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Simonsen S, Søgaard CK, Olsen JG, Otterlei M, Kragelund BB. The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery. Cell Mol Life Sci 2024; 81:245. [PMID: 38814467 DOI: 10.1007/s00018-024-05252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
DNA replication is a tightly coordinated event carried out by a multiprotein replication complex. An essential factor in the bacterial replication complex is the ring-shaped DNA sliding clamp, β-clamp, ensuring processive DNA replication and DNA repair through tethering of polymerases and DNA repair proteins to DNA. β -clamp is a hub protein with multiple interaction partners all binding through a conserved clamp binding sequence motif. Due to its central role as a DNA scaffold protein, β-clamp is an interesting target for antimicrobial drugs, yet little effort has been put into understanding the functional interactions of β-clamp. In this review, we scrutinize the β-clamp structure and dynamics, examine how its interactions with a plethora of binding partners are regulated through short linear binding motifs and discuss how contexts play into selection. We describe the dynamic process of clamp loading onto DNA and cover the recent advances in drug development targeting β-clamp. Despite decades of research in β-clamps and recent landmark structural insight, much remains undisclosed fostering an increased focus on this very central protein.
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Affiliation(s)
- Signe Simonsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Johan G Olsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Birthe B Kragelund
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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2
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Chen XR, Dixit K, Yang Y, McDermott MI, Imam HT, Bankaitis VA, Igumenova TI. A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated protein kinase C regulation. eLife 2024; 13:e92884. [PMID: 38687676 PMCID: PMC11060717 DOI: 10.7554/elife.92884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
Regulated hydrolysis of the phosphoinositide phosphatidylinositol(4,5)-bis-phosphate to diacylglycerol and inositol-1,4,5-P3 defines a major eukaryotic pathway for translation of extracellular cues to intracellular signaling circuits. Members of the lipid-activated protein kinase C isoenzyme family (PKCs) play central roles in this signaling circuit. One of the regulatory mechanisms employed to downregulate stimulated PKC activity is via a proteasome-dependent degradation pathway that is potentiated by peptidyl-prolyl isomerase Pin1. Here, we show that contrary to prevailing models, Pin1 does not regulate conventional PKC isoforms α and βII via a canonical cis-trans isomerization of the peptidyl-prolyl bond. Rather, Pin1 acts as a PKC binding partner that controls PKC activity via sequestration of the C-terminal tail of the kinase. The high-resolution structure of full-length Pin1 complexed to the C-terminal tail of PKCβII reveals that a novel bivalent interaction mode underlies the non-catalytic mode of Pin1 action. Specifically, Pin1 adopts a conformation in which it uses the WW and PPIase domains to engage two conserved phosphorylated PKC motifs, the turn motif and hydrophobic motif, respectively. Hydrophobic motif is a non-canonical Pin1-interacting element. The structural information combined with the results of extensive binding studies and experiments in cultured cells suggest that non-catalytic mechanisms represent unappreciated modes of Pin1-mediated regulation of AGC kinases and other key enzymes/substrates.
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Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Karuna Dixit
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Yuan Yang
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Mark I McDermott
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| | - Hasan Tanvir Imam
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Vytas A Bankaitis
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| | - Tatyana I Igumenova
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
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3
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Bonner X, Sondgeroth A, McCue A, Nicely N, Tripathy A, Spielvogel E, Moeser M, Ke R, Leiderman K, Joseph SB, Swanstrom R. Stoichiometry for entry and binding properties of the Env protein of R5 T cell-tropic HIV-1 and its evolutionary variant of macrophage-tropic HIV-1. mBio 2024; 15:e0032124. [PMID: 38426750 DOI: 10.1128/mbio.00321-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus type 1 typically requires a high density of CD4 for efficient entry as a mechanism to target CD4+ T cells (T-tropic), with CCR5 being used most often as the coreceptor. When target T cells are limiting, the virus can evolve to infect cells with a low density of CD4 such as macrophages (M-tropic). The entry phenotype is known to be encoded in the viral Env protein on the surface of the virus particle. Using data showing a dose response for infectivity based on CD4 surface density, we built a model consistent with T-tropic viruses requiring multiple CD4 molecules to mediate infection, whereas M-tropic viruses can infect cells using a single CD4 receptor molecule interaction. We also found that T-tropic viruses bound to the surface of cells with a low density of CD4 are released more slowly than M-tropic viruses which we modeled to be due to multiple interactions of the T-tropic virus with multiple CD4 molecules to allow the initial stable binding. Finally, we found that some M-tropic Env proteins, as the gp120 subunit, possess an enhanced affinity for CD4 compared with their T-tropic pair, indicating that the evolution of macrophage tropism can be reflected both in the closed Env trimer conformation on the virion surface and, in some cases, also in the open confirmation of gp120 Env. Collectively, these studies reveal differences in the stoichiometry of interaction of T-tropic and M-tropic viruses with CD4 and start to identify the basis of binding differences at the biochemical level. IMPORTANCE Human immunodeficiency virus type 1 normally targets CD4+ T cells for viral replication. When T cells are limiting, the virus can evolve to infect myeloid cells. The evolutionary step involves a change from requiring a high surface density of CD4 for entry to being able to infect cells with a low density of CD4, as is found on myeloid lineage cells such as macrophage and microglia. Viruses able to infect macrophages efficiently are most often found in the CNS late in the disease course, and such viruses may contribute to neurocognitive impairment. Here, we examine the CD4 binding properties of the viral Env protein to explore these two different entry phenotypes.
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Affiliation(s)
- Xavier Bonner
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amy Sondgeroth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amelia McCue
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathan Nicely
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ean Spielvogel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew Moeser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ruian Ke
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Karin Leiderman
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah B Joseph
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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4
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Katz M, Diskin R. The underlying mechanisms of arenaviral entry through matriglycan. Front Mol Biosci 2024; 11:1371551. [PMID: 38516183 PMCID: PMC10955480 DOI: 10.3389/fmolb.2024.1371551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
Matriglycan, a recently characterized linear polysaccharide, is composed of alternating xylose and glucuronic acid subunits bound to the ubiquitously expressed protein α-dystroglycan (α-DG). Pathogenic arenaviruses, like the Lassa virus (LASV), hijack this long linear polysaccharide to gain cellular entry. Until recently, it was unclear through what mechanisms LASV engages its matriglycan receptor to initiate infection. Additionally, how matriglycan is synthesized onto α-DG by the Golgi-resident glycosyltransferase LARGE1 remained enigmatic. Recent structural data for LARGE1 and for the LASV spike complex informs us about the synthesis of matriglycan as well as its usage as an entry receptor by arenaviruses. In this review, we discuss structural insights into the system of matriglycan generation and eventual recognition by pathogenic viruses. We also highlight the unique usage of matriglycan as a high-affinity host receptor compared with other polysaccharides that decorate cells.
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Affiliation(s)
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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5
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Kletzien OA, Wuttke DS, Batey RT. The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs. Biochemistry 2024. [PMID: 38329035 DOI: 10.1021/acs.biochem.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
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6
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van Weijsten MJ, Venrooij KR, Lelieveldt L, Kissel T, van Buijtenen E, van Dalen FJ, Verdoes M, Toes R, Bonger KM. Effect of Antigen Valency on Autoreactive B-Cell Targeting. Mol Pharm 2024; 21:481-490. [PMID: 37862070 PMCID: PMC10848265 DOI: 10.1021/acs.molpharmaceut.3c00527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023]
Abstract
Many autoimmune diseases are characterized by B cells that mistakenly recognize autoantigens and produce antibodies toward self-proteins. Current therapies aim to suppress the immune system, which is associated with adverse effects. An attractive and more specific approach is to target the autoreactive B cells selectively through their unique B-cell receptor (BCR) using an autoantigen coupled to an effector molecule able to modulate the B-cell activity. The cellular response upon antigen binding, such as receptor internalization, impacts the choice of effector molecule. In this study, we systematically investigated how a panel of well-defined mono-, di-, tetra-, and octavalent peptide antigens affects the binding, activation, and internalization of the BCR. To test our constructs, we used a B-cell line expressing a BCR against citrullinated antigens, the main autoimmune epitope in rheumatoid arthritis. We found that the dimeric antigen construct has superior targeting properties compared to those of its monomeric and multimeric counterparts, indicating that it can serve as a basis for future antigen-specific targeting studies for the treatment of RA.
