1
|
Mammoser CC, Agh RE, Garcia NM, Wang Y, Thielges M. Altered coordination in a blue copper protein upon association with redox partner revealed by carbon-deuterium vibrational probes. Phys Chem Chem Phys 2022; 24:21588-21592. [DOI: 10.1039/d2cp03314c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins tune the reactivity of metal sites; less understood is the impact of association with a redox partner. We demonstrate the utility of carbon-deuterium labels for selective analysis of delicate...
Collapse
|
2
|
Erv1 and Cytochrome c Mediate Rapid Electron Transfer via A Collision-Type Interaction. J Mol Biol 2021; 433:167045. [PMID: 33971209 DOI: 10.1016/j.jmb.2021.167045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/01/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Being essential for oxidative protein folding in the mitochondrial intermembrane space, the mitochondrial disulfide relay relies on the electron transfer (ET) from the sulfhydryl oxidase Erv1 to cytochrome c (Cc). Using solution NMR spectroscopy, we demonstrate that while the yeast Cc-Erv1 system is functionally active, no observable binding of the protein partners takes place. The transient interaction between Erv1 and Cc can be rationalized by molecular modeling, suggesting that a large surface area of Erv1 can sustain a fast ET to Cc via a collision-type mechanism, without the need for a canonical protein complex formation. We suggest that, by preventing the direct ET to molecular oxygen (O2), the collision-type Cc-Erv1 interaction plays a role in protecting the organism against reactive oxygen species.
Collapse
|
3
|
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
![]()
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.
Collapse
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
| |
Collapse
|
4
|
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: 10] [Impact Index Per Article: 2.5] [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.
Collapse
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
| |
Collapse
|
5
|
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
| |
Collapse
|
6
|
van Son M, Schilder JT, Di Savino A, Blok A, Ubbink M, Huber M. The Transient Complex of Cytochrome c and Cytochrome c Peroxidase: Insights into the Encounter Complex from Multifrequency EPR and NMR Spectroscopy. Chemphyschem 2020; 21:1060-1069. [PMID: 32301564 PMCID: PMC7317791 DOI: 10.1002/cphc.201901160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/03/2020] [Indexed: 12/31/2022]
Abstract
We present a novel approach to study transient protein‐protein complexes with standard, 9 GHz, and high‐field, 95 GHz, electron paramagnetic resonance (EPR) and paramagnetic NMR at ambient temperatures and in solution. We apply it to the complex of yeast mitochondrial iso‐1‐cytochrome c (Cc) with cytochrome c peroxidase (CcP) with the spin label [1‐oxyl‐2,2,5,5‐tetramethyl‐Δ3‐pyrroline‐3‐methyl)‐methanethiosulfonate] attached at position 81 of Cc (SL−Cc). A dissociation constant KD of 20±4×10−6 M (EPR and NMR) and an equal amount of stereo‐specific and encounter complex (NMR) are found. The EPR spectrum of the fully bound complex reveals that the encounter complex has a significant population (60 %) that shares important features, such as the Cc‐interaction surface, with the stereo‐specific complex.
Collapse
Affiliation(s)
- Martin van Son
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden (The, Netherlands
| | - Jesika T Schilder
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Antonella Di Savino
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Martina Huber
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden (The, Netherlands
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Fedorov VA, Kovalenko IB, Khruschev SS, Ustinin DM, Antal TK, Riznichenko GY, Rubin AB. Comparative analysis of plastocyanin-cytochrome f complex formation in higher plants, green algae and cyanobacteria. PHYSIOLOGIA PLANTARUM 2019; 166:320-335. [PMID: 30740703 DOI: 10.1111/ppl.12940] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Mechanisms of the complex formation between plastocyanin and cytochrome f in higher plants (Spinacia oleracea and Brassica rapa), green microalgae Chlamydomonas reinhardtii and two species of cyanobacteria (Phormidium laminosum and Nostoc sp.) were investigated using combined Brownian and molecular dynamics simulations and hierarchical cluster analysis. In higher plants and green algae, electrostatic interactions force plastocyanin molecule close to the heme of cytochrome f. In the subsequent rotation of plastocyanin molecule around the point of electrostatic contact in the vicinity of cytochrome f, copper (Cu) atom approaches cytochrome heme forming a stable configuration where cytochrome f molecule behaves as a rather rigid body without conformational changes. In Nostoc plastocyanin molecule approaches cytochrome f in a different orientation (head-on) where the stabilization of the plastocyanin-cytochrome f complex is accompanied by the conformational changes of the G188E189D190 loop that stabilizes the whole complex. In cyanobacterium P. laminosum, electrostatic preorientation of the approaching molecules was not detected, thus indicating that random motions rather than long-range electrostatic interactions are responsible for the proper mutual orientation. We demonstrated that despite the structural similarity of the investigated electron transport proteins in different photosynthetic organisms, the complexity of molecular mechanisms of the complex formation increases in the following sequence: non-heterocystous cyanobacteria - heterocystous cyanobacteria - green algae - flowering plants.
