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Hu CW, Wang A, Fan D, Worth M, Chen Z, Huang J, Xie J, Macdonald J, Li L, Jiang J. OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy. Proc Natl Acad Sci U S A 2024; 121:e2320867121. [PMID: 38838015 PMCID: PMC11181094 DOI: 10.1073/pnas.2320867121] [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: 11/27/2023] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
O-GlcNAcase (OGA) is the only human enzyme that catalyzes the hydrolysis (deglycosylation) of O-linked beta-N-acetylglucosaminylation (O-GlcNAcylation) from numerous protein substrates. OGA has broad implications in many challenging diseases including cancer. However, its role in cell malignancy remains mostly unclear. Here, we report that a cancer-derived point mutation on the OGA's noncatalytic stalk domain aberrantly modulates OGA interactome and substrate deglycosylation toward a specific set of proteins. Interestingly, our quantitative proteomic studies uncovered that the OGA stalk domain mutant preferentially deglycosylated protein substrates with +2 proline in the sequence relative to the O-GlcNAcylation site. One of the most dysregulated substrates is PDZ and LIM domain protein 7 (PDLIM7), which is associated with the tumor suppressor p53. We found that the aberrantly deglycosylated PDLIM7 suppressed p53 gene expression and accelerated p53 protein degradation by promoting the complex formation with E3 ubiquitin ligase MDM2. Moreover, deglycosylated PDLIM7 significantly up-regulated the actin-rich membrane protrusions on the cell surface, augmenting the cancer cell motility and aggressiveness. These findings revealed an important but previously unappreciated role of OGA's stalk domain in protein substrate recognition and functional modulation during malignant cell progression.
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Affiliation(s)
- Chia-Wei Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - Ao Wang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - Dacheng Fan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - Matthew Worth
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Junfeng Huang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - Jinshan Xie
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - John Macdonald
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
| | - Lingjun Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI53705
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2
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Parvathy J, Yazhini A, Srinivasan N, Sowdhamini R. Interfacial residues in protein-protein complexes are in the eyes of the beholder. Proteins 2024; 92:509-528. [PMID: 37982321 DOI: 10.1002/prot.26628] [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: 05/13/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
Abstract
Interactions between proteins are vital in almost all biological processes. The characterization of protein-protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein-protein complex are assumed to have the following two properties: (a) they always interact with a residue of a partner protein, which forms the basis for distance-based interface residue identification methods, and (b) they are solvent-exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)-based methods. The study interrogates this popular assumption by recognizing interface residues in protein-protein complexes through these two methods. The results show that a few residues are identified uniquely by each method, and the extent of conservation, propensities, and their contribution to the stability of protein-protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics, and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics, and function of protein-protein complexes are identified in a complementary manner.
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Affiliation(s)
- Jayadevan Parvathy
- Interdisciplinary Mathematical Sciences Initiative (IMI), Indian Institute of Science, Bangalore, India
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | | | - Ramanathan Sowdhamini
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
- National Center for Biological Sciences (NCBS), Bangalore, India
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3
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Shang W, Hu X, Lin X, Li S, Xiong S, Huang B, Wang X. Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies. Pharmaceuticals (Basel) 2024; 17:424. [PMID: 38675386 PMCID: PMC11054880 DOI: 10.3390/ph17040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.