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Affiliation(s)
- M. J. van Weijsten
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Institute
for Chemical Immunology, 6525 GA Nijmegen, The Netherlands
| | - K. R. Venrooij
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Institute
for Chemical Immunology, 6525 GA Nijmegen, The Netherlands
| | - L.P.W.M. Lelieveldt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Institute
for Chemical Immunology, 6525 GA Nijmegen, The Netherlands
| | - T. Kissel
- Department
of Rheumatology, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - E. van Buijtenen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - F. J. van Dalen
- Department
of Medical BioSciences, Radboudumc, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
- Institute
for Chemical Immunology, 6525 GA Nijmegen, The Netherlands
| | - M. Verdoes
- Department
of Medical BioSciences, Radboudumc, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
- Institute
for Chemical Immunology, 6525 GA Nijmegen, The Netherlands
| | - R.E.M. Toes
- Department
of Rheumatology, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - K. M. Bonger
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Institute
for Chemical Immunology, 6525 GA Nijmegen, The Netherlands
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7
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Romei MG, Leonard B, Katz ZB, Le D, Yang Y, Day ES, Koo CW, Sharma P, Bevers Iii J, Kim I, Dai H, Farahi F, Lin M, Shaw AS, Nakamura G, Sockolosky JT, Lazar GA. i-shaped antibody engineering enables conformational tuning of biotherapeutic receptor agonists. Nat Commun 2024; 15:642. [PMID: 38245524 PMCID: PMC10799922 DOI: 10.1038/s41467-024-44985-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
The ability to leverage antibodies to agonize disease relevant biological pathways has tremendous potential for clinical investigation. Yet while antibodies have been successful as antagonists, immune mediators, and targeting agents, they are not readily effective at recapitulating the biology of natural ligands. Among the important determinants of antibody agonist activity is the geometry of target receptor engagement. Here, we describe an engineering approach inspired by a naturally occurring Fab-Fab homotypic interaction that constrains IgG in a unique i-shaped conformation. i-shaped antibody (iAb) engineering enables potent intrinsic agonism of five tumor necrosis factor receptor superfamily (TNFRSF) targets. When applied to bispecific antibodies against the heterodimeric IL-2 receptor pair, constrained bispecific IgG formats recapitulate IL-2 agonist activity. iAb engineering provides a tool to tune agonist antibody function and this work provides a framework for the development of intrinsic antibody agonists with the potential for generalization across broad receptor classes.
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Affiliation(s)
- Matthew G Romei
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Brandon Leonard
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Zachary B Katz
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Daniel Le
- Department of Microchemistry, Proteomic, Lipidomics, and Next Generation Sequencing, Genentech Inc., South San Francisco, CA, USA
| | - Yanli Yang
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Eric S Day
- Department of Pharma Technical Development, Genentech Inc., South San Francisco, CA, USA
| | - Christopher W Koo
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Preeti Sharma
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Jack Bevers Iii
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Ingrid Kim
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Huiguang Dai
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Farzam Farahi
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - May Lin
- Department of Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Andrey S Shaw
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | | | - Greg A Lazar
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA.
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8
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Gormal RS, Martinez-Marmol R, Brooks AJ, Meunier FA. Location, location, location: Protein kinase nanoclustering for optimised signalling output. eLife 2024; 13:e93902. [PMID: 38206309 PMCID: PMC10783869 DOI: 10.7554/elife.93902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Protein kinases (PKs) are proteins at the core of cellular signalling and are thereby responsible for most cellular physiological processes and their regulations. As for all intracellular proteins, PKs are subjected to Brownian thermal energy that tends to homogenise their distribution throughout the volume of the cell. To access their substrates and perform their critical functions, PK localisation is therefore tightly regulated in space and time, relying upon a range of clustering mechanisms. These include post-translational modifications, protein-protein and protein-lipid interactions, as well as liquid-liquid phase separation, allowing spatial restriction and ultimately regulating access to their substrates. In this review, we will focus on key mechanisms mediating PK nanoclustering in physiological and pathophysiological processes. We propose that PK nanoclusters act as a cellular quantal unit of signalling output capable of integration and regulation in space and time. We will specifically outline the various super-resolution microscopy approaches currently used to elucidate the composition and mechanisms driving PK nanoscale clustering and explore the pathological consequences of altered kinase clustering in the context of neurodegenerative disorders, inflammation, and cancer.
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Affiliation(s)
- Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Ramon Martinez-Marmol
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Andrew J Brooks
- Frazer Institute, The University of QueenslandWoolloongabbaAustralia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
- School of Biomedical Sciences, The University of QueenslandSt LuciaAustralia
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9
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Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. Integrative spatiotemporal map of nucleocytoplasmic transport. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573409. [PMID: 38260487 PMCID: PMC10802240 DOI: 10.1101/2023.12.31.573409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The Nuclear Pore Complex (NPC) facilitates rapid and selective nucleocytoplasmic transport of molecules as large as ribosomal subunits and viral capsids. It is not clear how key emergent properties of this transport arise from the system components and their interactions. To address this question, we constructed an integrative coarse-grained Brownian dynamics model of transport through a single NPC, followed by coupling it with a kinetic model of Ran-dependent transport in an entire cell. The microscopic model parameters were fitted to reflect experimental data and theoretical information regarding the transport, without making any assumptions about its emergent properties. The resulting reductionist model is validated by reproducing several features of transport not used for its construction, such as the morphology of the central transporter, rates of passive and facilitated diffusion as a function of size and valency, in situ radial distributions of pre-ribosomal subunits, and active transport rates for viral capsids. The model suggests that the NPC functions essentially as a virtual gate whose flexible phenylalanine-glycine (FG) repeat proteins raise an entropy barrier to diffusion through the pore. Importantly, this core functionality is greatly enhanced by several key design features, including 'fuzzy' and transient interactions, multivalency, redundancy in the copy number of FG nucleoporins, exponential coupling of transport kinetics and thermodynamics in accordance with the transition state theory, and coupling to the energy-reliant RanGTP concentration gradient. These design features result in the robust and resilient rate and selectivity of transport for a wide array of cargo ranging from a few kilodaltons to megadaltons in size. By dissecting these features, our model provides a quantitative starting point for rationally modulating the transport system and its artificial mimics.
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10
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Baardsnes J, Paul-Roc B. SARS-CoV-2S-Protein-Ace2 Binding Analysis Using Surface Plasmon Resonance. Methods Mol Biol 2024; 2762:71-87. [PMID: 38315360 DOI: 10.1007/978-1-0716-3666-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Surface plasmon resonance (SPR) allows for the label-free determination of the binding affinity and rate constants of bimolecular interactions. Here, we describe the method used for the analysis of the Ace2-SARS-CoV2 S-protein interaction using indirect capture of the S-protein onto the SPR surface, and flowing monomeric Ace2. This method will allow for the determination of the rate constants for affinity, with additional analysis that is achievable using S-protein capture levels in conjunction with the sensorgram response for relative activity benchmarking.