Collapse
Affiliation(s)
- Vladimir A Fedorov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ilya B Kovalenko
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
- Institute of Physics and Mathematics, Astrakhan State University, Astrakhan, 414056, Russia
- Scientific and Technological Center of Unique Instrumentation of the Russian Academy of Sciences, Moscow, 117342, Russia
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
| | - Sergei S Khruschev
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitry M Ustinin
- Keldysh Institute of Applied Mathematics RAS, Moscow, 125047, Russia
| | - Taras K Antal
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | | | - Andrei B Rubin
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| |
Collapse
|
9
|
Ramos S, Le Sueur AL, Horness RE, Specker JT, Collins JA, Thibodeau KE, Thielges MC. Heterogeneous and Highly Dynamic Interface in Plastocyanin-Cytochrome f Complex Revealed by Site-Specific 2D-IR Spectroscopy. J Phys Chem B 2019; 123:2114-2122. [PMID: 30742428 DOI: 10.1021/acs.jpcb.8b12157] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Transient protein complexes are crucial for sustaining dynamic cellular processes. The complexes of electron-transfer proteins are a notable example, such as those formed by plastocyanin (Pc) and cytochrome f (cyt f) in the photosynthetic apparatus. The dynamic and heterogeneous nature of these complexes, however, makes their study challenging. To better elucidate the complex of Nostoc Pc and cyt f, 2D-IR spectroscopy coupled to site-specific labeling with cyanophenylalanine infrared (IR) probes was employed to characterize how the local environments at sites along the surface of Pc were impacted by cyt f binding. The results indicate that Pc most substantially engages with cyt f via the hydrophobic patch around the copper redox site. Complexation with cyt f led to an increase in inhomogeneous broadening of the probe absorptions, reflective of increased heterogeneity of interactions with their environment. Notably, most of the underlying states interconverted very rapidly (1 to 2 ps), suggesting a complex with a highly mobile interface. The data support a model of the complex consisting of a large population of an encounter complex. Additionally, the study demonstrates the application of 2D-IR spectroscopy with site-specifically introduced probes to reveal new quantitative insight about dynamic biochemical systems.
Collapse
Affiliation(s)
- Sashary Ramos
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| | - Amanda L Le Sueur
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| | - Rachel E Horness
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| | - Jonathan T Specker
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| | - Jessica A Collins
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| | - Katherine E Thibodeau
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Indiana University , Department of Chemistry , Bloomington , Indiana 47405 , United States
| |
Collapse
|
10
|
Foerster J, Poehner I, Ullmann GM. MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions. ACS OMEGA 2018; 3:6465-6475. [PMID: 31458826 PMCID: PMC6644659 DOI: 10.1021/acsomega.8b00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/22/2018] [Indexed: 06/10/2023]
Abstract
MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand-receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level. The application of MCMap is exemplified by the electron-transfer complex of cytochrome c peroxidase and cytochrome c from baker's yeast. The functionality of MCMap and the visualization of simulation data are in particular demonstrated by studying the dependence of the association on ionic strength and on the oxidation state of the binding partner. Furthermore, microscopically, a repulsion of a second ligand can be seen in the ternary complex upon the change of the oxidation state of the bound cytochrome c. The software is made available as open source software together with the example and can be downloaded free of charge from http://www.bisb.uni-bayreuth.de/index.php?page=downloads.
Collapse
|
11
|
Teilum K, Kunze MBA, Erlendsson S, Kragelund BB. (S)Pinning down protein interactions by NMR. Protein Sci 2017; 26:436-451. [PMID: 28019676 PMCID: PMC5326574 DOI: 10.1002/pro.3105] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 12/14/2016] [Accepted: 12/14/2016] [Indexed: 11/29/2022]
Abstract
Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions. These types of analyses determine the amounts and proportions of individual constituents that participate in a reaction as well as their rates of reactions and their thermodynamics. Although many different methods are available, there is currently no single method able to quantitatively capture and describe all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates, and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background and illustrate simple protein-ligand interactions as well as typical strategies for measuring binding constants using NMR spectroscopy. Finally, this review provides examples of caveats of the method as well as the options to improve the outcome of an NMR analysis of a protein interaction reaction.
