Bilayer-Protein Associations that are Transient

We deposited the first experimentally docked protein-lipid bilayer models accepted by the Protein Data Bank. We based these on improved distance estimates between enzyme and bilayers using paramagnetic NMR and some innovations in docking calculations that use these distance estimates (Koppisetti et al., 2014, Nat. Comms.; Prior et al., 2015, Structure; Marcink et al., 2019, Structure). This strategy readily detects transient interactions and a mixture of interactions. (This was supported by NIH GM057289).

NMR Structures

Earlier, we reported possibly the first NMR structure refined with residual dipolar couplings (RDCs) outside of NIH (Wu et al., 2000, JMB) and the first NMR structure of an RNA refined with RDCs (Leeper et al., 2002, Nat. Struct. Biol.).

More Accurate Interfaces

We introduced NMR mapping of protein-protein interfaces by exclusion of chelated, paramagnetic Gd(III) (Arumugam et al., 1998, Biochemistry) and demonstrated its accuracy within the interface and outside at a site exposed upon binding (Arumugam et al., 2003, Biochemistry). The method also seems reliable at modest affinities with protein and GAG partners (Garimella et al., 2006, Biochemistry; Fulcher et al., 2017, Structure).

When faced with extensive binding regions, we learned to prioritize the contacts most likely to shape specificity. We integrated Evolutionary trace identification of selectively conserved sites with the interfaces mapped by NMR using the chelated Gd(III) probe. This BINDSIght approach located exosites for binding of collagen and elastin to MMP-12 (Palmier et al., 2010, JBC; Fulcher et al., 2011, Biochemistry). (This was supported by NIH GM057289).

Publications cited:

Arumugam S, Hemme CL, Yoshida N, Suzuki K, Nagase H, Berjanskii M, Wu B, Van Doren SR. TIMP-1 contact sites and perturbations of stromelysin 1 mapped by NMR and a paramagnetic surface probe.Biochemistry. 1998 Jul 7;37(27):9650-7. https://pubs.acs.org/doi/10.1021/bi980128h

Fulcher YG, Prior SH, Masuko S, Li L, Pu D, Zhang F, Linhardt RJ, Van Doren SR. Glycan Activation of a Sheddase: Electrostatic Recognition between Heparin and proMMP-7. Structure. 2017 Jul 5;25(7):1100-1110.e5. https://doi.org/10.1016/j.str.2017.05.019

Fulcher YG, Van Doren SR. Remote exosites of the catalytic domain of matrix metalloproteinase-12 enhance elastin degradation. Biochemistry. 2011 Nov 8;50(44):9488-99. https://doi.org/10.1021/bi2009807

Garimella R, Liu X, Qiao W, Liang X, Zuiderweg ER, Riley MI, Van Doren SR. Hsc70 contacts helix III of the J domain from polyomavirus T antigens: addressing a dilemma in the chaperone hypothesis of how they release E2F from pRb. Biochemistry. 2006 Jun 6;45(22):6917-29. https://doi.org/10.1021/bi060411d

Koppisetti RK, Fulcher YG, Jurkevich A, Prior SH, Xu J, Lenoir M, Overduin M, Van Doren SR. Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12. Nat Commun. 2014 Nov 21;5:5552. https://doi.org/10.1038/ncomms6552

Leeper TC, Martin MB, Kim H, Cox S, Semenchenko V, Schmidt FJ, Van Doren SR. Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action. Nat Struct Biol. 2002 May;9(5):397-403. https://doi.org/10.1038/nsb775

Marcink TC, Simoncic JA, An B, Knapinska AM, Fulcher YG, Akkaladevi N, Fields GB, Van Doren SR. MT1-MMP Binds Membranes by Opposite Tips of Its β Propeller to Position It for Pericellular Proteolysis. Structure. 2019 Feb 5;27(2):281-292.e6. https://doi.org/10.1016/j.str.2018.10.008

Palmier MO, Fulcher YG, Bhaskaran R, Duong VQ, Fields GB, Van Doren SR. NMR and bioinformatics discovery of exosites that tune metalloelastase specificity for solubilized elastin and collagen triple helices. J Biol Chem. 2010 Oct 1;285(40):30918-30. https://doi.org/10.1074/jbc.M110.136903

Prior SH, Fulcher YG, Koppisetti RK, Jurkevich A, Van Doren SR. Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors. Structure. 2015 Nov 3;23(11):2099-110. https://doi.org/10.1016/j.str.2015.08.013

Wu B, Arumugam S, Gao G, Lee GI, Semenchenko V, Huang W, Brew K, Van Doren SR. NMR structure of tissue inhibitor of metalloproteinases-1 implicates localized induced fit in recognition of matrix metalloproteinases. J Mol Biol. 2000 Jan 14;295(2):257-68. https://doi.org/10.1006/jmbi.1999.3362