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Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

Covalent tethering of PPh2NC6H4C≡CH2 ligands (PPh2NC6H4C≡CH2 = 1,5-di-(4-ethynylphenyl)-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane) to planar, azide-terminated glassy carbon electrode surfaces has been accomplished using a CuI-catalyzed alkyne-azide cycloaddition (CuAAC) as the coupling reaction, using a BH3←P protection-deprotection strategy. Deprotected, surface-confined ligands were metallated using [NiII(MeCN)6](BF4)2. X-ray photoelectron spectroscopic measurements demonstrate that metallation introduced 1.3 equivalents NiII per diphosphine onto the electrode surface. Exposure of the surface to a second diphosphine ligand, PPh2NPh2, resulted in the removal of Ni from the surface. Protection, coupling, deprotection, and metallation conditions were optimized using solution-phase model systems, with benzyl azide as a model for the azide-terminated carbon surface; these reactions generate a [NiII(diphosphine)2]2+ complex. Acknowledgment. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. The XPS measurements were performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The x-ray crystal structure analysis was carried out by S.L., who was supported by a grant to Wendy J. Shaw from the Early Career Research Program through the U.S. Department of Energy, Office of Science. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, latin: dirigere: to guide or align). The first 3D structure of a DP [(+)-pinoresinol forming DP, 1.95 Å resolution, rhombohedral space group H32)] is reported herein. It has a tightly packed trimeric structure with an eight stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface, but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are 6 differentially conserved residues in DPs affording either the (+)- or (-)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.

A series of [Rh(PCH2XRCH2P)2]+ complexes were prepared to investigate second and outer coordination sphere effects on CO2 hydrogenation catalysis, where X is CH2 (dppp) or X-R is N-CH3, N-CH2COOH (glycine), N-CH2COOCH3 (Gly-OMe) or N-CH2C(O)N-CH(CH3)COOCH3 (GlyAla-OMe). All of these modified complexes were active for CO2 reduction to formate, with the N-CH3 derivative offering an eight-fold enhancement over dppp, which is consistent with decreased electron density around the phosphorous (and corresponding increase in electron density around the metal) observed in the 31P NMR spectrum. Despite the increase in rate with the addition of the pendant nitrogen, the addition of electron withdrawing amino acids and dipeptides to the amine resulted in complexes with reductions in rate of one to two orders of magnitude, most consistent with a change in pKa of the pendant amine resulting in lower activity. Collectively, the data suggests multiple contributions of the pendant amine in this catalytic system. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for the DOE by Battelle. A portion of this research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Porous graphene, which is a novel type of defective graphene, shows excellent potential as a support material for metal clusters. In this work, the stability and electronic structures of metal clusters (Pd, Ir, Rh) supported on pristine graphene and graphene with different sizes of nanopore were investigated by first-principle density functional theory (DFT) calculations. Thereafter, CO adsorption and oxidation reaction on the Pd-graphene system were chosen to evaluate its catalytic performance. Graphene with nanopore can strongly stabilize the metal clusters and cause a substantial downshift of the d-band center of the metal clusters, thus decreasing CO adsorption. All binding energies, d-band centers, and adsorption energies show a linear change with the size of the nanopore: a bigger size of nanopore corresponds to a stronger metal clusters bond to the graphene, lower downshift of the d-band center, and weaker CO adsorption. By using a suitable size nanopore, supported Pd clusters on the graphene will have similar CO and O2 adsorption ability, thus leading to superior CO tolerance. The DFT calculated reaction energy barriers show that graphene with nanopore is a superior catalyst for CO oxidation reaction. These properties can play an important role in instructing graphene-supported metal catalyst preparation to prevent the diffusion or agglomeration of metal clusters and enhance catalytic performance. This work was supported by National Basic Research Program of China (973Program) (2013CB733501), the National Natural Science Foundation of China (NSFC-21176221, 21136001, 21101137, 21306169, and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC).