Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains

Dasgupta, Soumyasri; Hu, Xiaoyu; Keizers, Peter H. J.; Liu, Weimin; Luchinat, Claudio; Nagulapalli, Malini; Overhand, Mark; Parigi, Giacomo; Sgheri, Luca; Ubbink, Marcellus

doi:10.1007/s10858-011-9532-2

Cited by 40 publications

(51 citation statements)

References 51 publications

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“…42). One of such methods consists of assigning to each conformer a value, called Maximum Occurrence (MaxOcc), which is defined as the highest fraction of time for which this conformer can exist in any optimized conformational ensemble without causing violations of the experimental averaged data (34,37,(43)(44)(45)(46)(47). It, thus, provides an upper bound for the population of each conformer in the real conformational ensemble of the system.…”

Section: −3mentioning

confidence: 99%

Identification of productive and futile encounters in an electron transfer protein complex

Andrałojć

Hiruma

Wei-min

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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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.paramagnetic NMR | encounter complex | cytochrome P450cam | putidaredoxin | maximum occurrence C rystal structures suggest that proteins assume unique, stereospecific orientations within protein-protein complexes. However, a number of studies in solution have made clear that encounter states are an inherent element of protein complexes (1-8), especially in electron transfer (ET), where the interactions are often extremely fast (9). In the encounter complex, the proteins assume multiple other orientations, often in equilibrium with the major stereospecific state. In low-affinity complexes with dissociation constant (K d ) values > 10 μM, the encounter complex can represent a sizeable fraction, and in some cases, a well-defined, stereospecific complex may even be absent (10-15). The presence of encounter states may be a consequence of the chemical nature of proteins. In nonobligate stereospecific complexes, the interface represents a small fraction of the total protein surface, and therefore, it is reasonable to assume that weak interactions also occur elsewhere. In the case in which protein pairs have evolved to exhibit a high association rate by using electrostatic preorientation, electrostatic patches seem to enhance the presence of encounter states (16,17). On the one hand, the preorientation reduces the surface area that is visited by the partner, thus enhancing the number of productive encounters, but on the other hand, highly charged patches can bind the oppositely charged protein in many orientations with a...

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Section: −3mentioning

confidence: 99%

Identification of productive and futile encounters in an electron transfer protein complex

Andrałojć

Hiruma

Wei-min

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…The MO of a given conformation is defined, and numerically calculated, as the maximum weight that this conformation can have in any suitable ensemble while still maintaining the ability of the ensemble to reproduce the experimental data. Paramagnetic NMR spectroscopic and small angle x-ray scattering (SAXS) data can be used as experimental restraints to calculate the MO of conformations of two-domain proteins, as previously demonstrated for calmodulin (CaM) alone (31,33,34) and its complexes with target peptides (30,35). The paramagnetic restraints originate FIGURE 1.…”

Section: Matrix Metalloproteinases (Mmps)mentioning

confidence: 99%

“…from the presence of paramagnetic metals, incorporated either in an existing metal binding site (36) or in a tag covalently bound to the protein (33). In the present case a lanthanide binding tag was used.…”

Section: Volume 288 • Number 42 • October 18 2013mentioning

confidence: 99%

Examination of Matrix Metalloproteinase-1 in Solution

Cerofolini¹,

Fields

Fragai

et al. 2013

Journal of Biological Chemistry

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Background: Matrix metalloproteinase-1 (MMP-1) collagenolysis relies on interdomain flexibility. Results: In all high maximum occurrence conformations, the MMP-1 hemopexin-like domain residues reported responsible for binding to the collagen triple-helix are solvent exposed. Conclusion: MMP-1 in solution is poised to interact with collagen and proceed along the steps of collagenolysis. Significance: The maximum occurrence approach can evaluate the predominant domain conformations for numerous multidomain enzymes.

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“…The advantages offered by paramagnetic restraints are more and more exploited thanks to the development of paramagnetic tags that can be attached to diamagnetic proteins, so that PCSs and RDCs can be easily measured also for molecules without a natural metal binding site (Wöhnert et al 2003;Rodriguez-Castañeda et al 2006;Su et al 2006;Su et al 2008a;Keizers et al 2008;Su et al 2008b;Zhuang et al 2008;Häussinger et al 2009;Su and Otting 2010;Hass et al 2010;Man et al 2010;Das Gupta et al 2011;Liu et al 2012;Cerofolini et al 2013;Yagi et al 2013a;Gempf et al 2013;Kobashigawa et al 2012;Saio et al 2011;Watanabe et al 2010;Loh et al 2013;Swarbrick et al 2011aSwarbrick et al , 2011b.…”

Section: Introductionmentioning

confidence: 99%

FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data

et al. 2014

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Pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) arising from the presence of paramagnetic metal ions in proteins as well as RDCs due to partial orientation induced by external orienting media are nowadays routinely measured as a part of the NMR characterization of biologically relevant systems. PCSs and RDCs are becoming more and more popular as restraints (1) to determine and/or refine protein structures in solution, (2) to monitor the extent of conformational heterogeneity in systems composed of rigid domains which can reorient with respect to one another, and (3) to obtain structural information in protein-protein complexes. The use of both PCSs and RDCs proceeds through the determination of the anisotropy tensors which are at the origin of these NMR observables. A new user-friendly web tool, called FANTEN (Finding ANisotropy TENsors), has been developed for the determination of the anisotropy tensors related to PCSs and RDCs and has been made freely available through the WeNMR ( http://fanten-enmr.cerm.unifi.it:8080 ) gateway. The program has many new features not available in other existing programs, among which the possibility of a joint analysis of several sets of PCS and RDC data and the possibility to perform rigid body minimizations.

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Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains

Cited by 40 publications

References 51 publications

Identification of productive and futile encounters in an electron transfer protein complex

Identification of productive and futile encounters in an electron transfer protein complex

Examination of Matrix Metalloproteinase-1 in Solution

FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data

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