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Affiliation(s)
- Jason Baardsnes
- Quality Attributes and Characterization, Human Health Therapeutics, National Research Council Canada, Montréal, QC, Canada.
| | - Béatrice Paul-Roc
- Quality Attributes and Characterization, Human Health Therapeutics, National Research Council Canada, Montréal, QC, Canada
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11
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Zak AJ, Hoang T, Yee CM, Rizvi SM, Prabhu P, Wen F. Pseudotyping Improves the Yield of Functional SARS-CoV-2 Virus-like Particles (VLPs) as Tools for Vaccine and Therapeutic Development. Int J Mol Sci 2023; 24:14622. [PMID: 37834067 PMCID: PMC10572262 DOI: 10.3390/ijms241914622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/08/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Virus-like particles (VLPs) have been proposed as an attractive tool in SARS-CoV-2 vaccine development, both as (1) a vaccine candidate with high immunogenicity and low reactogenicity and (2) a substitute for live virus in functional and neutralization assays. Though multiple SARS-CoV-2 VLP designs have already been explored in Sf9 insect cells, a key parameter ensuring VLPs are a viable platform is the VLP spike yield (i.e., spike protein content in VLP), which has largely been unreported. In this study, we show that the common strategy of producing SARS-CoV-2 VLPs by expressing spike protein in combination with the native coronavirus membrane and/or envelope protein forms VLPs, but at a critically low spike yield (~0.04-0.08 mg/L). In contrast, fusing the spike ectodomain to the influenza HA transmembrane domain and cytoplasmic tail and co-expressing M1 increased VLP spike yield to ~0.4 mg/L. More importantly, this increased yield translated to a greater VLP spike antigen density (~96 spike monomers/VLP) that more closely resembles that of native SARS-CoV-2 virus (~72-144 Spike monomers/virion). Pseudotyping further allowed for production of functional alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), and omicron (B.1.1.529) SARS-CoV-2 VLPs that bound to the target ACE2 receptor. Finally, we demonstrated the utility of pseudotyped VLPs to test neutralizing antibody activity using a simple, acellular ELISA-based assay performed at biosafety level 1 (BSL-1). Taken together, this study highlights the advantage of pseudotyping over native SARS-CoV-2 VLP designs in achieving higher VLP spike yield and demonstrates the usefulness of pseudotyped VLPs as a surrogate for live virus in vaccine and therapeutic development against SARS-CoV-2 variants.
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Affiliation(s)
| | | | | | | | | | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA (P.P.)
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12
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Chen XR, Dixit K, Yang Y, McDermott MI, Imam HT, Bankaitis VA, Igumenova TI. A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated Protein Kinase C regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558341. [PMID: 37781616 PMCID: PMC10541119 DOI: 10.1101/2023.09.18.558341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Regulated hydrolysis of the phosphoinositide phosphatidylinositol(4,5)-bis-phosphate to diacylglycerol and inositol-1,4,5-P3 defines a major eukaryotic pathway for translation of extracellular cues to intracellular signaling circuits. Members of the lipid-activated protein kinase C isoenzyme family (PKCs) play central roles in this signaling circuit. One of the regulatory mechanisms employed to downregulate stimulated PKC activity is via a proteasome-dependent degradation pathway that is potentiated by peptidyl-prolyl isomerase Pin1. Here, we show that contrary to prevailing models, Pin1 does not regulate conventional PKC isoforms α and βII via a canonical cis-trans isomerization of the peptidyl-prolyl bond. Rather, Pin1 acts as a PKC binding partner that controls PKC activity via sequestration of the C-terminal tail of the kinase. The high-resolution structure of Pin1 complexed to the C-terminal tail of PKCβII reveals that a novel bivalent interaction mode underlies the non-catalytic mode of Pin1 action. Specifically, Pin1 adopts a compact conformation in which it engages two conserved phosphorylated PKC motifs, the turn motif and hydrophobic motif, the latter being a non-canonical Pin1-interacting element. The structural information, combined with the results of extensive binding studies and in vivo experiments suggest that non-catalytic mechanisms represent unappreciated modes of Pin1-mediated regulation of AGC kinases and other key enzymes/substrates.
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13
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Jacobsen NL, Bloch M, Millard PS, Ruidiaz SF, Elsborg JD, Boomsma W, Hendus‐Altenburger R, Hartmann‐Petersen R, Kragelund BB. Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro. Protein Sci 2023; 32:e4733. [PMID: 37463013 PMCID: PMC10443397 DOI: 10.1002/pro.4733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) are often multifunctional and frequently posttranslationally modified. Deleted in split hand/split foot 1 (Dss1-Sem1 in budding yeast) is a highly multifunctional IDP associated with a range of protein complexes. However, it remains unknown if the different functions relate to different modified states. In this work, we show that Schizosaccharomyces pombe Dss1 is a substrate for casein kinase 2 in vitro, and we identify three phosphorylated threonines in its linker region separating two known disordered ubiquitin-binding motifs. Phosphorylations of the threonines had no effect on ubiquitin-binding but caused a slight destabilization of the C-terminal α-helix and mediated a direct interaction with the forkhead-associated (FHA) domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). The phosphorylation sites are not conserved and are absent in human Dss1. Sequence analyses revealed that the Txx(E/D) motif, which is important for phosphorylation and Dma1 binding, is not linked to certain branches of the evolutionary tree. Instead, we find that the motif appears randomly, supporting the mechanism of ex nihilo evolution of novel motifs. In support of this, other threonine-based motifs, although frequent, are nonconserved in the linker, pointing to additional functions connected to this region. We suggest that Dss1 acts as an adaptor protein that docks to Dma1 via the phosphorylated FHA-binding motifs, while the C-terminal α-helix is free to bind mitotic septins, thereby stabilizing the complex. The presence of Txx(D/E) motifs in the disordered regions of certain septin subunits may be of further relevance to the formation and stabilization of these complexes.
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Affiliation(s)
- Nina L. Jacobsen
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Magnus Bloch
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Peter S. Millard
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Sarah F. Ruidiaz
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
| | - Jonas D. Elsborg
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagen ØDenmark
| | | | - Rasmus Hartmann‐Petersen
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
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14
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Yin T, Xu L, Gil B, Merali N, Sokolikova MS, Gaboriau DCA, Liu DSK, Muhammad Mustafa AN, Alodan S, Chen M, Txoperena O, Arrastua M, Gomez JM, Ontoso N, Elicegui M, Torres E, Li D, Mattevi C, Frampton AE, Jiao LR, Ramadan S, Klein N. Graphene Sensor Arrays for Rapid and Accurate Detection of Pancreatic Cancer Exosomes in Patients' Blood Plasma Samples. ACS NANO 2023; 17:14619-14631. [PMID: 37470391 PMCID: PMC10416564 DOI: 10.1021/acsnano.3c01812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
Biosensors based on graphene field effect transistors (GFETs) have the potential to enable the development of point-of-care diagnostic tools for early stage disease detection. However, issues with reproducibility and manufacturing yields of graphene sensors, but also with Debye screening and unwanted detection of nonspecific species, have prevented the wider clinical use of graphene technology. Here, we demonstrate that our wafer-scalable GFETs array platform enables meaningful clinical results. As a case study of high clinical relevance, we demonstrate an accurate and robust portable GFET array biosensor platform for the detection of pancreatic ductal adenocarcinoma (PDAC) in patients' plasma through specific exosomes (GPC-1 expression) within 45 min. In order to facilitate reproducible detection in blood plasma, we optimized the analytical performance of GFET biosensors via the application of an internal control channel and the development of an optimized test protocol. Based on samples from 18 PDAC patients and 8 healthy controls, the GFET biosensor arrays could accurately discriminate between the two groups while being able to detect early cancer stages including stages 1 and 2. Furthermore, we confirmed the higher expression of GPC-1 and found that the concentration in PDAC plasma was on average more than 1 order of magnitude higher than in healthy samples. We found that these characteristics of GPC-1 cancerous exosomes are responsible for an increase in the number of target exosomes on the surface of graphene, leading to an improved signal response of the GFET biosensors. This GFET biosensor platform holds great promise for the development of an accurate tool for the rapid diagnosis of pancreatic cancer.
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Affiliation(s)
- Tianyi Yin
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Lizhou Xu
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Bruno Gil
- Hamlyn
Centre, Imperial College London, London SW7 2AZ, U.K.
| | - Nabeel Merali
- Oncology
Section, Surrey Cancer Research Institute, Department of Clinical
and Experimental Medicine, FHMS, University
of Surrey, The Leggett Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
- HPB
Surgical Unit, Royal Surrey NHS Foundation Trust, Guildford, Surrey GU2 7XX, U.K.
- Minimal Access
Therapy Training Unit (MATTU), University
of Surrey, The Leggett
Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
| | | | - David C. A. Gaboriau
- Facility
for Imaging By Light Microscopy, Imperial
College London, London SW7 2AZ, U.K.
| | - Daniel S. K. Liu
- Department
of Surgery & Cancer, Imperial College
London, Hammersmith Hospital
Campus, London W12 0NN, U.K.