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Affiliation(s)
| | | | | | | | | | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
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4
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Ntallis C, Tzoupis H, Tselios T, Chasapis CT, Vlamis-Gardikas A. Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands. Antioxidants (Basel) 2023; 13:15. [PMID: 38275635 PMCID: PMC10812433 DOI: 10.3390/antiox13010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In silico approaches were employed to examine the characteristics of interactions between human mitochondrial thioredoxin 2 (HsTrx2) and its 38 previously identified mitochondrial protein ligands. All interactions appeared driven mainly by electrostatic forces. The statistically significant residues of HsTrx2 for interactions were characterized as "contact hot spots". Since these were identical/adjacent to putative thermodynamic hot spots, an energy network approach identified their neighbors to highlight possible contact interfaces. Three distinct areas for binding emerged: (i) one around the active site for covalent interactions, (ii) another antipodal to the active site for strong non-covalent interactions, and (iii) a third area involved in both kinds of interactions. The contact interfaces of HsTrx2 were projected as respective interfaces for Escherichia coli Trx1 (EcoTrx1), 2, and HsTrx1. Comparison of the interfaces and contact hot spots of HsTrx2 to the contact residues of EcoTx1 and HsTrx1 from existing crystal complexes with protein ligands supported the hypothesis, except for a part of the cleft/groove adjacent to Trp30 preceding the active site. The outcomes of this study raise the possibility for the rational design of selective inhibitors for the interactions of HsTrx2 with specific protein ligands without affecting the entirety of the functions of the Trx system.
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Affiliation(s)
- Charalampos Ntallis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Haralampos Tzoupis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Theodore Tselios
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou 48, 11635 Athens, Greece;
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5
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Förste S, Vonshak O, Daube SS, Bar-Ziv RH, Lipowsky R, Rudorf S. Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. Microb Cell Fact 2023; 22:244. [PMID: 38037098 PMCID: PMC10688499 DOI: 10.1186/s12934-023-02237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system's three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes.
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Affiliation(s)
- Stefanie Förste
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Ohad Vonshak
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shirley S Daube
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Roy H Bar-Ziv
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, 30419, Hannover, Germany.
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6
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Hu CW, Wang A, Fan D, Worth M, Chen Z, Huang J, Xie J, Macdonald J, Li L, Jiang J. Cancer-derived mutation in the OGA stalk domain promotes cell malignancy through dysregulating PDLIM7 and p53. RESEARCH SQUARE 2023:rs.3.rs-2709128. [PMID: 36993758 PMCID: PMC10055641 DOI: 10.21203/rs.3.rs-2709128/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
O-GlcNAcase (OGA) is the sole enzyme that hydrolyzes O-GlcNAcylation from thousands of proteins and is dysregulated in many diseases including cancer. However, the substrate recognition and pathogenic mechanisms of OGA remain largely unknown. Here we report the first discovery of a cancer-derived point mutation on the OGA's non-catalytic stalk domain that aberrantly regulated a small set of OGA-protein interactions and O-GlcNAc hydrolysis in critical cellular processes. We uncovered a novel cancer-promoting mechanism in which the OGA mutant preferentially hydrolyzed the O-GlcNAcylation from modified PDLIM7 and promoted cell malignancy by down-regulating p53 tumor suppressor in different types of cells through transcription inhibition and MDM2-mediated ubiquitination. Our study revealed the OGA deglycosylated PDLIM7 as a novel regulator of p53-MDM2 pathway, offered the first set of direct evidence on OGA substrate recognition beyond its catalytic site, and illuminated new directions to interrogate OGA's precise role without perturbing global O-GlcNAc homeostasis for biomedical applications.