Collapse
Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Micha Ben Achim Kunze
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Simon Erlendsson
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| |
Collapse
|
12
|
Identification of productive and futile encounters in an electron transfer protein complex. Proc Natl Acad Sci U S A 2017; 114:E1840-E1847. [PMID: 28223532 DOI: 10.1073/pnas.1616813114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Well-defined, stereospecific states in protein complexes are often in exchange with an ensemble of more dynamic orientations: the encounter states. The structure of the stereospecific complex between cytochrome P450cam and putidaredoxin was solved recently by X-ray diffraction as well as paramagnetic NMR spectroscopy. Other than the stereospecific complex, the NMR data clearly show the presence of additional states in the complex in solution. In these encounter states, populated for a small percentage of the time, putidaredoxin assumes multiple orientations and samples a large part of the surface of cytochrome P450cam. To characterize the nature of the encounter states, an extensive paramagnetic NMR dataset has been analyzed using the Maximum Occurrence of Regions methodology. The analysis reveals the location and maximal spatial extent of the additional states needed to fully explain the NMR data. Under the assumption of sparsity of the size of the conformational ensemble, several minor states can be located quite precisely. The distribution of these minor states correlates with the electrostatic potential map around cytochrome P450cam. Whereas some minor states are on isolated positively charged patches, others are connected to the stereospecific site via positively charged paths. The existence of electrostatically favorable pathways between the stereospecific interaction site and the different minor states or lack thereof suggests a means to discriminate between productive and futile encounter states.
Collapse
|
13
|
Electron transfer and docking between cytochrome cd 1 nitrite reductase and different redox partners — A comparative study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1412-1421. [DOI: 10.1016/j.bbabio.2016.04.279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/30/2016] [Accepted: 04/27/2016] [Indexed: 11/21/2022]
|
14
|
Veit S, Nagadoi A, Rögner M, Rexroth S, Stoll R, Ikegami T. The cyanobacterial cytochrome b6f subunit PetP adopts an SH3 fold in solution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:705-14. [DOI: 10.1016/j.bbabio.2016.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/02/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
|
15
|
Zhang L, Borthakur S, Buck M. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations. Biophys J 2016; 110:877-86. [PMID: 26910424 PMCID: PMC4776036 DOI: 10.1016/j.bpj.2015.12.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 12/11/2022] Open
Abstract
The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in that it initially involves transitions to surfaces with fewer, less favorable contacts compared with those seen in the fully formed complex.
Collapse
Affiliation(s)
- Liqun Zhang
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Susmita Borthakur
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio; Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio.
| |
Collapse
|
16
|
Prior SH, Byrne TS, Tokmina-Roszyk D, Fields GB, Van Doren SR. Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12. J Biol Chem 2016; 291:7888-901. [PMID: 26887942 DOI: 10.1074/jbc.m115.703124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 11/06/2022] Open
Abstract
Collagenolysis is essential in extracellular matrix homeostasis, but its structural basis has long been shrouded in mystery. We have developed a novel docking strategy guided by paramagnetic NMR that positions a triple-helical collagen V mimic (synthesized with nitroxide spin labels) in the active site of the catalytic domain of matrix metalloproteinase-12 (MMP-12 or macrophage metalloelastase) primed for catalysis. The collagenolytically productive complex forms by utilizing seven distinct subsites that traverse the entire length of the active site. These subsites bury ∼1,080 Å(2)of surface area, over half of which is contributed by the trailing strand of the synthetic collagen V mimic, which also appears to ligate the catalytic zinc through the glycine carbonyl oxygen of its scissile G∼VV triplet. Notably, the middle strand also occupies the full length of the active site where it contributes extensive interfacial contacts with five subsites. This work identifies, for the first time, the productive and specific interactions of a collagen triple helix with an MMP catalytic site. The results uniquely demonstrate that the active site of the MMPs is wide enough to accommodate two strands from collagen triple helices. Paramagnetic relaxation enhancements also reveal an extensive array of encounter complexes that form over a large part of the catalytic domain. These transient complexes could possibly facilitate the formation of collagenolytically active complexes via directional Brownian tumbling.
