Identification of novel macrocyclic peptidase substrates via on-bead enzymatic cyclization

Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.     

An in situ atomic force microscopy study of uric acid crystal growth

Kidney stones are heterogeneous polycrystalline aggregates that can consist of several different building blocks. A significant number of human stones contain uric acid crystals as a crystalline component, though the molecular-level growth of this important biomaterial has not been previously well-characterized. In the present study, in situ atomic force microscopy (AFM) is used to investigate the real-time growth on the (100) surface of uric acid (UA) single crystals as a function of fundamental solution parameters. Layer-by-layer growth on UA (100) was found to be initiated at screw dislocation sites and to proceed via highly anisotropic rates which depend on the crystallographic direction. The smallest b-steps exhibited minimum heights corresponding to two molecular layers, while fast-moving c-steps more commonly showed monolayer heights. Growth kinetics measured under a range of flow rates, supersaturation levels, and pH values reveal linear trends in the growth kinetics, with faster growth attained in solutions with higher supersaturation and/or pH. The calculated kinetic parameters for UA growth derived from these experiments are in good agreement with the values reported for other crystal systems.     

Microfabrication of three-dimensional bioelectronic architectures

The functionality and structural diversity of biological macromolecules has motivated efforts to exploit proteins and DNA as templates for synthesis of electronic architectures. Although such materials offer promise for numerous applications in the fabrication of cellular interfaces, biosensors, and nanoelectronics, identification of techniques for positioning and ordering bioelectronic components into useful patterns capable of sophisticated function has presented a major challenge. Here, we describe the fabrication of electronic materials using biomolecular scaffolds that can be constructed with precisely defined topographies. In this approach, a tightly focused pulsed laser beam capable of promoting protein photo-cross-linking in specified femtoliter volume elements is scanned within a protein solution, creating biomolecular matrices that either remain in integral contact with a support surface or extend as free-standing structures through solution, tethered at their ends. Once fabricated, specific protein scaffolds can be selectively metallized via targeted deposition and growth of metal nanoparticles, yielding high-conductivity bioelectronic materials. This aqueous fabrication strategy opens new opportunities for creating electronic materials in chemically sensitive environments and may offer a general approach for creating microscopically defined inorganic landscapes.     

Electronic absorption and MCD spectra for Pt(AuPPh3)8(2+) and Au(AuPPh3)8(3+) cluster complexes in poly(methyl methacrylate) thin films at 295 and 10 K

Electronic absorption and 8 T magnetic circular dichroism (MCD) spectra are reported for nitrate salts of Pt(AuPPh3)8(2+) and Au(AuPPh3)8(3+) in poly(methyl methacrylate) (PMM) thin films at 295 and 10 K in the vis-UV region from 1.6 to 3.6 microm(-1) (1 microm(-1) = 10(4) cm(-1). Enhanced resolution is observed at low temperature, especially for Pt(AuPPh3)8(2+), which emphasizes the differences in the nature of the low-energy excited configurations and states between Pt(AuPPh3)8(2+) and Au(AuPPh3)8(3+). The absorption and MCD spectra for Pt(AuPPh3)8(2+) are interpreted in terms of a combination of excitations from filled Pt 5d orbitals to empty Au framework 6s orbitals and intraframework Au8(2+) (IF) transitions, whereas the spectra for Au(AuPPh3)8(3+) are ascribed entirely to Au IF transitions.     

Cooperative hydrogen-bonding effects in a water square: a single-crystal neutron and partial atomic charges and hardness analysis study

Four isomorphous complexes of formula [M(L)(4)(H(2)O)(2)]SO(4).2H(2)O (M = Co, 1a; Ni, 1b; Cu, 1c; Zn, 1d) have been isolated and characterized by single-crystal X-ray diffraction and neutron diffraction using the quasi-Laue diffractometer VIVALDI at the Institut Laue-Langevin as well as by thermogravimetric analysis. The structures contain a discrete, strongly hydrogen-bonded water tetramer which causes a significant distortion of the metal coordination sphere in each case. Partial atomic charges and hardness analysis (PACHA) calculations reveal that the shortest hydrogen bonds are not the strongest in this constrained, cyclic solid-state structure and show that the distortion at the metal center is caused by the drive to maintain the integrity of the water tetramer. The system undergoes a disorder-order transition on slow cooling that provides insight into the nature of communication between water squares.     

