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Dong X, Qin LY, Gong Z, Qin S, Zhou HX, Tang C. Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex. J Phys Chem Lett 2022; 13:792-800. [PMID: 35044179 PMCID: PMC8852806 DOI: 10.1021/acs.jpclett.1c03794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nonspecific binding of crowder proteins with functional proteins is likely prevalent in vivo, yet direct quantitative evidence, let alone residue-specific information, is scarce. Here we present nuclear magnetic resonance (NMR) characterization showing that bovine serum albumin weakly but preferentially interacts with the histidine carrier protein (HPr). Notably, the binding interface overlaps with that for HPr's specific partner protein, EIN, leading to competition. The crowder protein thus decreases the EIN-HPr binding affinity and accelerates the dissociation of the native complex. In contrast, Ficoll-70 stabilizes the native complex and slows its dissociation, as one would expect from excluded-volume and microviscosity effects. Our atomistic modeling of macromolecular crowding rationalizes the experimental data and provides quantitative insights into the energetics of protein-crowder interactions. The integrated NMR and modeling study yields benchmarks for the effects of crowded cellular environments on protein-protein specific interactions, with implications for evolution regarding how nonspecific binding can be minimized or exploited.
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Affiliation(s)
- Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ling-Yun Qin
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Sanbo Qin
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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2
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. Enhancing the population of the encounter complex affects protein complex formation efficiency. FEBS J 2021; 289:535-548. [PMID: 34403572 PMCID: PMC9293183 DOI: 10.1111/febs.16159] [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: 03/09/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Optimal charge distribution is considered to be important for efficient formation of protein complexes. Electrostatic interactions guide encounter complex formation that precedes the formation of an active protein complex. However, disturbing the optimized distribution by introduction of extra charged patches on cytochrome c peroxidase does not lead to a reduction in productive encounters with its partner cytochrome c. To test whether a complex with a high population of encounter complex is more easily affected by suboptimal charge distribution, the interactions of cytochrome c mutant R13A with wild‐type cytochrome c peroxidase and a variant with an additional negative patch were studied. The complex of the peroxidase and cytochrome c R13A was reported to have an encounter state population of 80%, compared to 30% for the wild‐type cytochrome c. NMR analysis confirms the dynamic nature of the interaction and demonstrates that the mutant cytochrome c samples the introduced negative patch. Kinetic experiments show that productive complex formation is fivefold to sevenfold slower at moderate and high ionic strength values for cytochrome c R13A but the association rate is not affected by the additional negative patch on cytochrome c peroxidase, showing that the total charge on the protein surface can compensate for less optimal charge distribution. At low ionic strength (44 mm), the association with the mutant cytochrome c reaches the same high rates as found for wild‐type cytochrome c, approaching the diffusion limit.
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3
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. The Charge Distribution on a Protein Surface Determines Whether Productive or Futile Encounter Complexes Are Formed. Biochemistry 2021; 60:747-755. [PMID: 33646750 PMCID: PMC8041253 DOI: 10.1021/acs.biochem.1c00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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Protein complex formation
depends strongly on electrostatic interactions.
The distribution of charges on the surface of redox proteins is often
optimized by evolution to guide recognition and binding. To test the
degree to which the electrostatic interactions between cytochrome c peroxidase (CcP) and cytochrome c (Cc)
are optimized, we produced five CcP variants, each with a different
charge distribution on the surface. Monte Carlo simulations show that
the addition of negative charges attracts Cc to the new patches, and
the neutralization of the charges in the regular, stereospecific binding
site for Cc abolishes the electrostatic interactions in that region
entirely. For CcP variants with the charges in the regular binding
site intact, additional negative patches slightly enhance productive
complex formation, despite disrupting the optimized charge distribution.