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Affiliation(s)
| | - Ao Wang
- University of Wisconsin-Madison
| | | | | | | | | | | | | | | | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison
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7
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Tight Complex Formation of the Fumarate Sensing DcuS-DcuR Two-Component System at the Membrane and Target Promoter Search by Free DcuR Diffusion. mSphere 2022; 7:e0023522. [PMID: 35862816 PMCID: PMC9429925 DOI: 10.1128/msphere.00235-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Signaling of two-component systems by phosphoryl transfer requires interaction of the sensor kinase with the response regulator. Interaction of the C4-dicarboxylate-responsive and membrane-integral sensor kinase DcuS with the response regulator DcuR was studied. In vitro, the cytoplasmic part of DcuS (PASC-Kin) was employed. Stable complexes were formed, when either DcuS or DcuR were phosphorylated (Kd 22 ± 11 and 28 ± 7 nM, respectively). The unphosphorylated proteins produced a more labile complex (Kd 1380 ± 395 nM). Bacterial two-hybrid studies confirm interaction of DcuR with DcuS (and PASC-Kin) in vivo. The absolute contents of DcuR (197-979 pmol mg−1 protein) in the bacteria exceeded those of DcuS by more than 1 order of magnitude. According to the Kd values, DcuS exists in complex, with phosphorylated but also unphosphorylated DcuR. In live cell imaging, the predominantly freely diffusing DcuR becomes markedly less mobile after phosphorylation and activation of DcuS by fumarate. Portions of the low mobility fraction accumulated at the cell poles, the preferred location of DcuS, and other portions within the cell, representing phosphorylated DcuR bound to promoters. In the model, acitvation of DcuS increases the affinity toward DcuR, leading to DcuS-P × DcuR formation and phosphorylation of DcuR. The complex is stable enough for phosphate-transfer, but labile enough to allow exchange between DcuR from the cytosol and DcuR-P of the complex. Released DcuR-P diffuses to target promoters and binds. Uncomplexed DcuR-P in the cytosol binds to nonactivated DcuS and becomes dephosphorylated. The lower affinity between DcuR and DcuS avoids blocking of DcuS and allows rapid exchange of DcuR. IMPORTANCE Complex formation of membrane-bound sensor kinases with the response regulators represents an inherent step of signaling from the membrane to the promoters on the DNA. In the C4-dicarboxylate-sensing DcuS-DcuR two-component system, complex formation is strengthened by activation (phosphorylation) in vitro and in vivo, with trapping of the response regulator DcuR at the membrane. Single-molecule tracking of DcuR in the bacterial cell demonstrates two populations of DcuR with decreased mobility in the bacteria after activation: one at the membrane, but a second in the cytosol, likely representing DNA-bound DcuR. The data suggest a model with binding of DcuR to DcuS-P for phosphorylation, and of DcuR-P to DcuS for dephosphorylation, allowing rapid adaptation of the DcuR phosphorylation state. DcuR-P is released and transferred to DNA by 3D diffusion.
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8
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Ghadie MA, Xia Y. Are transient protein-protein interactions more dispensable? PLoS Comput Biol 2022; 18:e1010013. [PMID: 35404956 PMCID: PMC9000134 DOI: 10.1371/journal.pcbi.1010013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are key drivers of cell function and evolution. While it is widely assumed that most permanent PPIs are important for cellular function, it remains unclear whether transient PPIs are equally important. Here, we estimate and compare dispensable content among transient PPIs and permanent PPIs in human. Starting with a human reference interactome mapped by experiments, we construct a human structural interactome by building three-dimensional structural models for PPIs, and then distinguish transient PPIs from permanent PPIs using several structural and biophysical properties. We map common mutations from healthy individuals and disease-causing mutations onto the structural interactome, and perform structure-based calculations of the probabilities for common mutations (assumed to be neutral) and disease mutations (assumed to be mildly deleterious) to disrupt transient PPIs and permanent PPIs. Using Bayes' theorem we estimate that a similarly small fraction (<~20%) of both transient and permanent PPIs are completely dispensable, i.e., effectively neutral upon disruption. Hence, transient and permanent interactions are subject to similarly strong selective constraints in the human interactome.
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Affiliation(s)
| | - Yu Xia
- Department of Bioengineering, McGill University, Montreal, Canada
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9
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Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein–Protein Interfaces, How and Why? Molecules 2022; 27:molecules27061841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022] Open
Abstract
Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface.
