Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.

The COP9 signalosome (CSN) is an evolutionarily conserved eight-subunit (CSN1-8) protein complex that controls protein ubiquitination by deneddylating Cullin-RING E3 ligases (CRLs). The activation and function of CSN hinges on its structural dynamics, which has been challenging to decipher by conventional tools. Here, we have developed a multichemistry cross-linking mass spectrometry approach enabled by three mass spectometry-cleavable cross-linkers to generate highly reliable cross-link data. We applied this approach with integrative structure modeling to determine the interaction and structural dynamics of CSN with the recently discovered ninth subunit, CSN9, in solution. Our results determined the localization of CSN9 binding sites and revealed CSN9-dependent structural changes of CSN. Together with biochemical analysis, we propose a structural model in which CSN9 binding triggers CSN to adopt a configuration that facilitates CSN-CRL interactions, thereby augmenting CSN deneddylase activity. Our integrative structure analysis workflow can be generalized to define in-solution architectures of dynamic protein complexes that remain inaccessible to other approaches.

Development of a Novel Sulfoxide-Containing MS-Cleavable Homobifunctional Cysteine-Reactive Cross-Linker for Studying Protein-Protein Interactions.

Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the most widely used cross-linking reagents target lysines. Although such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures. Although sulfhydryl-reactive cross-linkers are commercially available, their applications in XL-MS studies remain sparse, likely due to the difficulty in identifying cysteine cross-linked peptides. Previously, we developed a new class of sulfoxide-containing MS-cleavable cross-linkers to enable fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MS n). Here, we present the development of a new sulfoxide-containing MS-cleavable homobifunctional cysteine-reactive cross-linker, bismaleimide sulfoxide (BMSO). We demonstrate that BMSO-cross-linked peptides display the same characteristic fragmentation pattern during collision-induced dissociation (CID) as other sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MS n. Additionally, we show that BMSO can complement amine- and acidic-residue-reactive reagents for mapping protein-interaction regions. Collectively, this work not only enlarges the toolbox of MS-cleavable cross-linkers with diverse chemistries, but more importantly expands our capacity and capability of studying PPIs in general.

UV photodissociation dynamics of CHI2Cl and its role as a photolytic precursor for a chlorinated Criegee intermediate.

Photolysis of geminal diiodoalkanes in the presence of molecular oxygen has become an established route to the laboratory production of several Criegee intermediates, and such compounds also have marine sources. Here, we explore the role that the trihaloalkane, chlorodiiodomethane (CHI2Cl), may play as a photolytic precursor for the chlorinated Criegee intermediate ClCHOO. CHI2Cl has been synthesized and its UV absorption spectrum measured; relative to that of CH2I2 the spectrum is shifted to longer wavelength and the photolysis lifetime is calculated to be less than two minutes. The photodissociation dynamics have been investigated using DC slice imaging, probing ground state I and spin-orbit excited I* atoms with 2 + 1 REMPI and single-photon VUV ionization. Total translational energy distributions are bimodal for I atoms and unimodal for I*, with around 72% of the available energy partitioned in to the internal degrees of freedom of the CHICl radical product, independent of photolysis wavelength. A bond dissociation energy of D0 = 1.73 ± 0.11 eV is inferred from the wavelength dependence of the translational energy release, which is slightly weaker than typical C-I bonds. Analysis of the photofragment angular distributions indicate dissociation is prompt and occurs primarily via transitions to states of A'' symmetry. Complementary high-level MRCI calculations, including spin-orbit coupling, have been performed to characterize the excited states and confirm that states of A'' symmetry with highly mixed singlet and triplet character are predominantly responsible for the absorption spectrum. Transient absorption spectroscopy has been used to measure the absorption spectrum of ClCHOO produced from the reaction of CHICl with O2 over the range 345-440 nm. The absorption spectrum, tentatively assigned to the syn conformer, is at shorter wavelengths relative to that of CH2OO and shows far weaker vibrational structure.

The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress.

Oxidative stress has been implicated in multiple human neurological and other disorders. Proteasomes are multi-subunit proteases critical for the removal of oxidatively damaged proteins. To understand stress-associated human pathologies, it is important to uncover the molecular events underlying the regulation of proteasomes upon oxidative stress. To this end, we investigated H2O2 stress-induced molecular changes of the human 26S proteasome and determined that stress-induced 26S proteasome disassembly is conserved from yeast to human. Moreover, we developed and employed a new proteomic approach, XAP (in vivo cross-linking-assisted affinity purification), coupled with stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative MS, to capture and quantify several weakly bound proteasome-interacting proteins and examine their roles in stress-mediated proteasomal remodeling. Our results indicate that the adapter protein Ecm29 is the main proteasome-interacting protein responsible for stress-triggered remodeling of the 26S proteasome in human cells. Importantly, using a disuccinimidyl sulfoxide-based cross-linking MS platform, we mapped the interactions of Ecm29 within itself and with proteasome subunits and determined the architecture of the Ecm29-proteasome complex with integrative structure modeling. These results enabled us to propose a structural model in which Ecm29 intrudes on the interaction between the 20S core particle and the 19S regulatory particle in the 26S proteasome, disrupting the proteasome structure in response to oxidative stress.