- HPB
Surgical Unit, Imperial College Healthcare NHS Trust, Hammersmith
Hospital, London W12 0HS, U.K.
| | - Ahmad Nizamuddin Muhammad Mustafa
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
- FTKEE,
Universiti Teknikal Malaysia Melaka, 76100 Durian Tunggal, Melaka, Malaysia
| | - Sarah Alodan
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Michael Chen
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Oihana Txoperena
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - María Arrastua
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Juan Manuel Gomez
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Nerea Ontoso
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Marta Elicegui
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Elias Torres
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Danyang Li
- Research
Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
| | - Cecilia Mattevi
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Adam E. Frampton
- Oncology
Section, Surrey Cancer Research Institute, Department of Clinical
and Experimental Medicine, FHMS, University
of Surrey, The Leggett Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
- HPB
Surgical Unit, Royal Surrey NHS Foundation Trust, Guildford, Surrey GU2 7XX, U.K.
- Minimal Access
Therapy Training Unit (MATTU), University
of Surrey, The Leggett
Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
- Department
of Surgery & Cancer, Imperial College
London, Hammersmith Hospital
Campus, London W12 0NN, U.K.
| | - Long R. Jiao
- Department
of Surgery & Cancer, Imperial College
London, Hammersmith Hospital
Campus, London W12 0NN, U.K.
| | - Sami Ramadan
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Norbert Klein
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
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15
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Laroque S, Garcia Maset R, Hapeshi A, Burgevin F, Locock KES, Perrier S. Synthetic Star Nanoengineered Antimicrobial Polymers as Antibiofilm Agents: Bacterial Membrane Disruption and Cell Aggregation. Biomacromolecules 2023. [PMID: 37300501 DOI: 10.1021/acs.biomac.3c00150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance has become a worldwide issue, with multiresistant bacterial strains emerging at an alarming rate. Multivalent antimicrobial polymer architectures such as bottle brush or star polymers have shown great potential, as they could lead to enhanced binding and interaction with the bacterial cell membrane. In this study, a library of amphiphilic star copolymers and their linear copolymer equivalents, based on acrylamide monomers, were synthesized via RAFT polymerization. Their monomer distribution and molecular weight were varied. Subsequently, their antimicrobial activity toward a Gram-negative bacterium (Pseudomonas aeruginosa PA14) and a Gram-positive bacterium (Staphylococcus aureus USA300) and their hemocompatibility were investigated. The statistical star copolymer, S-SP25, showed an improved antimicrobial activity compared to its linear equivalent againstP. aeruginosaPA14. The star architecture enhanced its antimicrobial activity, causing bacterial cell aggregation, as revealed via electron microscopy. However, it also induced increased red blood cell aggregation compared to its linear equivalents. Changing/shifting the position of the cationic block to the core of the structure prevents the cell aggregation effect while maintaining a potent antimicrobial activity for the smallest star copolymer. Finally, this compound showed antibiofilm properties against a robust in vitro biofilm model.
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Affiliation(s)
- Sophie Laroque
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Ramón Garcia Maset
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Alexia Hapeshi
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Fannie Burgevin
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | | | - Sébastien Perrier
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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16
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Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
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Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
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17
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Zeder-Lutz G, Bornert O, Fellmann-Clauss R, Knittel-Obrecht A, Tranchant T, Bouteben S, Kaeffer J, Quillet R, Villa P, Wagner R, Lecat S, Simonin F. Characterization of anti-GASP motif antibodies that inhibit the interaction between GPRASP1 and G protein-coupled receptors. Anal Biochem 2023; 665:115062. [PMID: 36731712 DOI: 10.1016/j.ab.2023.115062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023]
Abstract
G protein-coupled receptor associated sorting protein 1 (GPRASP1) belongs to a family of 10 proteins that display sequence homologies in their C-terminal region. Several members including GPRASP1 also display a short repeated sequence called the GASP motif that is critically involved in protein-protein interactions with G protein-coupled receptors (GPCRs). Here, we characterized anti-GASP motif antibodies and investigated their potential inhibitory functions. We first showed that our in-house anti-GPRASP1 rabbit polyclonal serum contains anti-GASP motif antibodies and purified them by affinity chromatography. We further showed that these antibodies can detect GPRASP1 and GPRASP2 in Western blot, immunoprecipitation and immunofluorescence experiments while a mutant of GPRASP2, in which the most conserved hydrophobic core of the GASP motifs is mutated, was no more detected. Further characterization of anti-GASP motif antibodies by ELISA and Surface Plasmon Resonance assays suggests that GASP motifs function as multivalent epitopes. Finally, we set-up an Amplified Luminescent Proximity Homogeneous AlphaScreen® assay to detect the interaction between purified ADRB2 receptor and the central domain of GPRASP1 and showed that anti-GASP motif antibodies efficiently inhibit this interaction. Altogether, our results suggest that anti-GASP motif antibodies could represent a valuable tool to neutralize the interaction of GPRASP1 and GPRASP2 with different GPCRs.
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Affiliation(s)
- Gabrielle Zeder-Lutz
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Olivier Bornert
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Rosine Fellmann-Clauss
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Adeline Knittel-Obrecht
- Plateforme de Chimie Biologique integrative de Strasbourg, UAR3286, CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Thibaud Tranchant
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Sarah Bouteben
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France; Biotechnology and Cell Signaling, IMPReSs facility for Integral Membrane Proteins Research and Services, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Juliette Kaeffer
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Raphaëlle Quillet
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Pascal Villa
- Plateforme de Chimie Biologique integrative de Strasbourg, UAR3286, CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Renaud Wagner
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France; Biotechnology and Cell Signaling, IMPReSs facility for Integral Membrane Proteins Research and Services, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Sandra Lecat
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Frédéric Simonin
- Biotechnology and Cell Signaling, UMR7242 CNRS, University of Strasbourg, Illkirch-Graffenstaden, France.
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18
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Sladewski TE, Campbell PC, Billington N, D'Ordine A, Cole JL, de Graffenried CL. Cytokinesis in Trypanosoma brucei relies on an orphan kinesin that dynamically crosslinks microtubules. Curr Biol 2023; 33:899-911.e5. [PMID: 36787745 PMCID: PMC10023446 DOI: 10.1016/j.cub.2023.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023]
Abstract
Many single-celled eukaryotes have complex cell morphologies defined by microtubules arranged into higher-order structures. The auger-like shape of the parasitic protist Trypanosoma brucei (T. brucei) is mediated by a parallel array of microtubules that underlies the plasma membrane. The subpellicular array must be partitioned and segregated using a microtubule-based mechanism during cell division. We previously identified an orphan kinesin, KLIF, that localizes to the ingressing cleavage furrow and is essential for the completion of cytokinesis. We have characterized the biophysical properties of a truncated KLIF construct in vitro to gain mechanistic insight into the function of this novel kinesin. We find that KLIF is a non-processive dimeric kinesin that dynamically crosslinks microtubules. Microtubules crosslinked by KLIF in an antiparallel orientation are translocated relative to one another, while microtubules crosslinked parallel to one another remain static, resulting in the formation of organized parallel bundles. In addition, we find that KLIF stabilizes the alignment of microtubule plus ends. These features provide a mechanistic understanding for how KLIF functions to form a new pole of aligned microtubule plus ends that defines the shape of the new cell posterior, which is an essential requirement for the completion of cytokinesis in T. brucei.
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Affiliation(s)
- Thomas E Sladewski
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Paul C Campbell
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Neil Billington
- Laboratory of Physiology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda 20892, USA
| | - Alexandra D'Ordine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - James L Cole
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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19
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Flowers D, Bassen D, Kapitanov GI, Marcantonio D, Burke JM, Apgar JF, Betts A, Hua F. A next generation mathematical model for the in vitro to clinical translation of T-cell engagers. J Pharmacokinet Pharmacodyn 2023; 50:215-227. [PMID: 36790614 DOI: 10.1007/s10928-023-09846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023]
Abstract
T-cell engager (TCE) molecules activate the immune system and direct it to kill tumor cells. The key mechanism of action of TCEs is to crosslink CD3 on T cells and tumor associated antigens (TAAs) on tumor cells. The formation of this trimolecular complex (i.e. trimer) mimics the immune synapse, leading to therapeutic-dependent T-cell activation and killing of tumor cells. Computational models supporting TCE development must predict trimer formation accurately. Here, we present a next-generation two-step binding mathematical model for TCEs to describe trimer formation. Specifically, we propose to model the second binding step with trans-avidity and as a two-dimensional (2D) process where the reactants are modeled as the cell-surface density. Compared to the 3D binding model where the reactants are described in terms of concentration, the 2D model predicts less sensitivity of trimer formation to varying cell densities, which better matches changes in EC50 from in vitro cytotoxicity assay data with varying E:T ratios. In addition, when translating in vitro cytotoxicity data to predict in vivo active clinical dose for blinatumomab, the choice of model leads to a notable difference in dose prediction. The dose predicted by the 2D model aligns better with the approved clinical dose and the prediction is robust under variations in the in vitro to in vivo translation assumptions. In conclusion, the 2D model with trans-avidity to describe trimer formation is an improved approach for TCEs and is likely to produce more accurate predictions to support TCE development.
