1
|
Ravera E, Gigli L, Fiorucci L, Luchinat C, Parigi G. The evolution of paramagnetic NMR as a tool in structural biology. Phys Chem Chem Phys 2022; 24:17397-17416. [PMID: 35849063 DOI: 10.1039/d2cp01838a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic NMR data contain extremely accurate long-range information on metalloprotein structures and, when used in the frame of integrative structural biology approaches, they allow for the retrieval of structural details to a resolution that is not achievable using other techniques. Paramagnetic data thus represent an extremely powerful tool to refine protein models in solution, especially when coupled to X-ray or cryoelectron microscopy data, to monitor the formation of complexes and determine the relative arrangements of their components, and to highlight the presence of conformational heterogeneity. More recently, theoretical and computational advancements in quantum chemical calculations of paramagnetic NMR observables are progressively opening new routes in structural biology, because they allow for the determination of the structure within the coordination sphere of the metal center, thus acting as a loupe on sites that are difficult to observe but very important for protein function.
Collapse
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Letizia Fiorucci
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| |
Collapse
|
2
|
Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
Collapse
Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| |
Collapse
|
3
|
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.
Collapse
|
4
|
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: 6] [Impact Index Per Article: 2.0] [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
|
5
|
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] [MESH Headings] [Grants] [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 LaboratoryLeiden UniversityNiels Bohrweg 22333 CALeiden (TheNetherlands
| | - Jesika T. Schilder
- Leiden Institute of ChemistryLeiden University, Gorlaeus LaboratoriesEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Antonella Di Savino
- Leiden Institute of ChemistryLeiden University, Gorlaeus LaboratoriesEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Anneloes Blok
- Leiden Institute of ChemistryLeiden University, Gorlaeus LaboratoriesEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Marcellus Ubbink
- Leiden Institute of ChemistryLeiden University, Gorlaeus LaboratoriesEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Martina Huber
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes LaboratoryLeiden UniversityNiels Bohrweg 22333 CALeiden (TheNetherlands
| |
Collapse
|
6
|
Pachis ST, Hiruma Y, Tromer EC, Perrakis A, Kops GJPL. Interactions between N-terminal Modules in MPS1 Enable Spindle Checkpoint Silencing. Cell Rep 2020; 26:2101-2112.e6. [PMID: 30784592 DOI: 10.1016/j.celrep.2019.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/13/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022] Open
Abstract
Faithful chromosome segregation relies on the ability of the spindle assembly checkpoint (SAC) to delay anaphase onset until chromosomes are attached to the mitotic spindle via their kinetochores. MPS1 kinase is recruited to kinetochores to initiate SAC signaling and is removed from kinetochores once stable microtubule attachments have been formed to allow normal mitotic progression. Here, we show that a helical fragment within the kinetochore-targeting N-terminal extension (NTE) module of MPS1 is required for interactions with kinetochores and forms intramolecular interactions with its adjacent tetratricopeptide repeat (TPR) domain. Bypassing this NTE-TPR interaction results in high MPS1 levels at kinetochores due to loss of regulatory input into MPS1 localization, inefficient MPS1 delocalization upon microtubule attachment, and SAC silencing defects. These results show that SAC responsiveness to attachments relies on regulated intramolecular interactions in MPS1 and highlight the sensitivity of mitosis to perturbations in the dynamics of the MPS1-NDC80-C interactions.
Collapse
Affiliation(s)
- Spyridon T Pachis
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, the Netherlands
| | - Yoshitaka Hiruma
- Department of Biochemistry, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands
| | - Eelco C Tromer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Anastassis Perrakis
- Department of Biochemistry, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, the Netherlands.
| |
Collapse
|
7
|
Miao Q, Liu WM, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019; 58:13093-13100. [PMID: 31314159 PMCID: PMC6771572 DOI: 10.1002/anie.201906049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/15/2019] [Indexed: 01/20/2023]
Abstract
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.
