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Gurusinghe SN, Oppenheimer B, Shifman JM. Cold spots are universal in protein-protein interactions. Protein Sci 2022; 31:e4435. [PMID: 36173158 PMCID: PMC9490803 DOI: 10.1002/pro.4435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/22/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022]
Abstract
Proteins interact with each other through binding interfaces that differ greatly in size and physico-chemical properties. Within the binding interface, a few residues called hot spots contribute the majority of the binding free energy and are hence irreplaceable. In contrast, cold spots are occupied by suboptimal amino acids, providing possibility for affinity enhancement through mutations. In this study, we identify cold spots due to cavities and unfavorable charge interactions in multiple protein-protein interactions (PPIs). For our cold spot analysis, we first use a small affinity database of PPIs with known structures and affinities and then expand our search to nearly 4000 homo- and heterodimers in the Protein Data Bank (PDB). We observe that cold spots due to cavities are present in nearly all PPIs unrelated to their binding affinity, while unfavorable charge interactions are relatively rare. We also find that most cold spots are located in the periphery of the binding interface, with high-affinity complexes showing fewer centrally located colds spots than low-affinity complexes. A larger number of cold spots is also found in non-cognate interactions compared to their cognate counterparts. Furthermore, our analysis reveals that cold spots are more frequent in homo-dimeric complexes compared to hetero-complexes, likely due to symmetry constraints imposed on sequences of homodimers. Finally, we find that glycines, glutamates, and arginines are the most frequent amino acids appearing at cold spot positions. Our analysis emphasizes the importance of cold spot positions to protein evolution and facilitates protein engineering studies directed at enhancing binding affinity and specificity in a wide range of applications.
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Affiliation(s)
- Sagara N.S. Gurusinghe
- Department of Biological ChemistryThe Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalemIsrael
| | - Ben Oppenheimer
- Department of Biological ChemistryThe Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalemIsrael
| | - Julia M. Shifman
- Department of Biological ChemistryThe Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalemIsrael
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2
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Magits W, Sablina AA. The regulation of the protein interaction network by monoubiquitination. Curr Opin Struct Biol 2022; 73:102333. [PMID: 35176591 DOI: 10.1016/j.sbi.2022.102333] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/24/2021] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
The conjugation of a single ubiquitin or monoubiquitination acts as a versatile signal that can have both degradative and non-degradative functions. The latter is of particular interest as emerging evidence indicates that ubiquitin-driven alterations of the protein interaction landscape play a key role in multiple signaling pathways. Whereas early studies were focused on how monoubiquitination alters the interactions of proteins containing ubiquitin-binding domains, more recent reports demonstrate that ubiquitin conjugation can also affect the binding mode by changing the surface of the ubiquitinated substrate. Furthermore, monoubiquitination modulates the interactions with other macromolecules, such as DNA or lipids, underscoring the diverse role of monoubiquitination in cellular processes. In this review, we discussed how monoubiquitination achieves its function by modulating the interaction landscape.
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Affiliation(s)
- Wout Magits
- VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Anna A Sablina
- VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
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3
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Petell CJ, Randene K, Pappas M, Sandoval D, Strahl BD, Harrison JS, Steimel JP. Mechanically transduced immunosorbent assay to measure protein-protein interactions. eLife 2021; 10:67525. [PMID: 34581668 PMCID: PMC8479797 DOI: 10.7554/elife.67525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. We use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Kathyrn Randene
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Michael Pappas
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Diego Sandoval
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, United States
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4
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Ruidiaz SF, Dreier JE, Hartmann-Petersen R, Kragelund BB. The disordered PCI-binding human proteins CSNAP and DSS1 have diverged in structure and function. Protein Sci 2021; 30:2069-2082. [PMID: 34272906 PMCID: PMC8442969 DOI: 10.1002/pro.4159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) regularly constitute components of larger protein assemblies contributing to architectural stability. Two small, highly acidic IDPs have been linked to the so-called PCI complexes carrying PCI-domain subunits, including the proteasome lid and the COP9 signalosome. These two IDPs, DSS1 and CSNAP, have been proposed to have similar structural propensities and functions, but they display differences in their interactions and interactome sizes. Here we characterized the structural properties of human DSS1 and CSNAP at the residue level using NMR spectroscopy and probed their propensities to bind ubiquitin. We find that distinct structural features present in DSS1 are completely absent in CSNAP, and vice versa, with lack of relevant ubiquitin binding to CSNAP, suggesting the two proteins to have diverged in both structure and function. Our work additionally highlights that different local features of seemingly similar IDPs, even subtle sequence variance, may endow them with different functional traits. Such traits may underlie their potential to engage in multiple interactions thereby impacting their interactome sizes.
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Affiliation(s)
- Sarah F Ruidiaz
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Jesper E Dreier
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,REPIN, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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5
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Bonadio A, Shifman JM. Computational design and experimental optimization of protein binders with prospects for biomedical applications. Protein Eng Des Sel 2021; 34:gzab020. [PMID: 34436606 PMCID: PMC8388154 DOI: 10.1093/protein/gzab020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 11/12/2022] Open
Abstract
Protein-based binders have become increasingly more attractive candidates for drug and imaging agent development. Such binders could be evolved from a number of different scaffolds, including antibodies, natural protein effectors and unrelated small protein domains of different geometries. While both computational and experimental approaches could be utilized for protein binder engineering, in this review we focus on various computational approaches for protein binder design and demonstrate how experimental selection could be applied to subsequently optimize computationally-designed molecules. Recent studies report a number of designed protein binders with pM affinities and high specificities for their targets. These binders usually characterized with high stability, solubility, and low production cost. Such attractive molecules are bound to become more common in various biotechnological and biomedical applications in the near future.
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Affiliation(s)
- Alessandro Bonadio
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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Yokoyama H, Sawada JI, Sato K, Ogo N, Kamei N, Ishikawa Y, Hara K, Asai A, Hashimoto H. Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. ACS OMEGA 2018; 3:12284-12294. [PMID: 31459302 PMCID: PMC6644766 DOI: 10.1021/acsomega.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/22/2018] [Indexed: 06/10/2023]
Abstract
For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S-trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para-methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty
of Pharmaceutical Sciences, Tokyo University
of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kohei Sato
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Naohisa Ogo
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Nanami Kamei
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Akira Asai
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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7
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Fennell LM, Rahighi S, Ikeda F. Linear ubiquitin chain-binding domains. FEBS J 2018; 285:2746-2761. [PMID: 29679476 DOI: 10.1111/febs.14478] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/08/2018] [Accepted: 04/13/2018] [Indexed: 12/25/2022]
Abstract
Ubiquitin modification (ubiquitination) of target proteins can vary with respect to chain lengths, linkage type, and chain forms, such as homologous, mixed, and branched ubiquitin chains. Thus, ubiquitination can generate multiple unique surfaces on a target protein substrate. Ubiquitin-binding domains (UBDs) recognize ubiquitinated substrates, by specifically binding to these unique surfaces, modulate the formation of cellular signaling complexes and regulate downstream signaling cascades. Among the eight different homotypic chain types, Met1-linked (also termed linear) chains are the only chains in which linkage occurs on a non-Lys residue of ubiquitin. Linear ubiquitin chains have been implicated in immune responses, cell death and autophagy, and several UBDs - specific for linear ubiquitin chains - have been identified. In this review, we describe the main principles of ubiquitin recognition by UBDs, focusing on linear ubiquitin chains and their roles in biology.
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Affiliation(s)
- Lilian M Fennell
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Health Science Campus, Chapman University, Irvine, CA, USA
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
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