(s)
| | - T Michael Sabo
- Chemistry Department, University of Louisville, Louisville, Kentucky 40292
| | - Muriel C Maurer
- Chemistry Department, University of Louisville, Louisville, Kentucky 40292.
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Abstract
A major component of a hydrogen exchange mass spectrometry experiment is the analysis of protein and peptide mass spectra to yield information about deuterium incorporation. The processing of data that are produced includes the identification of each peptic peptide to create a master table/array of peptide sequence, retention time and retention time range, mass range, and undeuterated mass. The amount of deuterium incorporated into each of the peptides in this array must then be determined. Various software platforms have been developed in order to perform this specific type of data analysis. We describe the fundamental parameters to be considered at each step along the way and how data processing, either by an individual or by software, must approach the analysis.
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