Dynamic Structural Changes Are Observed upon Collagen and Metal Ion Binding to the Integrin α1 I Domain

Weinreb, Paul H.; Li, Sheng; Gao, Sharon X.; Liu, Tong; Pepinsky, R. Blake; Caravella, Justin A.; Lee, Jun H.; Woods, Virgil L.

doi:10.1074/jbc.m112.354365

Cited by 15 publications

(17 citation statements)

References 76 publications

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“…These structural rearrangements are consistent with those observed in the structure of the ␣2I upon binding to GFOGER. Further validation of the current structure is provided by a recent analysis of the dynamics of ␣1I in complex with collagen type IV using hydrogen-deuterium exchange mass spectroscopy (57). The study provided evidence of increased conformational mobility in the region between residues 283 and 290, corresponding to loop ␤E-␣6 (including the uncoiled C helix), as well as the region between residues 318 and 332, which corresponds to helix 7.…”

Section: Discussionmentioning

confidence: 67%

The Structure of Integrin α1I Domain in Complex with a Collagen-mimetic Peptide

Chin¹,

Headey²,

Mohanty

et al. 2013

Journal of Biological Chemistry

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Background: Collagen-binding integrins bind differentially to different types of collagen. Results: The solution structure of integrin ␣1I domain in complex with a collagen-mimetic peptide was determined. Conclusion: Integrin ␣1I domain binds collagen in a distinct orientation compared with ␣2I, but the signal transduction mechanisms appear to be conserved. Significance: Understanding the collagen binding specificity of integrins might enable their selective modulation in disease.

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Section: Discussionmentioning

confidence: 67%

The Structure of Integrin α1I Domain in Complex with a Collagen-mimetic Peptide

Chin¹,

Headey²,

Mohanty

et al. 2013

Journal of Biological Chemistry

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“…The quality of each peptide was monitored by individually examining each measured isotopic envelope spectrum for the entire time-course exchange. The deuterium content was calculated for each time point by using specialized software as previously described (26,30).…”

Section: Methodsmentioning

confidence: 99%

Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1

Tamir¹,

Rotem‐Bamberger

Katz

et al. 2014

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

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Life requires orchestrated control of cell proliferation, cell maintenance, and cell death. Involved in these decisions are protein complexes that assimilate a variety of inputs that report on the status of the cell and lead to an output response. Among the proteins involved in this response are nutrient-deprivation autophagy factor-1 (NAF-1)-and Bcl-2. NAF-1 is a homodimeric member of the novel Fe-S protein NEET family, which binds two 2Fe-2S clusters. NAF-1 is an important partner for Bcl-2 at the endoplasmic reticulum to functionally antagonize Beclin 1-dependent autophagy [Chang NC, Nguyen M, Germain M, Shore GC (2010) EMBO J 29 (3):606-618]. We used an integrated approach involving peptide array, deuterium exchange mass spectrometry (DXMS), and functional studies aided by the power of sufficient constraints from direct coupling analysis (DCA) to determine the dominant docked conformation of the NAF-1-Bcl-2 complex. NAF-1 binds to both the pro-and antiapoptotic regions (BH3 and BH4) of Bcl-2, as demonstrated by a nested protein fragment analysis in a peptide array and DXMS analysis. A combination of the solution studies together with a new application of DCA to the eukaryotic proteins NAF-1 and Bcl-2 provided sufficient constraints at amino acid resolution to predict the interaction surfaces and orientation of the protein-protein interactions involved in the docked structure. The specific integrated approach described in this paper provides the first structural information, to our knowledge, for future targeting of the NAF-1-Bcl-2 complex in the regulation of apoptosis/ autophagy in cancer biology.ife requires a controlled balance of energy conversion and utilization. These critical processes are governed by an elaborate set of reactions involving numerous protein-protein interactions. Among them is the ability of organisms to control the recycling of high-energy compounds and to control cell proliferation. These processes are, at least in part, under the control of cell survival and programmed cell death (autophagic and apoptotic) processes. Misregulation of these processes leads to many diseases, including cancer. Among the key proteins involved in these processes are Bcl-2 (1, 2) and the more recently identified iron-sulfur (Fe-S) protein nutrient-deprivation autophagy factor-1 (NAF-1) (also known as Cisd2, Miner1, Eris, and Noxp70) (3-5).NAF-1 is important for human health and disease. Missplicing of NAF-1 causes Wolfram syndrome 2 (6). NAF-1 is also functionally linked to the regulation of autophagy in cancer, and aging (3-5, 7, 8). This protein is a member of the 2Fe-2S cluster NEET family. NAF-1 has a similar backbone fold and 3Cys-1His coordination of the 2Fe-2S cluster as found in the founding member of the NEET family, mitoNEET (mNT). NAF-1 differs from mNT in the distribution of charged and aromatic surface residues (9, 10). These differences alter the 3D shape and electrostatics of the surfaces of mNT and NAF-1, leading to interactions with distinct binding partners. In fact, recent work identifi...

