Formation of transient protein complexes

Schilder, Jesika T.; Ubbink, Marcellus

doi:10.1016/j.sbi.2013.07.009

Cited by 62 publications

(56 citation statements)

References 54 publications

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“…However, a number of studies in solution have made clear that encounter states are an inherent element of protein complexes (1)(2)(3)(4)(5)(6)(7)(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.…”

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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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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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“…It has been suggested that these regions might confer higher thermodynamic stability, thus indirectly contributing to binding energy (33), or provide a larger capture radius for long range electrostatic interactions that may facilitate the formation of an "encounter complex" or an ensemble of encounter complexes that later evolve into the final complex (34,35). Indeed, it was shown previously that the C70WT construct is considerably more stable than the C53WT construct (33,36).…”

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confidence: 99%

Synergic Role of Nucleophosmin Three-helix Bundle and a Flanking Unstructured Tail in the Interaction with G-quadruplex DNA

Arcovito

Chiarella

Longa

et al. 2014

Journal of Biological Chemistry

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Background: Nucleophosmin is a nucleolar protein that interacts with G-quadruplexes. Results: Site-directed mutagenesis and molecular dynamics unravel the role of single residues in complex formation. Conclusion: A disordered segment of nucleophosmin contributes to G-quadruplex recognition by facilitating the formation of an encounter complex and transiently interacting with the G-quadruplex. Significance: Understanding the role played by flanking fuzziness is an important issue in protein/DNA interactions.

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“…Such perturbations of NMR peaks are minimal in encounter complexes (32). NMR detection of the line broadening of one partner introduced by an unpaired electron on the other partner provides an excellent means to characterize both specific and lightly populated nonspecific modes of binding (32)(33)(34)(35). The unpaired electron, typically introduced in a nitroxide group, has such a strong magnetic moment that its dipole-dipole broadening of the NMR peaks of neighboring protons reaches up to around 25 Å despite its steep decline proportional to 1/r 6 (36).…”

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“…These 1 H NMR line broadenings are measured as paramagnetic relaxation enhancements (PREs) most reliably as transverse relaxation rate constants, ⌫ 2 (35). The insights from PREs into complexes of lower affinity (35) have been exploited to characterize the structures of mixtures of specific and nonspecific protein complexes with DNA (33), proteins (34), redox protein partners (32,37,38), and bilayer mimics (39,40). Synthesis of a nitroxide-containing artificial amino acid into key locations within a triple-helical peptide model of collagens I-III enabled structural capture of its transient complex with a domain of MT1-MMP (41).…”

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Path to Collagenolysis

Prior

Byrne

Tokmina‐Roszyk

et al. 2016

Journal of Biological Chemistry

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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 ϳ1,080 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 GϳVV 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.Collagens comprise around 30% of the protein mass of the body (1) and resist general proteolysis. Matrix metalloproteinases (MMPs) 2 degrade collagen during cancer cell migration (2), angiogenesis (3, 4), destabilization of atherosclerotic plaques (5), and arthritis (6) and after myocardial infarction (7). For instance, plaques contain a collagen-rich cap and are sensitive to MMP-12 secreted by macrophages that makes them more vulnerable to rupture, precipitating myocardial infarction, or stroke (8).Collagen fibrils are bundles of staggered triple helices. Each triple helix comprises three extended strands twisted into a right-handed superhelix with hydrogen bonding between chains (9). Each collagen chain is a long series of GXY triplets in which the glycine is in the interior, X is often proline, and Y is often a stabilizing 4-hydroxyproline (Hyp). Because each chain is offset by one residue, the chains have been named leading, middle, and trailing (10). Lack of Pro and Hyp in four GXY triplets on the C-terminal side of the MMP scissile bond in interstitial collagens (types I, II, and III) was proposed to loosen the triple helix (1); this was later observed as 10-fold symmetry (11).Protease substrates are labeled by increasing distance from the scissile peptide bond with a prime indicating the C-terminal side: P 4 -P 3 -P-P 1 ϳP 1 Ј-P 2 Ј-P 3 Ј-P 4 Ј where ϳ denotes the scissile peptide bond. We refer to the residues on the N-terminal side of the scissile bond as "unprimed" and those on the C-terminal side as "primed." The...

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Formation of transient protein complexes

Cited by 62 publications

References 54 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

Synergic Role of Nucleophosmin Three-helix Bundle and a Flanking Unstructured Tail in the Interaction with G-quadruplex DNA

Path to Collagenolysis

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