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Affiliation(s)
| | | | | | | | | | | | | | - Fei Hua
- Applied BioMath, Concord, MA, USA.
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20
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Macdonald R, Mahoney BJ, Soule J, Goring AK, Ford J, Loo JA, Cascio D, Clubb RT. The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme-iron from human hemoglobin. Proc Natl Acad Sci U S A 2023; 120:e2211939120. [PMID: 36693107 PMCID: PMC9945957 DOI: 10.1073/pnas.2211939120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023] Open
Abstract
Streptococcus pyogenes (group A Streptococcus) is a clinically important microbial pathogen that requires iron in order to proliferate. During infections, S. pyogenes uses the surface displayed Shr receptor to capture human hemoglobin (Hb) and acquires its iron-laden heme molecules. Through a poorly understood mechanism, Shr engages Hb via two structurally unique N-terminal Hb-interacting domains (HID1 and HID2) which facilitate heme transfer to proximal NEAr Transporter (NEAT) domains. Based on the results of X-ray crystallography, small angle X-ray scattering, NMR spectroscopy, native mass spectrometry, and heme transfer experiments, we propose that Shr utilizes a "cap and release" mechanism to gather heme from Hb. In the mechanism, Shr uses the HID1 and HID2 modules to preferentially recognize only heme-loaded forms of Hb by contacting the edges of its protoporphyrin rings. Heme transfer is enabled by significant receptor dynamics within the Shr-Hb complex which function to transiently uncap HID1 from the heme bound to Hb's β subunit, enabling the gated release of its relatively weakly bound heme molecule and subsequent capture by Shr's NEAT domains. These dynamics may maximize the efficiency of heme scavenging by S. pyogenes, enabling it to preferentially recognize and remove heme from only heme-loaded forms of Hb that contain iron.
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Affiliation(s)
- Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Brendan J. Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Jess Soule
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Jordan Ford
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
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21
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Ito K, Matsuda Y, Mine A, Miyairi K, Kikuchi Y, Konishi A. Bacterially Secretable Single-Chain Tandem Macrocyclic Peptides for High Affinity and Inhibitory Activity. Chembiochem 2023; 24:e202200599. [PMID: 36409290 DOI: 10.1002/cbic.202200599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The inhibition of protein-protein interactions (PPIs) is an effective approach for therapy. Owing to their large binding surface areas to target proteins, macrocyclic peptides are suitable molecules for PPI inhibition. In this study, we developed single-chain tandem macrocyclic peptides (STaMPtides) that inhibits the vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2). They were artificially designed to comprise two different VEGFR2-binding macrocyclic peptides linked in tandem by peptide linkers and secreted by Corynebacterium glutamicum. Most potent VEGFR2-inhibitory STaMPtides with length-optimized linkers exhibited >1000 times stronger inhibitory activity than their parental monomeric peptides, possibly due to the avidity effect of heterodimerization. Our approach of using STaMPtides for PPI inhibition may be used to inhibit other extracellular factors, such as growth factors and cytokines.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
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22
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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23
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Zambo B, Morlet B, Negroni L, Trave G, Gogl G. Native holdup (nHU) to measure binding affinities from cell extracts. SCIENCE ADVANCES 2022; 8:eade3828. [PMID: 36542723 PMCID: PMC9770967 DOI: 10.1126/sciadv.ade3828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Characterizing macromolecular interactions is essential for understanding cellular processes, yet most methods currently used to detect protein interactions from cells are qualitative. Here, we introduce the native holdup (nHU) approach to estimate equilibrium binding constants of protein interactions directly from cell extracts. Compared to other pull-down-based assays, nHU requires less sample preparation and can be coupled to any analytical methods as readouts, such as Western blotting or mass spectrometry. We use nHU to explore interactions of SNX27, a cargo adaptor of the retromer complex and find good agreement between in vitro affinities and those measured directly from cell extracts using nHU. We discuss the strengths and limitations of nHU and provide simple protocols that can be implemented in most laboratories.
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Affiliation(s)
- Boglarka Zambo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Gilles Trave
- Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
- Corresponding author. (G.T.); (G.G.)
| | - Gergo Gogl
- Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
- Corresponding author. (G.T.); (G.G.)
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24
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Bila H, Paloja K, Caroprese V, Kononenko A, Bastings MM. Multivalent Pattern Recognition through Control of Nano-Spacing in Low-Valency Super-Selective Materials. J Am Chem Soc 2022; 144:21576-21586. [DOI: 10.1021/jacs.2c08529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Hale Bila
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Kaltrina Paloja
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Vincenzo Caroprese
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Artem Kononenko
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Maartje M.C. Bastings
- Programmable Biomaterials Laboratory (PBL), Institute of Materials (IMX), Interfaculty Bioengineering Institute (IBI), School of Engineering (STI), Ecole Polytechnique Fédérale Lausanne (EPFL), Lausanne 1015, Switzerland
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25
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Ebrahimi F, Noaparast Z, Abedi SM, Hosseinimehr SJ. Homodimer 99mTc-HYNIC-E(SSSLTVPWY) 2 peptide improved HER2-overexpressed tumor targeting and imaging. Med Oncol 2022; 39:204. [PMID: 36175805 DOI: 10.1007/s12032-022-01798-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/15/2022] [Indexed: 06/16/2023]
Abstract
We hypothesized that a novel design of the LTVPWY (LY) peptide might exhibit a great potential for improving binding affinity and targeting HER2-overexpressed tumors. Hence, new dimer construction of 99mTc-labeled LY [99mTc-HYNIC-E(SSSLTVPWY)2] (99mTc-DLY) was introduced. Afterward, a head-to-head comparison of in vitro and in vivo experiments was performed between 99mTc-DLY and 99mTc-HYNIC-SSSLTVPWY as the monomer analog. The blocking dosage of trastuzumab reduced the uptake of the dimer about 20% more efficiently than the monomer in the SKOV-3 cell line. A twofold increase in competitive binding affinity and biological half-life was observed for 99mTc-DLY. The ovarian-tumor-bearing mice were detected with high contrast where the tumor-to-muscle ratio of 99mTc-DLY was notably increased about 40% using a gamma camera. The biodistribution experiment revealed an approximately 10% enhancement in tumor/blood, tumor/muscle, and tumor/bone ratios for the dimer. More rapid blood clearance was another achievement of the homodimer design. Overall, 99mTc-DLY successfully affected the pharmacokinetics and consequently the visualization of HER2-overexpressing tumors.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zohreh Noaparast
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Mohammad Abedi
- Department of Radiology and Nuclear Medicine, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Jalal Hosseinimehr
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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26
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Dreier JE, Prestel A, Martins JM, Brøndum SS, Nielsen O, Garbers AE, Suga H, Boomsma W, Rogers JM, Hartmann-Petersen R, Kragelund BB. A context-dependent and disordered ubiquitin-binding motif. Cell Mol Life Sci 2022; 79:484. [PMID: 35974206 PMCID: PMC9381478 DOI: 10.1007/s00018-022-04486-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023]
Abstract
Ubiquitin is a small, globular protein that is conjugated to other proteins as a posttranslational event. A palette of small, folded domains recognizes and binds ubiquitin to translate and effectuate this posttranslational signal. Recent computational studies have suggested that protein regions can recognize ubiquitin via a process of folding upon binding. Using peptide binding arrays, bioinformatics, and NMR spectroscopy, we have uncovered a disordered ubiquitin-binding motif that likely remains disordered when bound and thus expands the palette of ubiquitin-binding proteins. We term this motif Disordered Ubiquitin-Binding Motif (DisUBM) and find it to be present in many proteins with known or predicted functions in degradation and transcription. We decompose the determinants of the motif showing it to rely on features of aromatic and negatively charged residues, and less so on distinct sequence positions in line with its disordered nature. We show that the affinity of the motif is low and moldable by the surrounding disordered chain, allowing for an enhanced interaction surface with ubiquitin, whereby the affinity increases ~ tenfold. Further affinity optimization using peptide arrays pushed the affinity into the low micromolar range, but compromised context dependence. Finally, we find that DisUBMs can emerge from unbiased screening of randomized peptide libraries, featuring in de novo cyclic peptides selected to bind ubiquitin chains. We suggest that naturally occurring DisUBMs can recognize ubiquitin as a posttranslational signal to act as affinity enhancers in IDPs that bind to folded and ubiquitylated binding partners.