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Affiliation(s)
- Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
- Correspondence:
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10
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Sagar A, Herranz-Trillo F, Langkilde AE, Vestergaard B, Bernadó P. Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets. Structure 2021; 29:1074-1090.e4. [PMID: 33862013 DOI: 10.1016/j.str.2021.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Transient biomolecular interactions play crucial roles in many cellular signaling and regulation processes. However, deciphering the structure of these assemblies is challenging owing to the difficulties in isolating complexes from the individual partners. The additive nature of small-angle X-ray scattering (SAXS) data allows for probing the species present in these mixtures, but decomposition into structural and thermodynamic information is difficult. We present a chemometric approach enabling the decomposition of titration SAXS data into species-specific information. Using extensive synthetic SAXS data, we demonstrate that robust decomposition can be achieved for titrations with a maximum fraction of complex of 0.5 that can be extended to 0.3 when two orthogonal titrations are simultaneously analyzed. The effect of the structural features, titration points, relative concentrations, and noise are thoroughly analyzed. The validation of the strategy with experimental data highlights the power of the approach to provide unique insights into this family of biomolecular assemblies.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
| | - Fátima Herranz-Trillo
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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11
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Tandon H, Melarkode Vattekatte A, Srinivasan N, Sandhya S. Molecular and Structural Basis of Cross-Reactivity in M. tuberculosis Toxin-Antitoxin Systems. Toxins (Basel) 2020; 12:E481. [PMID: 32751054 PMCID: PMC7472061 DOI: 10.3390/toxins12080481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 01/12/2023] Open
Abstract
Mycobacterium tuberculosis genome encodes over 80 toxin-antitoxin (TA) systems. While each toxin interacts with its cognate antitoxin, the abundance of TA systems presents an opportunity for potential non-cognate interactions. TA systems mediate manifold interactions to manage pathogenicity and stress response network of the cell and non-cognate interactions may play vital roles as well. To address if non-cognate and heterologous interactions are feasible and to understand the structural basis of their interactions, we have performed comprehensive computational analyses on the available 3D structures and generated structural models of paralogous M. tuberculosis VapBC and MazEF TA systems. For a majority of the TA systems, we show that non-cognate toxin-antitoxin interactions are structurally incompatible except for complexes like VapBC15 and VapBC11, which show similar interfaces and potential for cross-reactivity. For TA systems which have been experimentally shown earlier to disfavor non-cognate interactions, we demonstrate that they are structurally and stereo-chemically incompatible. For selected TA systems, our detailed structural analysis identifies specificity conferring residues. Thus, our work improves the current understanding of TA interfaces and generates a hypothesis based on congenial binding site, geometric complementarity, and chemical nature of interfaces. Overall, our work offers a structure-based explanation for non-cognate toxin-antitoxin interactions in M. tuberculosis.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; (H.T.); (A.M.V.)
| | - Akhila Melarkode Vattekatte
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; (H.T.); (A.M.V.)
- Biologie Intégrée du Globule Rouge UMR_S1134, INSERM, Université Paris, Université de la Réunion, Université des Antilles, F-75739 Paris, France
- Laboratoire d’Excellence GR-Ex, F-75739 Paris, France
- Faculté des Sciences et Technologies, Saint Denis Messag, F-97715 La Réunion, France
- Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France
| | - Narayanaswamy Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; (H.T.); (A.M.V.)
| | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; (H.T.); (A.M.V.)