Collapse
Affiliation(s)
- Stephen H Prior
- From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Todd S Byrne
- From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Dorota Tokmina-Roszyk
- the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, and
| | - Gregg B Fields
- the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, and the Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458
| | - Steven R Van Doren
- From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211,
| |
Collapse
|
17
|
Abstract
Many biomolecular interactions proceed via lowly populated, transient intermediates. Believed to facilitate formation of a productive complex, these short-lived species are inaccessible to conventional biophysical and structural techniques and, until recently, could only be studied by theoretical simulations. Recent development of experimental approaches sensitive to the presence of minor species--in particular paramagnetic relaxation enhancement (PRE) NMR spectroscopy--has enabled direct visualization and detailed characterization of such lowly populated states. Collectively referred to as an encounter complex, the binding intermediates are particularly important in transient protein interactions, such as those orchestrating signaling cascades or energy-generating electron transfer (ET) chains. Here I discuss encounter complexes of redox proteins mediating biological ET reactions, which are essential for many vital cellular activities including oxidative phosphorylation and photosynthesis. In particular, this Account focuses on the complex of cytochrome c (Cc) and cytochrome c peroxidase (CcP), which is a paradigm of biomolecular ET and an attractive system for studying protein binding and enzymatic catalysis. The Cc-CcP complex formation proceeds via an encounter state, consisting of multiple protein-protein orientations sampled in the search of the dominant, functionally active bound form and exhibiting a broad spatial distribution, in striking agreement with earlier theoretical simulations. At low ionic strength, CcP binds another Cc molecule to form a weak ternary complex, initially inferred from kinetics experiments and postulated to account for the measured ET activity. Despite strenuous efforts, the ternary complex could not be observed directly and remained eagerly sought for the past two decades. Very recently, we have solved its structure in solution and shown that it consists of two binding forms: the dominant, ET-inactive geometry and an ensemble of lowly populated species with short separations between Cc and CcP cofactors, which summarily account for the measured ET rate. Unlike most protein complexes, which require accurate alignment of the binding surfaces in a single, well-defined orientation to carry out their function, redox proteins can form multiple productive complexes. As fast ET will occur any time the redox centers of the binding partners are close enough to ensure efficient electron tunneling across the interface, many protein-protein orientations are expected to be ET active. The present analysis confirms that the low-occupancy states can support the functional ET activity and contribute to the stability of redox protein complexes. As illustrated here, boundaries between the dominant and the encounter forms become blurred for many dynamic ET systems, which are more aptly described by ensembles of functionally and structurally heterogeneous bound forms.
Collapse
Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, and Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| |
Collapse
|
18
|
Owens CP, Katz FEH, Carter CH, Luca MA, Tezcan FA. Evidence for Functionally Relevant Encounter Complexes in Nitrogenase Catalysis. J Am Chem Soc 2015; 137:12704-12. [PMID: 26360912 PMCID: PMC4809638 DOI: 10.1021/jacs.5b08310] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nitrogenase is the only enzyme that can convert atmospheric dinitrogen (N2) into biologically usable ammonia (NH3). To achieve this multielectron redox process, the nitrogenase component proteins, MoFe-protein (MoFeP) and Fe-protein (FeP), repeatedly associate and dissociate in an ATP-dependent manner, where one electron is transferred from FeP to MoFeP per association. Here, we provide experimental evidence that encounter complexes between FeP and MoFeP play a functional role in nitrogenase catalysis. The encounter complexes are stabilized by electrostatic interactions involving a positively charged patch on the β-subunit of MoFeP. Three single mutations (βAsn399Glu, βLys400Glu, and βArg401Glu) in this patch were generated in Azotobacter vinelandii MoFeP. All of the resulting variants displayed decreases in specific catalytic activity, with the βK400E mutation showing the largest effect. As simulated by the Thorneley-Lowe kinetic scheme, this single mutation lowered the rate constant for FeP-MoFeP association 5-fold. We also found that the βK400E mutation did not affect the coupling of ATP hydrolysis with electron transfer (ET) between FeP and MoFeP. These data suggest a mechanism where FeP initially forms encounter complexes on the MoFeP β-subunit surface en route to the ATP-activated, ET-competent complex over the αβ-interface.