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Affiliation(s)
- Jesper E Dreier
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - João M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Sebastian S Brøndum
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Olaf Nielsen
- Functional Genomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna E Garbers
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen Ø, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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27
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Macadangdang BR, Makanani SK, Miller JF. Accelerated Evolution by Diversity-Generating Retroelements. Annu Rev Microbiol 2022; 76:389-411. [PMID: 35650669 DOI: 10.1146/annurev-micro-030322-040423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Diversity-generating retroelements (DGRs) create vast amounts of targeted, functional diversity by facilitating the rapid evolution of ligand-binding protein domains. Thousands of DGRs have been identified in bacteria, archaea, and their respective viruses. They are broadly distributed throughout the microbial world, with enrichment observed in certain taxa and environments. The diversification machinery works through a novel mechanism termed mutagenic retrohoming, whereby nucleotide sequence information is copied from an invariant DNA template repeat (TR) into an RNA intermediate, selectively mutagenized at TR adenines during cDNA synthesis by a DGR-encoded reverse transcriptase, and transferred to a variable repeat (VR) region within a variable-protein gene (54). This unidirectional flow of information leaves TR-DNA sequences unmodified, allowing for repeated rounds of mutagenic retrohoming to optimize variable-protein function. DGR target genes are often modular and can encode one or more of a wide variety of discrete functional domains appended to a diversifiable ligand-binding motif. Bacterial variable proteins often localize to cell surfaces, although a subset appear to be cytoplasmic, while phage-encoded DGRs commonly diversify tail fiber-associated receptor-binding proteins. Here, we provide a comprehensive review of the mechanism and consequences of accelerated protein evolution by these unique and beneficial genetic elements. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Benjamin R Macadangdang
- Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California, USA; .,California NanoSystems Institute, University of California, Los Angeles, California, USA
| | - Sara K Makanani
- California NanoSystems Institute, University of California, Los Angeles, California, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; .,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA;
| | - Jeff F Miller
- California NanoSystems Institute, University of California, Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA; .,Molecular Biology Institute, University of California, Los Angeles, California, USA
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28
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Pone EJ, Hernandez-Davies JE, Jan S, Silzel E, Felgner PL, Davies DH. Multimericity Amplifies the Synergy of BCR and TLR4 for B Cell Activation and Antibody Class Switching. Front Immunol 2022; 13:882502. [PMID: 35663959 PMCID: PMC9161726 DOI: 10.3389/fimmu.2022.882502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Sustained signaling through the B cell antigen receptor (BCR) is thought to occur only when antigen(s) crosslink or disperse multiple BCR units, such as by multimeric antigens found on the surfaces of viruses or bacteria. B cell-intrinsic Toll-like receptor (TLR) signaling synergizes with the BCR to induce and shape antibody production, hallmarked by immunoglobulin (Ig) class switch recombination (CSR) of constant heavy chains from IgM/IgD to IgG, IgA or IgE isotypes, and somatic hypermutation (SHM) of variable heavy and light chains. Full B cell differentiation is essential for protective immunity, where class switched high affinity antibodies neutralize present pathogens, memory B cells are held in reserve for future encounters, and activated B cells also serve as semi-professional APCs for T cells. But the rules that fine-tune B cell differentiation remain partially understood, despite their being essential for naturally acquired immunity and for guiding vaccine development. To address this in part, we have developed a cell culture system using splenic B cells from naive mice stimulated with several biotinylated ligands and antibodies crosslinked by streptavidin reagents. In particular, biotinylated lipopolysaccharide (LPS), a Toll-like receptor 4 (TLR4) agonist, and biotinylated anti-IgM were pre-assembled (multimerized) using streptavidin, or immobilized on nanoparticles coated with streptavidin, and used to active B cells in this precisely controlled, high throughput assay. Using B cell proliferation and Ig class switching as metrics for successful B cell activation, we show that the stimuli are both synergistic and dose-dependent. Crucially, the multimerized immunoconjugates are most active over a narrow concentration range. These data suggest that multimericity is an essential requirement for B cell BCR/TLRs ligands, and clarify basic rules for B cell activation. Such studies highlight the importance in determining the choice of single vs multimeric formats of antigen and PAMP agonists during vaccine design and development.
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29
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Imran A, Moyer BS, Wolfe AJ, Cosgrove MS, Makarov DE, Movileanu L. Interplay of Affinity and Surface Tethering in Protein Recognition. J Phys Chem Lett 2022; 13:4021-4028. [PMID: 35485934 PMCID: PMC9106920 DOI: 10.1021/acs.jpclett.2c00621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/27/2022] [Indexed: 05/10/2023]
Abstract
Surface-tethered ligand-receptor complexes are key components in biological signaling and adhesion. They also find increasing utility in single-molecule assays and biotechnological applications. Here, we study the real-time binding kinetics between various surface-immobilized peptide ligands and their unrestrained receptors. A long peptide tether increases the association of ligand-receptor complexes, experimentally proving the fly casting mechanism where the disorder accelerates protein recognition. On the other hand, a short peptide tether enhances the complex dissociation. Notably, the rate constants measured for the same receptor, but under different spatial constraints, are strongly correlated to one another. Furthermore, this correlation can be used to predict how surface tethering on a ligand-receptor complex alters its binding kinetics. Our results have immediate implications in the broad areas of biomolecular recognition, intrinsically disordered proteins, and biosensor technology.
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Affiliation(s)
- Ali Imran
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor
Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United
States
- Lewis
School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor
Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United
States
- Lewis
School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
- Department
of Chemistry, State University of New York
College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Michael S. Cosgrove
- Department
of Biochemistry and Molecular Biology, State
University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving
Avenue, Syracuse, New York 13210, United States
| | - Dmitrii E. Makarov
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Oden
Institute
for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United
States
- The BioInspired
Institute, Syracuse University, Syracuse, New York 13244, United States
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30
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Ebrahimi F, Hosseinimehr SJ. Homomultimer strategy for improvement of radiolabeled peptides and antibody fragments in tumor targeting. Curr Med Chem 2022; 29:4923-4957. [PMID: 35450521 DOI: 10.2174/0929867329666220420131836] [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: 11/23/2021] [Revised: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
Abstract
A homomultimeric radioligand is composed of multiple identical ligands connected to the linker and radionuclide to detect a variety of overexpressed receptors on cancer cells. Multimer strategy holds great potential for introducing new radiotracers based on peptide and monoclonal antibody (mAb) derivatives in molecular imaging and therapy. It offers a reliable procedure for the preparation of biological-based targeting with diverse affinities and pharmacokinetics. In this context, we provide a useful summary and interpretation of the main results by a comprehensive look at multimeric radiopharmaceuticals in nuclear oncology. Therefore, there will be explanations for the strategy mechanisms and the main variables affecting the biodistribution results. The discussion is followed by highlights of recent work in the targeting of various types of receptors. The consequences are expressed based on comparing some parameters between monomer and multimer counterparts in each relevant section.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Jalal Hosseinimehr
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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31
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Dunlap T, Cao Y. Physiological Considerations for Modeling in vivo Antibody-Target Interactions. Front Pharmacol 2022; 13:856961. [PMID: 35281913 PMCID: PMC8912916 DOI: 10.3389/fphar.2022.856961] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The number of therapeutic antibodies in development pipelines is increasing rapidly. Despite superior success rates relative to small molecules, therapeutic antibodies still face many unique development challenges. There is often a translational gap from their high target affinity and specificity to the therapeutic effects. Tissue microenvironment and physiology critically influence antibody-target interactions contributing to apparent affinity alterations and dynamic target engagement. The full potential of therapeutic antibodies will be further realized by contextualizing antibody-target interactions under physiological conditions. Here we review how local physiology such as physical stress, biological fluid, and membrane characteristics could influence antibody-target association, dissociation, and apparent affinity. These physiological factors in the early development of therapeutic antibodies are valuable toward rational antibody engineering, preclinical candidate selection, and lead optimization.