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“…These studies have captured static conformational “snapshots” of the collagen binding α1 I in three different conformations: a closed‐unbound structure determined by X‐ray, a transitional conformation adopted by the gain‐of‐function E317A/α1 I mutant determined by X‐ray, and an open‐bound form determined by solution NMR with a complexed GLOGEN THP . The first glimpse of α1 I slow dynamics originated from a HDX mass spectroscopy study on a α1 I rat‐human chimera and provided important insights on the impact of different ligands on integrin activation . To assess the role of intrinsic conformational fluctuations on the structural switch, our studies focus on elucidating the dynamics of unbound human α1 I integrin and its activating E317A mutant at the atomic level by HDX NMR spectroscopy in combination with ITC to evaluate the binding energetics.…”

Section: Discussionmentioning

confidence: 99%

“…7 The first glimpse of a1 I slow dynamics originated from a HDX mass spectroscopy study on a a1 I rat-human chimera and provided important insights on the impact of different ligands on integrin activation. 42 To assess the role of intrinsic conformational fluctuations on the structural switch, our studies focus on elucidating the dynamics of unbound human a1 I integrin and its activating E317A mutant at the atomic level by HDX NMR spectroscopy in combination with ITC to evaluate the binding energetics. The resultant data suggest that slow timescale motions may be an integral determinant of aI-domain propensity to undergo significant structural changes upon collagen binding.…”

Section: Discussionmentioning

confidence: 99%

Intrinsic local destabilization of the C‐terminus predisposes integrin α1 I domain to a conformational switch induced by collagen binding

et al. 2016

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Integrin-collagen interactions play a critical role in a myriad of cellular functions that include immune response, and cell development and differentiation, yet their mechanism of binding is poorly understood. There is increasing evidence that conformational flexibility assumes a central role in the molecular mechanisms of protein-protein interactions and here we employ NMR hydrogen-deuterium exchange (HDX) experiments to explore the impact of slower timescale dynamic events. To gain insight into the mechanisms underlying collagen-induced conformational switches, we have undertaken a comparative study between the wild type integrin a1 I and a gain-of-function E317A mutant. NMR HDX results suggest a relationship between regions exhibiting a reduced local stability in the unbound I domain and those that undergo significant conformational changes upon binding. Specifically, the aC and a7 helices within the C-terminus are at the center of such major perturbations and present reduced local stabilities in the unbound state relative to other structural elements. Complementary isothermal titration calorimetry experiments have been performed to derive complete thermodynamic binding profiles for association of the collagen-like triple-helical peptide with wild type a1 I and E317A mutant. The differential energetics observed for E317A are consistent with the HDX experiments and support a model in which intrinsically destabilized regions predispose Abbreviations: a1 I, alpha1 I domain; NMR, nuclear magnetic resonance; HDX, hydrogen-deuterium exchange; HSCQ, heteronuclear single-quantum correlation; MIDAS, metal ion-dependent adhesion site; THP, collagen-like triple helical peptide; ITC, isothermal titration calorimetry; CD, circular dichroism.Additional Supporting Information may be found in the online version of this article.Integrin-collagen interactions play a critical role in cell adhesion processes. To gain insight into the mechanisms underlying collageninduced conformational switches, we have undertaken a comparative NMR study between the human integrin a1 I and a gain-offunction E317A mutant. Our results, supported by thermodynamic measurements, suggest that intrinsically destabilized regions facilitate conformational rearrangements of integrin I domain. This study highlights the importance of exploring slow dynamics to delineate allosteric and binding events. Published by Wiley-Blackwell. V C 2016 The Protein Society conformational rearrangement in the integrin I domain. This study highlights the importance of exploring different timescales to delineate allosteric and binding events.

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Dynamic Structural Changes Are Observed upon Collagen and Metal Ion Binding to the Integrin α1 I Domain

Cited by 15 publications

References 76 publications

The Structure of Integrin α1I Domain in Complex with a Collagen-mimetic Peptide

The Structure of Integrin α1I Domain in Complex with a Collagen-mimetic Peptide

Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1

Intrinsic local destabilization of the C‐terminus predisposes integrin α1 I domain to a conformational switch induced by collagen binding

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