Removal of the charges in the regular binding site results in a dramatic
decrease in the complex formation rate, even in the presence of highly
negative patches elsewhere on the surface. We conclude that additional
charge patches can result in either productive or futile encounter
complexes, depending on whether negative residues are located also
in the regular binding site.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447 Bayreuth, Germany
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447 Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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4
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020; 59:23239-23243. [PMID: 32827196 PMCID: PMC7756542 DOI: 10.1002/anie.202010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 12/14/2022]
Abstract
Electrostatic interactions can strongly increase the efficiency of protein complex formation. The charge distribution in redox proteins is often optimized to steer a redox partner to the electron transfer active binding site. To test whether the optimized distribution is more important than the strength of the electrostatic interactions, an additional negative patch was introduced on the surface of cytochrome c peroxidase, away from the stereospecific binding site, and its effect on the encounter complex as well as the rate of complex formation was determined. Monte Carlo simulations and paramagnetic relaxation enhancement NMR experiments indicate that the partner, cytochrome c, interacts with the new patch. Unexpectedly, the rate of the active complex formation was not reduced, but rather slightly increased. The findings support the idea that for efficient protein complex formation the strength of the electrostatic interaction is more critical than an optimized charge distribution.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Thijmen La Haye
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands.,Present address: University of Delft, TNW Applied Sciences, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anneloes Blok
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Monika Timmer
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
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5
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome
c
Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonella Di Savino
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Johannes M. Foerster
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Thijmen La Haye
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
- Present address: University of Delft TNW Applied Sciences Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Anneloes Blok
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Monika Timmer
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - G. Matthias Ullmann
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Marcellus Ubbink
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
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Kale S, Strickland M, Peterkofsky A, Liu J, Tjandra N. Model of a Kinetically Driven Crosstalk between Paralogous Protein Encounter Complexes. Biophys J 2019; 117:1655-1665. [PMID: 31623885 DOI: 10.1016/j.bpj.2019.09.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 10/25/2022] Open
Abstract
Proteins interact with one another across a broad spectrum of affinities. Our understanding of the low end of this spectrum, as characterized by millimolar dissociation constants, relies on a handful of cases in which weak encounters have experimentally been identified. These weak interactions away from the specific target binding site can lead toward a higher-affinity complex. Recently, we detected weak encounters between two paralogous phosphotransferase pathways of Escherichia coli, which regulate various metabolic processes and stress responses. In addition to encounters that are known to occur between cognate proteins, i.e., those that can exchange phosphate groups with each other, surprisingly, encounters involving noncognates were also observed. It is not clear whether these "futile" encounters have a cooperative or competitive role. Using agent-based simulations, we find that the encounter complexes can be cooperative or competitive so as to increase or lower the effective binding affinity of the specific complex under different circumstances. This finding invites further questions into how organisms might exploit such low affinities to connect their signaling components.
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Affiliation(s)
- Seyit Kale
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland; National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland.
| | - Madeleine Strickland
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Alan Peterkofsky
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Jian Liu
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, John Hopkins University, Baltimore, Maryland
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland.
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Li ZL, Buck M. Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein-Protein Interactions. J Chem Theory Comput 2019; 15:4318-4331. [PMID: 31241940 DOI: 10.1021/acs.jctc.9b00195] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water interaction in the CHARMM36 force field, in order to better fit the solvation free energy of amino acids side-chain analogues. We find that the molecular dynamics simulation with the scaled force field, CHARMM36s, as well as a recently released version, CHARMM36m, effectively improve on the overly sticky association of proteins, such as ubiquitin. We investigate the formation of a heterodimer protein complex between the SAM domains of the EphA2 receptor and the SHIP2 enzyme by performing a combined total of 48 μs simulations with the different potential functions. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% with CHARMM36s, and to 18.3% with CHARMM36m. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a preorientation guided by Coulomb interactions, consistent with an electrostatic steering mechanism. In 12 cases, the complex could directly transform to the native protein interaction surfaces with only small adjustments in domain orientation. In the other 13 cases, orientational and/or translational adjustments are needed to reach the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a dissociation followed by a reassociation to the correct complex structure is still rare. Instead, the remaining non-native complexes undergo configurational changes/surface searching, which, however, rarely leads to native structures on a time scale of 250 ns. These observations provide a rich picture of the mechanisms of protein-protein complex formation and suggest that computational predictions of native complex PPIs could be improved further.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States.,Departments of Pharmacology and Neurosciences, and Case Comprehensive Cancer Center , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
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Strickland M, Kale S, Strub MP, Schwieters CD, Liu J, Peterkofsky A, Tjandra N. Potential Regulatory Role of Competitive Encounter Complexes in Paralogous Phosphotransferase Systems. J Mol Biol 2019; 431:2331-2342. [PMID: 31071328 DOI: 10.1016/j.jmb.2019.04.040] [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] [Received: 02/26/2019] [Revised: 04/22/2019] [Accepted: 04/28/2019] [Indexed: 11/28/2022]
Abstract
There are two paralogous Escherichia coli phosphotransferase systems, one for sugar import (PTSsugar) and one for nitrogen regulation (PTSNtr), that utilize proteins enzyme Isugar (EIsugar) and HPr, and enzyme INtr (EINtr) and NPr, respectively. The enzyme I proteins have similar folds, as do their substrates HPr and NPr, yet they show strict specificity for their cognate partner both in stereospecific protein-protein complex formation and in reversible phosphotransfer. Here, we investigate the mechanism of specific EINtr:NPr complex formation by the study of transient encounter complexes. NMR paramagnetic relaxation enhancement experiments demonstrated transient encounter complexes of EINtr not only with the expected partner, NPr, but also with the unexpected partner, HPr. HPr occupies transient sites on EINtr but is unable to complete stereospecific complex formation. By occupying the non-productive transient sites, HPr promotes NPr transient interaction to productive sites closer to the stereospecific binding site and actually enhances specific complex formation between NPr and EINtr. The cellular level of HPr is approximately 150 times higher than that of NPr. Thus, our finding suggests a potential mechanism for cross-regulation of enzyme activity through formation of competitive encounter complexes.
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Affiliation(s)
- Madeleine Strickland
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seyit Kale
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jian Liu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan Peterkofsky
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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