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Affiliation(s)
- Tyler Dunlap
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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32
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Verkhivker G. Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering. Int J Mol Sci 2022; 23:ijms23062928. [PMID: 35328351 PMCID: PMC8951411 DOI: 10.3390/ijms23062928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Nanobodies provide important advantages over traditional antibodies, including their smaller size and robust biochemical properties such as high thermal stability, high solubility, and the ability to be bioengineered into novel multivalent, multi-specific, and high-affinity molecules, making them a class of emerging powerful therapies against SARS-CoV-2. Recent research efforts on the design, protein engineering, and structure-functional characterization of nanobodies and their binding with SARS-CoV-2 S proteins reflected a growing realization that nanobody combinations can exploit distinct binding epitopes and leverage the intrinsic plasticity of the conformational landscape for the SARS-CoV-2 S protein to produce efficient neutralizing and mutation resistant characteristics. Structural and computational studies have also been instrumental in quantifying the structure, dynamics, and energetics of the SARS-CoV-2 spike protein binding with nanobodies. In this review, a comprehensive analysis of the current structural, biophysical, and computational biology investigations of SARS-CoV-2 S proteins and their complexes with distinct classes of nanobodies targeting different binding sites is presented. The analysis of computational studies is supplemented by an in-depth examination of mutational scanning simulations and identification of binding energy hotspots for distinct nanobody classes. The review is focused on the analysis of mechanisms underlying synergistic binding of multivalent nanobodies that can be superior to single nanobodies and conventional nanobody cocktails in combating escape mutations by effectively leveraging binding avidity and allosteric cooperativity. We discuss how structural insights and protein engineering approaches together with computational biology tools can aid in the rational design of synergistic combinations that exhibit superior binding and neutralization characteristics owing to avidity-mediated mechanisms.
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Affiliation(s)
- Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; ; Tel.: +1-714-516-4586
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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33
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Kumar P, Lavis LD. Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience. Annu Rev Neurosci 2022; 45:131-150. [PMID: 35226826 DOI: 10.1146/annurev-neuro-110520-030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced general strategies to combine the molecular specificity of small-molecule tools with the cellular specificity of genetically encoded reagents. Here, we survey the application, refinement, and extension of these hybrid small-molecule:protein methods to problems in neuroscience, which yields powerful reagents to precisely measure and manipulate neural systems. Expected final online publication date for the Annual Review of Neuroscience, Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pratik Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA;
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA;
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34
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Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core. Nat Commun 2022; 13:1002. [PMID: 35194049 PMCID: PMC8863989 DOI: 10.1038/s41467-022-28654-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/03/2022] [Indexed: 12/29/2022] Open
Abstract
The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
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Affiliation(s)
- Alexander J Pak
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
| | - Alvin Yu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Zunlong Ke
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- James Franck Institute, The University of Chicago, Chicago, IL, USA.
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35
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Gutgsell A, Gunnarsson A, Forssén P, Gordon E, Fornstedt T, Geschwindner S. Biosensor-Enabled Deconvolution of the Avidity-Induced Affinity Enhancement for the SARS-CoV-2 Spike Protein and ACE2 Interaction. Anal Chem 2022; 94:1187-1194. [PMID: 34964599 PMCID: PMC8751012 DOI: 10.1021/acs.analchem.1c04372] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022]
Abstract
Avidity is an effective and frequent phenomenon employed by nature to achieve extremely high-affinity interactions. As more drug discovery efforts aim to disrupt protein-protein interactions, it is becoming increasingly common to encounter systems that utilize avidity effects and to study these systems using surface-based technologies, such as surface plasmon resonance (SPR) or biolayer interferometry. However, heterogeneity introduced from multivalent binding interactions complicates the analysis of the resulting sensorgram. A frequently applied practice is to fit the data based on a 1:1 binding model, and if the fit does not describe the data adequately, then the experimental setup is changed to favor a 1:1 binding interaction. This reductionistic approach is informative but not always biologically relevant. Therefore, we aimed to develop an SPR-based assay that would reduce the heterogeneity to enable the determination of the kinetic rate constants for multivalent binding interactions using the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the human receptor angiotensin-converting enzyme 2 (ACE2) as a model system. We employed a combinatorial approach to generate a sensor surface that could distinguish between monovalent and multivalent interactions. Using advanced data analysis algorithms to analyze the resulting sensorgrams, we found that controlling the surface heterogeneity enabled the deconvolution of the avidity-induced affinity enhancement for the SARS-CoV-2 spike protein and ACE2 interaction.
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Affiliation(s)
- Aspen
Rene Gutgsell
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Anders Gunnarsson
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Patrik Forssén
- Department
of Engineering and Chemical Sciences, Karlstad
University, SE-651 88 Karlstad, Sweden
| | - Euan Gordon
- Discovery
Biology, Discovery Sciences, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Torgny Fornstedt
- Department
of Engineering and Chemical Sciences, Karlstad
University, SE-651 88 Karlstad, Sweden
| | - Stefan Geschwindner
- Mechanistic
& Structural Biology, Discovery Sciences, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
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36
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Ito K, Matsuda Y, Mine A, Shikida N, Takahashi K, Miyairi K, Shimbo K, Kikuchi Y, Konishi A. Single-chain tandem macrocyclic peptides as a scaffold for growth factor and cytokine mimetics. Commun Biol 2022; 5:56. [PMID: 35031676 PMCID: PMC8760323 DOI: 10.1038/s42003-022-03015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022] Open
Abstract
Mimetics of growth factors and cytokines are promising tools for culturing large numbers of cells and manufacturing regenerative medicine products. In this study, we report single-chain tandem macrocyclic peptides (STaMPtides) as mimetics in a new multivalent peptide format. STaMPtides, which contain two or more macrocyclic peptides with a disulfide-closed backbone and peptide linkers, are successfully secreted into the supernatant by Corynebacterium glutamicum-based secretion technology. Without post-secretion modification steps, such as macrocyclization or enzymatic treatment, bacterially secreted STaMPtides form disulfide bonds, as designed; are biologically active; and show agonistic activities against respective target receptors. We also demonstrate, by cell-based assays, the potential of STaMPtides, which mimic growth factors and cytokines, in cell culture. The STaMPtide technology can be applied to the design, screening, and production of growth factor and cytokine mimetics.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan.
