Insight into Protein Conformation and Subcharging by DMSO from Native Ion Mobility Mass Spectrometry

Electrospray ionization-mass spectrometry (ESI-MS) interfaced with ion-mobility (IM) spectrometry has enabled the study of protein structure and interactions under native-like conditions. In biological assays, dimethyl sulfoxide (DMSO) is often included as a co-solvent to dissolve organic molecules. While low levels of DMSO are known to reduce the charge of protein ions generated by ESI, the exact mechanism by which this occurs has been debated. In this study, we describe the first application of IM–MS to study the effect of DMSO subcharging on native protein conformation. We find that at low concentrations, DMSO induces modest (1-2 %), but repeatable, reductions in protein collision-cross sections (CCSs) of four different protein complexes, avidin, concanavalin A, alcohol dehydrogenase, and pyruvate kinase, as measured by traveling-wave (TW) IM–MS. Individual protein charge states also experienced compaction in size, suggesting that this effect could not be attributed to the shift of charge state distribution by DMSO alone.D.S.-H. Chan acknowledges the support of the Croucher Foundation and the Cambridge Commonwealth, European and International Trust for receipt of a Croucher Cambridge International Scholarship

Effect of DMSO on Protein Structure and Interactions Assessed by Collision-Induced Dissociation and Unfolding

Given the frequent use of DMSO in biochemical and biophysical assays, it is desirable to understand the influence of DMSO concentration on the dissociation or unfolding behavior of proteins. In this study, the effects of DMSO on the structure and interactions of avidin and Mycobacterium tuberculosis (Mtb) CYP142A1 were assessed through collision-induced dissociation (CID) and collision-induced unfolding (CIU) as monitored by nanoelectrospray ionization–ion mobility–mass spectrometry (nESI-IM-MS). DMSO concentrations higher than 4% (v/v) destabilize the avidin tetramer toward dissociation and unfolding, via both its effects on charge state distribution (CSD) as well as at the level of individual charge states. In contrast, DMSO both protects against heme loss and increases the stability of CYP142A1 toward unfolding even up to 40% DMSO. Tandem MS/MS experiments showed that DMSO could modify the dissociation pathway of CYP142A1, while CIU revealed the protective effect of the heme group on the structure of CYP142A1.D.S.-H.C. acknowledges the Croucher Foundation and the Cambridge Commonwealth, European and International Trust for receipt of a Croucher Cambridge International Scholarship. M.E.K. was supported by a Commonwealth (University of Cambridge) Scholarship awarded in conjunc-tion with the Cambridge Commonwealth Trust and Cam-bridge Overseas Trust. K.J.M. and A.G.C. were supported by grants from the UK BBSRC (Biotechnology and Biological Sciences Research Council (BB/I019669/1 and BB/I019227/1)

An artificial CO-releasing metalloprotein built by histidine-selective metallation.

We report the design and synthesis of an aquacarbonyl Ru(II) dication cis-[Ru(CO)2(H2O)4](2+) reagent for histidine (His)-selective metallation of interleukin (IL)-8 at site 33. The artificial, non-toxic interleukin (IL)-8-Ru(II)(CO)2 metalloprotein retained IL-8-dependent neutrophil chemotactic activity and was shown to spontaneously release CO in live cells.We thank the European Commission (Marie Curie CIG to G.J.L.B., Marie Curie IEF to O.B.), FCT Portugal (FCT Investigator to G.J.L.B.) and the EPSRC for generous funding.This is the final published version. It first appeared at http://pubs.rsc.org/en/Content/ArticleLanding/2015/CC/c4cc10204e#!divAbstract

Mining 2:2 Complexes from 1:1 Stoichiometry: Formation of Cucurbit[8]uril−Diarylviologen Quaternary Complexes Favored by Electron-Donating Substituents

A 1:1 binding stoichiometry of a host−guest complex need not consist of a single host and guest. Diarylviologens containing electron-donating substituents complexed with cucurbit[8]uril (CB[8]) in a 1:1 stoichiometry exhibit abnormally large binding enthalpies compared to typical enthalpy changes observed for 1:1 binary complexes. Here, several CB[8]-mediated host−guest complexes, which were previously reported as 1:1 binary complexes, are verified to be 2:2 quaternary complexes by a combination of isothermal titration calorimetry, $^1$H, NOESY, and ROESY NMR, and ion mobility mass spectrometry, clearly indicating a binding motif of two partially overlapping diarylviologens held in place with two CB[8] molecules. Formation of 2:2 quaternary complexes is favored by electron-donating substituents, while electron-withdrawing substituents typically result in 1:1 binary complexes. The stacking of two highly conjugated diarylviologens in one quaternary motif affords the complexes enhanced conductance when considered as a single-molecular conductor. Moreover, an additional conducting signal previously observed for this “supramolecular” conductor can be readily understood with our 2:2 complexation model, corresponding to a parallel conductance pathway. Therefore, a 2:2 quaternary complex model grants a greater understanding of such supramolecular complexes, enabling the design of engineered, hierarchical structures and functional materials.The authors thank the Leverhulme Trust (project: ‘Natural material innovation for sustainable living’), the Marie Curie FP7 SASSYPOL ITN (607602) programme, and EPSRC (EP/ L504920/1) for funding