Collapse
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New, Taipei City, 24205, Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| |
Collapse
|
8
|
Miao Q, Liu W, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double‐Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Wei‐Min Liu
- Department of Chemistry Fu Jen Catholic University No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205 Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| |
Collapse
|
9
|
Paramagnetic NMR as a new tool in structural biology. Emerg Top Life Sci 2018; 2:19-28. [DOI: 10.1042/etls20170084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022]
Abstract
NMR (nuclear magnetic resonance) investigation through the exploitation of paramagnetic effects is passing from an approach limited to few specialists in the field to a generally applicable method that must be considered, especially for the characterization of systems hardly affordable with other techniques. This is mostly due to the fact that paramagnetic data are long range in nature, thus providing information for the structural and dynamic characterization of complex biomolecular architectures in their native environment. On the other hand, this information usually needs to be complemented by data from other sources. Integration of paramagnetic NMR with other techniques, and the development of protocols for a joint analysis of all available data, is fundamental for achieving a comprehensive characterization of complex biological systems. We describe here a few examples of the new possibilities offered by paramagnetic data used in integrated structural approaches.
Collapse
|
10
|
Gentry KA, Prade E, Barnaba C, Zhang M, Mahajan M, Im SC, Anantharamaiah GM, Nagao S, Waskell L, Ramamoorthy A. Kinetic and Structural Characterization of the Effects of Membrane on the Complex of Cytochrome b 5 and Cytochrome c. Sci Rep 2017; 7:7793. [PMID: 28798301 PMCID: PMC5552742 DOI: 10.1038/s41598-017-08130-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Cytochrome b5 (cytb5) is a membrane protein vital for the regulation of cytochrome P450 (cytP450) metabolism and is capable of electron transfer to many redox partners. Here, using cyt c as a surrogate for cytP450, we report the effect of membrane on the interaction between full-length cytb5 and cyt c for the first time. As shown through stopped-flow kinetic experiments, electron transfer capable cytb5 - cyt c complexes were formed in the presence of bicelles and nanodiscs. Experimentally measured NMR parameters were used to map the cytb5-cyt c binding interface. Our experimental results identify differences in the binding epitope of cytb5 in the presence and absence of membrane. Notably, in the presence of membrane, cytb5 only engaged cyt c at its lower and upper clefts while the membrane-free cytb5 also uses a distal region. Using restraints generated from both cytb5 and cyt c, a complex structure was generated and a potential electron transfer pathway was identified. These results demonstrate the importance of studying protein-protein complex formation in membrane mimetic systems. Our results also demonstrate the successful preparation of novel peptide-based lipid nanodiscs, which are detergent-free and possesses size flexibility, and their use for NMR structural studies of membrane proteins.
Collapse
Affiliation(s)
| | - Elke Prade
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlo Barnaba
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meng Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mukesh Mahajan
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - G M Anantharamaiah
- Department of Medicine, UAB Medical Center, Birmingham, Alabama, 35294, USA
| | - Satoshi Nagao
- Graduate School of Material Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and Veterans Affairs Medical Center, Ann Arbor, Michigan, 48105, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
11
|
Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
Collapse
|
12
|
Schilder J, Ubbink M. Weak self-association of cytochrome c peroxidase molecules observed by paramagnetic NMR. JOURNAL OF BIOMOLECULAR NMR 2016; 65:29-40. [PMID: 27236778 PMCID: PMC4908164 DOI: 10.1007/s10858-016-0035-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/03/2016] [Indexed: 06/05/2023]
Abstract
There is growing experimental evidence that many proteins exhibit a tendency for (ultra)weak homo- or hetero- oligomerization interactions. With the development of paramagnetic relaxation enhancement NMR spectroscopy it has become possible to characterize weak complexes experimentally and even detect complexes with affinities in the 1-25 mM range. We present evidence for a weak complex between cytochrome c peroxidase (CcP) molecules. In a previous study, we attached nitroxide based spin labels at three positions on CcP with the intent of observing intramolecular PRE effects. However, several intermolecular PRE effects were also observed suggesting a weak self-association between CcP molecules. The CcP-CcP complex was characterized using paramagnetic NMR and protein docking. The interaction occurs between the surface that is also part of the stereo-specific binding site for its physiological partner, cytochrome c (Cc), and several small, positively charged patches on the "back" of CcP. The CcP-CcP complex is not a stereo-specific complex. It is a dynamic ensemble of orientations, characteristic of an encounter state. The contact areas resemble those observed for CcP molecules in crystals. The CcP-CcP complex formation competes with that of the CcP-Cc complex. However, the affinity for Cc is much larger and thus it is expected that, under physiological conditions, auto-inhibition will be limited. A weak self-association between cytochrome c peroxidase molecules was characterized using paramagnetic NMR.