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12
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The Molecular Interaction Process. J Pharm Sci 2020; 109:154-160. [DOI: 10.1016/j.xphs.2019.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 01/14/2023]
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13
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Hadi-Alijanvand H. Soft regions of protein surface are potent for stable dimer formation. J Biomol Struct Dyn 2019; 38:3587-3598. [PMID: 31476974 DOI: 10.1080/07391102.2019.1662328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins' quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids' affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. AbbreviationsAABaverage affinity for bindingANManisotropic network modelAPCaffinity propagation clusteringASAaccessible surface areaCCDinter residues distanceCSCcomplex stability codeDMdistance matrixΔGdissPISA-computed dissociation free energyGNMGaussian normal mode analysisNMAnormal mode analysisPBPprotein binding patchPISAproteins, interfaces, structures and assembliesrASArelative accessible area in respect to unfolded state of residuesRMrecurrence matrixrPrelative protrusionRPrecurrence plotRQArecurrence quantitative analysisSEMstandard error of meanCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamid Hadi-Alijanvand
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
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14
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Humphreys SC, Thayer MB, Lade JM, Wu B, Sham K, Basiri B, Hao Y, Huang X, Smith R, Rock BM. Plasma and Liver Protein Binding of N-Acetylgalactosamine–Conjugated Small Interfering RNA. Drug Metab Dispos 2019; 47:1174-1182. [DOI: 10.1124/dmd.119.086967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022] Open
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15
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Jayashree S, Murugavel P, Sowdhamini R, Srinivasan N. Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions. Biol Direct 2019; 14:1. [PMID: 30646935 PMCID: PMC6334431 DOI: 10.1186/s13062-019-0232-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/07/2019] [Indexed: 11/29/2022] Open
Abstract
Background Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of residues at the interface of protein-protein complexes in conferring stability and specificity to the complex. Interface residues in a protein are well known for their interactions with sidechain and main chain atoms with the interacting protein. However, the extent of intra-protein interactions involving interface residues in a protein-protein complex and their relative contribution in comparison to inter-protein interactions are not clearly understood. This paper probes this feature using a dataset of protein-protein complexes of known 3-D structure. Results We have analysed a dataset of 45 transient protein-protein complex structures with at least one of the interacting proteins with a known structure available also in the unbound form. We observe that a large proportion of interface residues (1608 out of 2137 interface residues, 75%) are involved in intra and inter-protein interactions simultaneously. The amino acid propensities of such interfacial residues involved in bifurcated interactions are found to be highly similar to the general propensities to occur at protein-protein interfaces. Finally, we observe that a majority (83%) of intra-protein interactions of interface residues with bifurcated interactions, are also observed in the protein uncomplexed form. Conclusions We have shown, to the best of our knowledge for the first time, that a vast majority of the protein-protein interface residues are involved in extensive intra-protein interactions apart from inter-protein interactions. For a majority of such interface residues the microenvironment in the tertiary structure is pre-formed and retained upon complex formation with its cognate partner during transient interactions. Reviewers This article was reviewed by Arumay Pal and Mallur Madhusudhan. Electronic supplementary material The online version of this article (10.1186/s13062-019-0232-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srinivasan Jayashree
- School of Bioscience & Technology, Vellore Institute of Technology, VIT University, Vellore, 632014, India
| | - Pavalam Murugavel
- National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bellary road, Bangalore, 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, UAS-GKVK Campus, Bellary road, Bangalore, 560065, India
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16
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Bakhman A, Rabinovich E, Shlamkovich T, Papo N, Kosloff M. Residue-level determinants of angiopoietin-2 interactions with its receptor Tie2. Proteins 2018; 87:185-197. [PMID: 30520519 DOI: 10.1002/prot.25638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/04/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
Abstract
We combined computational and experimental methods to interrogate the binding determinants of angiopoietin-2 (Ang2) to its receptor tyrosine kinase (RTK) Tie2-a central signaling system in angiogenesis, inflammation, and tumorigenesis. We used physics-based electrostatic and surface-area calculations to identify the subset of interfacial Ang2 and Tie2 residues that can affect binding directly. Using random and site-directed mutagenesis and yeast surface display (YSD), we validated these predictions and identified additional Ang2 positions that affected receptor binding. We then used burial-based calculations to classify the larger set of Ang2 residues that are buried in the Ang2 core, whose mutations can perturb the Ang2 structure and thereby affect interactions with Tie2 indirectly. Our analysis showed that the Ang2-Tie2 interface is dominated by nonpolar contributions, with only three Ang2 and two Tie2 residues that contribute electrostatically to intermolecular interactions. Individual interfacial residues contributed only moderately to binding, suggesting that engineering of this interface will require multiple mutations to reach major effects. Conversely, substitutions in substantially buried Ang2 residues were more prevalent in our experimental screen, reduced binding substantially, and are therefore more likely to have a deleterious effect that might contribute to oncogenesis. Computational analysis of additional RTK-ligand complexes, c-Kit-SCF and M-CSF-c-FMS, and comparison to previous YSD results, further show the utility of our combined methodology.