Collapse
Affiliation(s)
- Cedric P. Owens
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - Faith E. H. Katz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - Cole H. Carter
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - Maria A. Luca
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92039, United States
| |
Collapse
|
19
|
Khruschev SS, Abaturova AM, Fedorov VA, Kovalenko IB, Riznichenko GY, Rubin AB. The identification of intermediate states of the electron-transfer proteins plastocyanin and cytochrome f diffusional encounters. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
20
|
Landrieu I, Verger A, Baert JL, Rucktooa P, Cantrelle FX, Dewitte F, Ferreira E, Lens Z, Villeret V, Monté D. Characterization of ERM transactivation domain binding to the ACID/PTOV domain of the Mediator subunit MED25. Nucleic Acids Res 2015; 43:7110-21. [PMID: 26130716 PMCID: PMC4538835 DOI: 10.1093/nar/gkv650] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/28/2015] [Indexed: 01/12/2023] Open
Abstract
The N-terminal acidic transactivation domain (TAD) of ERM/ETV5 (ERM38–68), a PEA3 group member of Ets-related transcription factors, directly interacts with the ACID/PTOV domain of the Mediator complex subunit MED25. Molecular details of this interaction were investigated using nuclear magnetic resonance (NMR) spectroscopy. The TAD is disordered in solution but has a propensity to adopt local transient secondary structure. We show that it folds upon binding to MED25 and that the resulting ERM–MED25 complex displays characteristics of a fuzzy complex. Mutational analysis further reveals that two aromatic residues in the ERM TAD (F47 and W57) are involved in the binding to MED25 and participate in the ability of ERM TAD to activate transcription. Mutation of a key residue Q451 in the VP16 H1 binding pocket of MED25 affects the binding of ERM. Furthermore, competition experiments show that ERM and VP16 H1 share a common binding interface on MED25. NMR data confirms the occupancy of this binding pocket by ERM TAD. Based on these experimental data, a structural model of a functional interaction is proposed. This study provides mechanistic insights into the Mediator–transactivator interactions.
Collapse
Affiliation(s)
- Isabelle Landrieu
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Alexis Verger
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Jean-Luc Baert
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Prakash Rucktooa
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - François-Xavier Cantrelle
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Frédérique Dewitte
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Elisabeth Ferreira
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Zoé Lens
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Vincent Villeret
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| | - Didier Monté
- CNRS UMR 8576, Université de Lille, Parc CNRS de la Haute Borne, 50 avenue de Halley, B.P. 70478, 59658 Villeneuve d'Ascq Cedex, France
| |
Collapse
|
21
|
Khruschev SS, Abaturova AM, Diakonova AN, Fedorov VA, Ustinin DM, Kovalenko IB, Riznichenko GY, Rubin AB. Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
22
|
Moreno-Beltrán B, Díaz-Moreno I, González-Arzola K, Guerra-Castellano A, Velázquez-Campoy A, De la Rosa MA, Díaz-Quintana A. Respiratory complexes III and IV can each bind two molecules of cytochrome c at low ionic strength. FEBS Lett 2015; 589:476-83. [PMID: 25595453 DOI: 10.1016/j.febslet.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/26/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022]
Abstract
The transient interactions of respiratory cytochrome c with complexes III and IV is herein investigated by using heterologous proteins, namely human cytochrome c, the soluble domain of plant cytochrome c1 and bovine cytochrome c oxidase. The binding molecular mechanisms of the resulting cross-complexes have been analyzed by Nuclear Magnetic Resonance and Isothermal Titration Calorimetry. Our data reveal that the two cytochrome c-involving adducts possess a 2:1 stoichiometry - that is, two cytochrome c molecules per adduct - at low ionic strength. We conclude that such extra binding sites at the surfaces of complexes III and IV can facilitate the turnover and sliding of cytochrome c molecules and, therefore, the electron transfer within respiratory supercomplexes.
Collapse
Affiliation(s)
- Blas Moreno-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain.
| | - Katiuska González-Arzola
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandra Guerra-Castellano
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI) - Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Maria de Luna 11, 50018 Zaragoza, Spain
| | - Miguel A De la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla-CSIC, Avda. Américo Vespucio 49, Sevilla 41092, Spain
| |
Collapse
|
23
|
Zheng T, Boyle A, Robson Marsden H, Valdink D, Martelli G, Raap J, Kros A. Probing coiled-coil assembly by paramagnetic NMR spectroscopy. Org Biomol Chem 2015; 13:1159-68. [DOI: 10.1039/c4ob02125h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Here a new method to determine the orientation of coiled-coil peptide motifs is described.