Collapse
Affiliation(s)
- Jesika Schilder
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| |
Collapse
|
13
|
Schilder J, Liu WM, Kumar P, Overhand M, Huber M, Ubbink M. Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement. Phys Chem Chem Phys 2016; 18:5729-42. [DOI: 10.1039/c5cp03781f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The effect of spin label mobility on the accuracy of protein–protein docking calculations was investigated using inter- and intra-molecular PRE data.
Collapse
Affiliation(s)
- Jesika Schilder
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| | - Wei-Min Liu
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| | - Pravin Kumar
- Department of Physics
- Huygens-Kamerlingh Onnes Laboratory
- Leiden University
- 2333 CA Leiden
- The Netherlands
| | - Mark Overhand
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| | - Martina Huber
- Department of Physics
- Huygens-Kamerlingh Onnes Laboratory
- Leiden University
- 2333 CA Leiden
- The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| |
Collapse
|
14
|
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
|
15
|
Erman JE, Vitello LB, Pearl NM, Jacobson T, Francis M, Alberts E, Kou A, Bujarska K. Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry. Biochemistry 2015. [PMID: 26212209 DOI: 10.1021/acs.biochem.5b00686] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, we constructed, expressed, and purified 46 charge-reversal mutants of yeast cytochrome c peroxidase (CcP) and determined their electronic absorption spectra, their reaction with H2O2, and their steady-state catalytic properties [ Pearl , N. M. et al. (2008) Biochemistry 47 , 2766 - 2775 ]. Forty-four of the mutants involve the conversion of either an aspartate or glutamate residue to a lysine residue, while two are positive-to-negative mutations, R31E and K149D. In this paper, we report on a calorimetric study of the interaction of each charge-reversal mutant (excluding the internal mutants D76K and D235K) with recombinant yeast iso-1 ferricytochrome c(C102T) (yCc) under conditions where only one-to-one yCc/CcP complex formation is observed. Thirteen of the 44 surface-site charge-reversal mutants decrease the binding affinity for yCc by a factor of 2 or more. Eight of the 13 mutations (E32K, D33K, D34K, E35K, E118K, E201K, E290K, E291K) occur within, or on the immediate periphery, of the crystallographically defined yCc binding site [ Pelletier , H. and Kraut , J. (1992) Science 258 , 1748 - 1755 ], three of the mutations (D37K, E98K, E209K) are slightly removed from the crystallographic site, and two of the mutations (D165K, D241K) occur on the "back-side" of CcP. The current study is consistent with a model for yCc binding to CcP in which yCc binds predominantly near the region defined by crystallographic structure of the 1:1 yCc-CcP complex, whether as a stable electron-transfer active complex or as part of a dynamic encounter complex.
Collapse
Affiliation(s)
- James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Lidia B Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Naw May Pearl
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Timothy Jacobson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Meka Francis
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Erik Alberts
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Allen Kou
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Kathy Bujarska
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| |
Collapse
|