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Affiliation(s)
- Anna Bakhman
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Eitan Rabinovich
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tomer Shlamkovich
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
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17
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Sun T, Mu D, Cui J. Mathematical model identifies effective P53 accumulation with target gene binding affinity in DNA damage response for cell fate decision. Cell Cycle 2018; 17:2716-2730. [PMID: 30488759 DOI: 10.1080/15384101.2018.1553342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Functional p53 signaling is essential for appropriate responses to diverse stimuli. P53 dynamics employs the information from the stimulus leading to selective gene expression and cell fate decision. However, the decoding mechanism of p53 dynamics under DNA damage challenge remains poorly understood. Here we mathematically modeled the recently dual-phase p53 dynamics under doxorubicin treatment. We found that p53 could perform sequential pulses followed by a high-amplitude terminal pulse at relatively low doxorubicin treatment, whereas p53 became steadily accumulated when damage level was high. The effective p53 integral above a threshold but not the absolute accumulation of p53 precisely discriminated survival and death. Silencing negative regulators in p53 network might promote the occurrence of terminal pulse. Furthermore, lower binding affinity and degradation rate of p53 target genes could favorably discriminate high and low dose doxorubicin treatment. Grouping by temporal profiles suggested that the p53 dynamics rather than the doxorubicin doses could better discriminate cellular outcomes and confer less variation for effective p53 integral reemphasizing the importance of p53 level regulation. Our model has established a theoretical framework that p53 dynamics can work cooperatively with its binding affinity to target genes leading to cell fate choice, providing new clues of optimized clinical design by manipulating p53 dynamics.
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Affiliation(s)
- Tingzhe Sun
- a School of Life Sciences , Anqing Normal University , Anqing , Anhui , China
| | - Dan Mu
- a School of Life Sciences , Anqing Normal University , Anqing , Anhui , China
| | - Jun Cui
- b MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences , Sun Yat-sen University , Guangzhou , Guangdong , China
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18
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Khan MF, Spurgeon SK, Yan XG. Modeling and Dynamic Behavior of eIF2 Dependent Regulatory System With Disturbances. IEEE Trans Nanobioscience 2018; 17:518-524. [PMID: 30281470 DOI: 10.1109/tnb.2018.2873027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Eukaryotic initiation factor 2 (eIF2) is a central controller of the eukaryotic translational machinery. To sustain the on-going translation activity, eIF2 cycles between its GTP and GDP bound states. However, in response to cellular stresses, the phosphorylation of eIF2 takes place, which acts as an inhibitor of the guanine nucleotide exchange factor eIF2B and switches the translation activity on physiological timescales. The main objective of this paper is to investigate the stability of the regulatory system under nominal conditions, parametric fluctuations, and structural damages. In this paper, a mathematical model of eIF2-dependent regulatory system is used to identify the stability-conferring features within the system with the help of direct and indirect methods of Lyapunov stability theory. To investigate the impact of intrinsic fluctuations and structural damages on the stability of regulatory system, the mathematical model has been linearized around feasible equilibrium point and the variation of system poles has been observed. The investigations have revealed that the regulatory model is stable and able to tolerate the intrinsic stressors but becomes unstable when particular complex is targeted to override the undesirable interaction. Our analyses indicate that, the stability is a collective property and damage in the structure of the system changes the stability of the system.
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19
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Mazumder A, Batabyal S, Mondal M, Mondol T, Choudhury S, Ghosh R, Chatterjee T, Bhattacharyya D, Pal SK, Roy S. Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation. Phys Chem Chem Phys 2017; 19:14781-14792. [PMID: 28548177 DOI: 10.1039/c7cp01193h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA-protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes.
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Affiliation(s)
- Abhishek Mazumder
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700 032, India
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