Collapse
Affiliation(s)
- TingTing Zheng
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Aimee Boyle
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Hana Robson Marsden
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Dayenne Valdink
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Giuliana Martelli
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Jan Raap
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| | - Alexander Kros
- Dept. Supramolecular & Biomaterials Chemistry
- Leiden Institute of Chemistry
- Leiden University
- Leiden
- The Netherlands
| |
Collapse
|
24
|
Bashir Q, Meulenbroek EM, Pannu NS, Ubbink M. Engineering specificity in a dynamic protein complex with a single conserved mutation. FEBS J 2014; 281:4892-905. [DOI: 10.1111/febs.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Navraj S. Pannu
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| |
Collapse
|
25
|
The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1305-15. [DOI: 10.1016/j.bbabio.2014.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/13/2014] [Accepted: 03/16/2014] [Indexed: 11/23/2022]
|
26
|
Guan JY, Foerster JM, Drijfhout JW, Timmer M, Blok A, Ullmann GM, Ubbink M. An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy. Chembiochem 2014; 15:556-66. [DOI: 10.1002/cbic.201300623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Indexed: 12/21/2022]
|
27
|
Hass MAS, Ubbink M. Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints. Curr Opin Struct Biol 2014; 24:45-53. [DOI: 10.1016/j.sbi.2013.11.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 10/25/2022]
|
28
|
Liu Y, Gridnev ID, Zhang W. Mechanism of the Asymmetric Hydrogenation of Exocyclic α,β-Unsaturated Carbonyl Compounds with an Iridium/BiphPhox Catalyst: NMR and DFT Studies. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309677] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
29
|
Liu Y, Gridnev ID, Zhang W. Mechanism of the Asymmetric Hydrogenation of Exocyclic α,β-Unsaturated Carbonyl Compounds with an Iridium/BiphPhox Catalyst: NMR and DFT Studies. Angew Chem Int Ed Engl 2014; 53:1901-5. [DOI: 10.1002/anie.201309677] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Indexed: 11/09/2022]
|
30
|
Scanu S, Foerster JM, Timmer M, Ullmann GM, Ubbink M. Loss of electrostatic interactions causes increase of dynamics within the plastocyanin-cytochrome f complex. Biochemistry 2013; 52:6615-26. [PMID: 23984801 DOI: 10.1021/bi400450q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent studies on the electron transfer complex formed by cytochrome f and plastocyanin from Nostoc revealed that both hydrophobic and electrostatic interactions play a role in the process of complex formation. To study the balance between these two types of interactions in the encounter and the final state, the complex between plastocyanin from Phormidium laminosum and cytochrome f from Nostoc sp. PCC 7119 was investigated using NMR spectroscopy and Monte Carlo docking. Cytochrome f has a highly negative charge. Phormidium plastocyanin is similar to that from Nostoc, but the net charge of the protein is negative rather than positive. NMR titrations of Zn-substituted Phormidium plastocyanin and Nostoc cytochrome f indicated that a complex with an affinity intermediate between those of the Nostoc and Phormidium complexes is formed. Plastocyanin was found in a head-on orientation, as determined using pseudocontact shifts, similar to that in the Phormidium complex, in which the hydrophobic patch represents the main site of interaction on plastocyanin. However, the interaction in the cross-complex is dependent on electrostatics, similar to that in the Nostoc complex. The negative charge of plastocyanin decreases, but not abolishes, the attraction to cytochrome f, resulting in the formation of a more diffuse encounter complex than in the Nostoc case, as could be determined using paramagnetic relaxation spectroscopy. This work illustrates the subtle interplay of electrostatic and hydrophobic interactions in the formation of transient protein complexes. The results are discussed in the context of a model for association on the basis of hydrophobic contacts in the encounter state.
Collapse
Affiliation(s)
- Sandra Scanu
- Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | | | | | | |
Collapse
|
31
|
Schilder J, Ubbink M. Formation of transient protein complexes. Curr Opin Struct Biol 2013; 23:911-8. [PMID: 23932200 DOI: 10.1016/j.sbi.2013.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/11/2013] [Accepted: 07/11/2013] [Indexed: 01/16/2023]
Abstract
The encounter complex of two proteins is a dynamic intermediate state that guides proteins to their binding site, thus enhancing the rate of complex formation. It is particularly useful for complexes that must balance a biological requirement for high turnover with the need for specific binding, such as electron transfer complexes. Here, we describe the current methods for studying and visualizing encounter complexes. We discuss recent developments in mapping the energy landscapes, the role of hydrophobic interactions during encounter complex formation and the discovery of futile encounter complexes. These studies have not only provided insight into encounter complexes of electron transfer proteins, but also opened up new questions and approaches for studying encounter complexes in other weakly associated proteins.
Collapse
Affiliation(s)
- Jesika Schilder
- Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | |
Collapse
|