Computational protein design: Advances in the design and redesign of biomolecular nanostructures

Computational protein design facilitates the continued development of methods for the design of biomolecular structure, sequence and function. Recent applications include the design of novel protein sequences and structures, proteins incorporating nonbiological components, protein assemblies, soluble variants of membrane proteins, and proteins that modulate membrane function.     

Chemistry of the oxophosphinidene ligand. 2. Reactivity of the anionic complexes [MCp{P(O)R*}(CO)(2)](-) (M = Mo, W; R* = 2,4,6-C(6)H(2)(t)Bu(3)) toward electrophiles based on elements different from carbon

The anionic oxophosphinidene complexes (H-DBU)[MCp{P(O)R*}(CO)(2)] (M = Mo, W; R* = 2,4,6-C(6)H(2)(t)Bu(3); Cp = η(5)-C(5)H(5), DBU = 1,8-diazabicyclo [5.4.0] undec-7-ene) displayed multisite reactivity when faced with different electrophilic reagents. The reactions with the group 14 organochloride compounds ER(4-x)Cl(x) (E = Si, Ge, Sn, Pb) led to either phosphide-like, oxophosphinidene-bridged derivatives [MCp{P(OE')R*}(CO)(2)] (E' = SiMe(3), SiPh(3), GePh(3), GeMe(2)Cl) or to terminal oxophosphinidene complexes [MCp{P(O)R*}(CO)(2)(E')] (E' = SnPh(3), SnPh(2)Cl, PbPh(3); Mo-Pb = 2.8845(4) ? for the MoPb compound). A particular situation was found in the reaction with SnMe(3)Cl, this giving a product existing in both tautomeric forms, with the phosphide-like complex [MCp{P(OSnMe(3))R*}(CO)(2)] prevailing at room temperature and the tautomer [MCp{P(O)R*}(CO)(2)(SnMe(3))] being the unique species present below 203 K in dichloromethane solution. The title anions also showed a multisite behavior when reacting with transition-metal based electrophiles. Thus, the reactions with the complexes [M'Cp(2)Cl(2)] (M' = Ti, Zr) gave phosphide-like derivatives [MCp{P(OM')R*}(CO)(2)] (M = Mo, M' = TiCp(2)Cl, ZrCp(2)Cl; M = W, M' = ZrCp(2)Cl), displaying a bridging κ(1),κ(1)-P,O- oxophosphinidene ligand connecting MCp(CO)(2) and M'Cp(2)Cl metal fragments (W-P = 2.233(1) ?, O-Zr = 2.016(4) ? for the WZr compound]. In contrast, the reactions with the complex [AuCl{P(p-tol)(3)}] gave the metal-metal bonded derivatives trans-[MCp{P(O)R*}(CO)(2){AuP(p-tol)(3)}] (M = Mo, W; Mo-Au = 2.7071(7) ?). From all the above results it was concluded that the terminal oxophosphinidene complexes are preferentially formed under conditions of orbital control, while charge-controlled reactions tend to give derivatives with the electrophilic fragment bound to the oxygen atom of the oxophosphinidene ligand (phosphide-like, oxophosphinidene-bridged derivatives).     

A general preparation of (Z)-1-fluorostilbene derivatives for the design of conformationally restricted peptidomimetics

The preparation of (Z)-1-fluoro-2-bromostyrenes provides a general route for the formation of (Z)-1-fluorostilbene derivatives as configurationally stable spacial linkers for the design of conformationally restricted peptidomimetics. Palladium-catalyzed aryl Suzuki and Stille cross-coupling reactions have been surveyed to proceed with complete retention of fluoroalkene geometry, and permit the direct incorporation of a variety of aryl and heteroaromatic substituents.     

Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics

Asparagine glycosylation is one of the most common and important post-translational modifications of proteins in eukaryotic cells. N-glycosylation occurs when a triantennary glycan precursor is transferred en bloc to a nascent polypeptide (harboring the N-X-T/S sequon) as the peptide is cotranslationally translocated into the endoplasmic reticulum (ER). In addition to facilitating binding interactions with components of the ER proteostasis network, N-glycans can also have intrinsic effects on protein folding by directly altering the folding energy landscape. Previous work from our laboratories (Hanson et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 109, 3131-3136; Shental-Bechor, D.; Levy, Y. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8256-8261) suggested that the three sugar residues closest to the protein are sufficient for accelerating protein folding and stabilizing the resulting structure in vitro; even a monosaccharide can have a dramatic effect. The highly conserved nature of these three proximal sugars in N-glycans led us to speculate that introducing an N-glycosylation site into a protein that is not normally glycosylated would stabilize the protein and increase its folding rate in a manner that does not depend on the presence of specific stabilizing protein-saccharide interactions. Here, we test this hypothesis experimentally and computationally by incorporating an N-linked GlcNAc residue at various positions within the Pin WW domain, a small β-sheet-rich protein. The results show that an increased folding rate and enhanced thermodynamic stability are not general, context-independent consequences of N-glycosylation. Comparison between computational predictions and experimental observations suggests that generic glycan-based excluded volume effects are responsible for the destabilizing effect of glycosylation at highly structured positions. However, this reasoning does not adequately explain the observed destabilizing effect of glycosylation within flexible loops. Our data are consistent with the hypothesis that specific, evolved protein-glycan contacts must also play an important role in mediating the beneficial energetic effects on protein folding that glycosylation can confer.     

Tuning Internal Strain in Metal–Organic Frameworks via Vapor Phase Infiltration for CO2 Reduction

A gas‐phase approach to form Zn coordination sites on metal–organic frameworks (MOFs) by vapor‐phase infiltration (VPI) was developed. Compared to Zn sites synthesized by the solution‐phase method, VPI samples revealed approximately 2.8 % internal strain. Faradaic efficiency towards conversion of CO₂ to CO was enhanced by up to a factor of four, and the initial potential was positively shifted by 200–300 mV. Using element‐specific X‐ray absorption spectroscopy, the local coordination environment of the Zn center was determined to have square‐pyramidal geometry with four Zn?N bonds in the equatorial plane and one Zn‐OH₂ bond in the axial plane. The fine‐tuned internal strain was further supported by monitoring changes in XRD and UV/Visible absorption spectra across a range of infiltration cycles. The ability to use internal strain to increase catalytic activity of MOFs suggests that applying this strategy will enhance intrinsic catalytic capabilities of a variety of porous materials.     

Synthesis of bis N-heterocyclic carbenes,derivatives and metal complexes

A method for the synthesis and isolation of 1,1′-methylene-bis-(3-aryl-imidazol-2-ylidene) ligands, aryl = 2,6-diisopropyl-phenyl (DiPP), L^DiPP, mesityl (mes), L^mes, is reported, which provides synthetically useful quantities of high purity. Derivatisation of L^DiPP with chalcogenides gave the adducts L^DiPPE₂, E = S, Se, Te. Reaction of L^DiPP with [Pd(tmeda)Me₂], [Pt(μ-SMe₂)Me₂]₂, [Ir(1,5-COD)(μ-Cl)]₂/KPF₆ and [NiBr₂(dme)] gave [Pd(L^DiPP)Me₂] (1), [Pt(L^DiPP)Me₂] (2), [Ir(L^DiPP)(1,5-COD)](PF₆) (3) and [Ni(L^DiPP)Br₂] (4), respectively. The latter was reduced in the presence of CO to [Ni(L^DiPP)(CO)₂] (5). The structures of L^mes, L^DiPPTe₂, and 1–5 are also reported.     

Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4

Theoretical studies are presented into the experimentally observed regioselectivity difference of testosterone hydroxylation by cytochrome P450 3A4 at the 1β, 2β, 6β, and 15β positions. Such regioselectivity is investigated by density functional theory calculations on a model system. The barrier heights of hydrogen abstraction, which are corrected by zero-point vibrational energies, are computed to be about 10.1, 13.6, 14.4, and 16.2 kcal/mol for the 6β-, 2β-, 15β-, and 1β-positions, respectively. The calculated barriers suggest the regioselectivity preference of 6β ? 2β > 15β > 1β, which is in good agreement with experimental findings.