Solvent content of protein crystals from diffraction intensities by Independent Component Analysis

An analysis of the protein content of several crystal forms of proteins has been performed. We apply a new numerical technique, the Independent Component Analysis (ICA), to determine the volume fraction of the asymmetric unit occupied by the protein. This technique requires only the crystallographic data of structure factors as input.Comment: 9 pages, 2 figures, 1 tabl

Structural characterization of CYP144A1 - a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis (TB). The virulent Mtb H37Rv strain encodes 20 cytochrome P450 (CYP) enzymes, many of which are implicated in Mtb survival and pathogenicity in the human host. Bioinformatics analysis revealed that CYP144A1 is retained exclusively within the Mycobacterium genus, particularly in species causing human and animal disease. Transcriptomic annotation revealed two possible CYP144A1 start codons, leading to expression of (i) a "full-length" 434 amino acid version (CYP144A1-FLV) and (ii) a "truncated" 404 amino acid version (CYP144A1-TRV). Computational analysis predicted that the extended N-terminal region of CYP144A1-FLV is largely unstructured. CYP144A1 FLV and TRV forms were purified in heme-bound states. Mass spectrometry confirmed production of intact, His6-tagged forms of CYP144A1-FLV and -TRV, with EPR demonstrating cysteine thiolate coordination of heme iron in both cases. Hydrodynamic analysis indicated that both CYP144A1 forms are monomeric. CYP144A1-TRV was crystallized and the first structure of a CYP144 family P450 protein determined. CYP144A1-TRV has an open structure primed for substrate binding, with a large active site cavity. Our data provide the first evidence that Mtb produces two different forms of CYP144A1 from alternative transcripts, with CYP144A1-TRV generated from a leaderless transcript lacking a 5'-untranslated region and Shine-Dalgarno ribosome binding site

Crystallographic study of mutant Lys120Leu Xenopus laevis Cu,Zn superoxide dismutase

Theoretical calculations and experimental measurements on the Xenopus laevis Cu,Zn superoxide dismutase (XSODB) wild-type protein and on some of its engineered mutants showed that the electrostatic arrangement around the active site channel plays a fundamental role in determining the catalytic properties of the enzyme. Lys120, which lies on the lip of the active site channel, about 11 Angstrom from the catalytic copper ion, influences the enzyme electrostatic environment and binding selectivity. Neutralization of this residue has the effect of decreasing the activity of the enzyme versus the negatively charged substrate. In order to get precise information about the mutated residue and its effects on the structure of the engineered protein, the crystal structure of single site Lys120Leu mutant XSODB was determined at 2.0 Angstrom resolution, and refined to an R-factor value of 0.181. The structure of Lys120Leu mutant XSODB is little affected by the amino-acid substitution, suggesting that the main effect-of the mutation is perturbation of the electrostatic properties of the SOD catalytic center

Purification of Recombinant α-synuclein: A Comparison of Commonly Used Protocols.

The initial state of the intrinsically disordered protein α-synuclein (aSyn), e.g., the presence of oligomers and degradation products, or the presence of contaminants and adducts can greatly influence the aggregation kinetics and toxicity of the protein. Here, we compare four commonly used protocols for the isolation of recombinant aSyn from Escherichia coli: boiling, acid precipitation, ammonium sulfate precipitation, and periplasmic lysis followed by ion exchange chromatography and gel filtration. We identified, using nondenaturing electrospray ionization mass spectrometry, that aSyn isolated by acid precipitation and periplasmic lysis was the purest and yielded the highest percentage of monomeric protein, 100% and 96.5%, respectively. We then show that aSyn purified by the different protocols exerts different metabolic stresses in cells, with the more multimeric/degraded and least pure samples leading to a larger increase in cell vitality. However, the percentage of monomeric protein and the purity of the samples did not correlate with aSyn aggregation propensity. This study highlights the importance of characterizing monomeric aSyn after purification, as the choice of purification method can significantly influence the outcome of a subsequent study

Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions.

XRCC4 (X-ray cross-complementation group 4) and XLF (XRCC4-like factor) are two essential interacting proteins in the human NHEJ (non-homologous end-joining) pathway that repairs DNA DSBs (double-strand breaks). The individual crystal structures show that the dimeric proteins are homologues with protomers containing head domains and helical coiled-coil tails related by approximate two-fold symmetry. Biochemical, mutagenesis, biophysical and structural studies have identified the regions of interaction between the two proteins and suggested models for the XLF-XRCC4 complex. An 8.5 Å (1 Å = 0.1 nm) resolution crystal structure of XLF-XRCC4 solved by molecular replacement, together with gel filtration and nano-ESI (nano-electrospray ionization)-MS results, demonstrates that XLF and XRCC4 dimers interact through their head domains and form an alternating left-handed helical structure with polypeptide coiled coils and pseudo-dyads of individual XLF and XRCC4 dimers at right angles to the helical axis