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Natsuki Shikida
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kazutoshi Takahashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kazutaka Shimbo
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
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37
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Kovermann M, Weininger U, Löw C. Completing the family of human EH domains: Solution structure of the internal EH domain of γ-synergin. Protein Sci 2021; 31:811-821. [PMID: 34967068 PMCID: PMC8927860 DOI: 10.1002/pro.4269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/11/2021] [Accepted: 12/24/2021] [Indexed: 11/05/2022]
Abstract
Eps15 homology (EH) domains are universal interaction domains to establish networks of protein-protein interactions in the cell. These networks mainly coordinate cellular functions including endocytosis, actin remodeling and other intracellular signaling pathways. They are well characterized in structural terms, except for the internal EH domain from human γ-synergin (EHγ). Here, we complete the family of EH domain structures by determining the solution structure of the EHγ domain. The structural ensemble follows the canonical EH domain fold and the identified binding site is similar to other known EH domains. But EHγ differs significantly in the N- and C-terminal regions. The N-terminal α-helix is shortened compared to known homologs, while the C-terminal one is fully formed. A significant proportion of the remaining N- and C-terminal regions are well structured, a feature not seen in other EH domains. Single mutations in both the N-terminal and the C-terminal structured extensions lead to the loss of the distinct three-dimensional fold and turn EHγ into a molten globule like state. Therefore, we propose that the structural extensions in EHγ function as a clamp and are undoubtedly required to maintain its tertiary fold. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
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38
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Spatial control of avidity regulates initiation and progression of selective autophagy. Nat Commun 2021; 12:7194. [PMID: 34893607 PMCID: PMC8664900 DOI: 10.1038/s41467-021-27420-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/17/2021] [Indexed: 11/11/2022] Open
Abstract
Autophagosomes form at the endoplasmic reticulum in mammals, and between the vacuole and the endoplasmic reticulum in yeast. However, the roles of these sites and the mechanisms regulating autophagosome formation are incompletely understood. Vac8 is required for autophagy and recruits the Atg1 kinase complex to the vacuole. Here we show that Vac8 acts as a central hub to nucleate the phagophore assembly site at the vacuolar membrane during selective autophagy. Vac8 directly recruits the cargo complex via the Atg11 scaffold. In addition, Vac8 recruits the phosphatidylinositol 3-kinase complex independently of autophagy. Cargo-dependent clustering and Vac8-dependent sequestering of these early autophagy factors, along with local Atg1 activation, promote phagophore assembly site assembly at the vacuole. Importantly, ectopic Vac8 redirects autophagosome formation to the nuclear membrane, indicating that the vacuolar membrane is not specifically required. We propose that multiple avidity-driven interactions drive the initiation and progression of selective autophagy. The molecular principles governing the initiation of autophagosome formation are not clearly understood. Here we show that the vacuolar protein Vac8 coordinates this process by promoting an avidity-driven assembly of several autophagy factors.
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39
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Dillen A, Mohrbacher A, Lammertyn J. A Versatile One-Step Competitive Fiber Optic Surface Plasmon Resonance Bioassay Enabled by DNA Nanotechnology. ACS Sens 2021; 6:3677-3684. [PMID: 34633181 DOI: 10.1021/acssensors.1c01447] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fiber optic surface plasmon resonance (FO-SPR)-based biosensors have emerged as powerful tools for biomarker detection due to their ability for real-time analysis of biomolecular interactions, cost-effectiveness, and user-friendliness. However, as (FO-)SPR signals are determined by the mass of the target molecules, the detection of low-molecular-weight targets remains challenging and currently requires tedious labeling and preparation steps. Therefore, in this work, we established a new concept for low-molecular-weight target detection by implementing duplexed aptamers on an FO-SPR sensor. In this manner, we enabled one-step competitive detection and could achieve significant signals, independent of the weight of the target molecules, without requiring labeling or preprocessing steps. This was demonstrated for the detection of a small molecule (ATP), protein (thrombin), and ssDNA target, thereby reaching detection limits of 72 μM, 36 nM, and 30 nM respectively and proving the generalizability of the proposed bioassay. Furthermore, target detection was successfully achieved in 10-fold diluted plasma, which demonstrated the applicability of the assay in biologically relevant matrices. Altogether, the developed one-step competitive FO-SPR bioassay opens up possibilities for the detection of low-molecular-weight targets in a fast and straightforward manner.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems − Biosensors Group, Willem de Croylaan 42, Box 2428, Leuven 3001, Belgium
| | - Aurélie Mohrbacher
- KU Leuven, Department of Biosystems − Biosensors Group, Willem de Croylaan 42, Box 2428, Leuven 3001, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems − Biosensors Group, Willem de Croylaan 42, Box 2428, Leuven 3001, Belgium
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40
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Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms. ACS OMEGA 2021; 6:26354-26371. [PMID: 34660995 PMCID: PMC8515575 DOI: 10.1021/acsomega.1c03558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/10/2021] [Indexed: 05/11/2023]
Abstract
Structure-functional studies have recently revealed a spectrum of diverse high-affinity nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience against mutational escape. In this study, we combine atomistic simulations with the ensemble-based mutational profiling of binding for the SARS-CoV-2 S-RBD complexes with a wide range of nanobodies to identify dynamic and binding affinity fingerprints and characterize the energetic determinants of nanobody-escaping mutations. Using an in silico mutational profiling approach for probing the protein stability and binding, we examine dynamics and energetics of the SARS-CoV-2 complexes with single nanobodies Nb6 and Nb20, VHH E, a pair combination VHH E + U, a biparatopic nanobody VHH VE, and a combination of the CC12.3 antibody and VHH V/W nanobodies. This study characterizes the binding energy hotspots in the SARS-CoV-2 protein and complexes with nanobodies providing a quantitative analysis of the effects of circulating variants and escaping mutations on binding that is consistent with a broad range of biochemical experiments. The results suggest that mutational escape may be controlled through structurally adaptable binding hotspots in the receptor-accessible binding epitope that are dynamically coupled to the stability centers in the distant binding epitope targeted by VHH U/V/W nanobodies. This study offers a plausible mechanism in which through cooperative dynamic changes, nanobody combinations and biparatopic nanobodies can elicit the increased binding affinity response and yield resilience to common escape mutants.
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Affiliation(s)
- Gennady M. Verkhivker
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Steve Agajanian
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Deniz Yasar Oztas
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Grace Gupta
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
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41
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Addonizio CJ, Gates BD, Webber MJ. Supramolecular "Click Chemistry" for Targeting in the Body. Bioconjug Chem 2021; 32:1935-1946. [PMID: 34415139 DOI: 10.1021/acs.bioconjchem.1c00326] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The fields of precision imaging and drug delivery have revealed a number of tools to improve target specificity and increase efficacy in diagnosing and treating disease. Biological molecules, such as antibodies, continue to be the primary means of assuring active targeting of various payloads. However, molecular-scale recognition motifs have emerged in recent decades to achieve specificity through the design of interacting chemical motifs. In this regard, an assortment of bioorthogonal covalent conjugations offer possibilities for in situ complexation under physiological conditions. Herein, a related concept is discussed that leverages interactions from noncovalent or supramolecular motifs to facilitate in situ recognition and complex formation in the body. Classic supramolecular motifs based on host-guest complexation offer one such means of facilitating recognition. In addition, synthetic bioinspired motifs based on oligonucleotide hybridization and coiled-coil peptide bundles afford other routes to form complexes in situ. The architectures to include recognition of these various motifs for targeting enable both monovalent and multivalent presentation, seeking high affinity or engineered avidity to facilitate conjugation even under dilute conditions of the body. Accordingly, supramolecular "click chemistry" offers a complementary tool in the growing arsenal targeting improved healthcare efficacy.
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Affiliation(s)
- Christopher J Addonizio
- University of Notre Dame, Department of Chemical & Biomolecular Engineering, Notre Dame, Indiana 46556 United States
| | - Brant D Gates
- University of Notre Dame, Department of Chemical & Biomolecular Engineering, Notre Dame, Indiana 46556 United States
| | - Matthew J Webber
- University of Notre Dame, Department of Chemical & Biomolecular Engineering, Notre Dame, Indiana 46556 United States
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42
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Jiang Z, Nero T, Mukherjee S, Olson R, Yan J. Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces. Front Microbiol 2021; 12:686793. [PMID: 34305846 PMCID: PMC8295476 DOI: 10.3389/fmicb.2021.686793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 01/01/2023] Open
Abstract
Bacterial biofilms are communities of cells enclosed in an extracellular polymeric matrix in which cells adhere to each other and to foreign surfaces. The development of a biofilm is a dynamic process that involves multiple steps, including cell-surface attachment, matrix production, and population expansion. Increasing evidence indicates that biofilm adhesion is one of the main factors contributing to biofilm-associated infections in clinics and biofouling in industrial settings. This review focuses on describing biofilm adhesion strategies among different bacteria, including Vibrio cholerae, Pseudomonas aeruginosa, and Staphylococcus aureus. Techniques used to characterize biofilm adhesion are also reviewed. An understanding of biofilm adhesion strategies can guide the development of novel approaches to inhibit or manipulate biofilm adhesion and growth.
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Affiliation(s)
- Zhaowei Jiang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Thomas Nero
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Sampriti Mukherjee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, United States
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States.,Quantitative Biology Institute, Yale University, New Haven, CT, United States
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43
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On the specificity of protein-protein interactions in the context of disorder. Biochem J 2021; 478:2035-2050. [PMID: 34101805 PMCID: PMC8203207 DOI: 10.1042/bcj20200828] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.
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