Comparison of whole blood, plasma and nails as monitors for the dietary intake of selenium

Haem peroxidases are globular proteins with an iron-porphyrin complex as prosthetic group. They catalyze the oxidation of substrate by peroxides, frequently via free-radical intermediates. The catalytic cycle involves changes in the redox states of the prosthetic group, that can be monitored by changes in the intense absorption spectra. During the past decades, considerable scientific effort has been put into the elucidation of the mechanisms of reactions catalyzed by these enzymes. Radiation-chemical techniques have made an important contribution by providing information on the redox states of the enzymes and their interconversions, as well as on the properties of the free-radical intermediates involved.     

Comparison of the electrophilic and free-radical addition of halogens with hexafluoro-1,3-butadiene and 1,3-butadiene

Ionic and photochemical reaction of chlorine (Cl₂), bromine (Br₂) and iodine monochloride (ICl) to hexafluoro-1,3-butadiene (1) and 1,3-butadiene (2) were carried out under conditions that would provide product distributions under controlled ionic or free-radical conditions. Product distributions for ionic reaction of Cl₂ and Br₂ with 1 are similar and suggest a weakly-bridged halonium ion species. Theoretical calculations support weakly-bridged chloronium and bromonium ions for both dienes 1 and 2. There are more of the 1,4-dihalo-2-butene products from ionic halogenation of 1 than 2 which correlates with the greater charge density on carbon-4 of halonium ions from 1. Ionic and free-radical reactions of ICl with 1 give 8 and 2% of 3-chloro-4-iodohexafluoro-1-butene and 4-chloro-3-iodohexafluoro-1-butene, respectively. The minor cis-1,4-dihalo-2-butene products from 1 and 2 are reported when formed.     

Transferable atom equivalent multicentered multipole expansion method

The transferability of atomic and functional group properties is an implicit concept in chemistry. The work presented here describes the use of Transferable Atom Equivalents (TAE) to represent molecular electrostatic potential fields through the use of integrated atomic multipole moments that are associated with each TAE atom type used in the reconstruction. TAE molecular surface distributions of electrostatic potentials are compared with analytical ab initio and empirical (Gasteiger) partial charge reference models for several conformations of test peptides. Surface electrostatic potential distributions computed using TAE multipole representations were found to converge at the octopole level, with incremental improvement observed when hexadecapoles were included. Molecular electrostatic potential fields that were produced using the TAE method were observed to be responsive to conformational changes and to compare well with ab initio reference distributions. Generation of TAE atom types and their associated multipoles does not involve fitting to sample electrostatic potential fields, but rather utilizes integrated AIM atomic electron density distributions within representative chemical environments. The RECON program was used for TAE reconstruction. RECON is capable of processing 5,000 drug-sized molecules or 25 proteins per minute per 1.7 GHz P4 Linux processor.     

Bis(m-phenylene)-32-crown-10-based cryptands, powerful hosts for paraquat derivatives

Four new bis(m-phenylene)-32-crown-10-based cryptands with different third bridges were prepared. Their complexes with paraquat derivatives were studied by proton NMR spectroscopy, mass spectrometry, and X-ray analysis. It was found that these cryptands bind paraquat derivatives very strongly. Specifically, a diester cryptand with a pyridyl nitrogen atom located at a site occupied by either water or a PF(6) anion in analogous complexes exhibited the highest association constant K(a) = 5.0 x 10(6) M(-1) in acetone with paraquat, 9000 times greater than the crown ether system. X-ray structures of this and analogous complexes demonstrate that improved complexation with this host is a consequence of preorganization, adequate ring size for occupation by the guest, and the proper location of the pyridyl N-atom for binding to the beta-pyridinium hydrogens of the paraquat guests. This readily accessible cryptand is one of the most powerful hosts reported for paraquats.     

Field gradient electrophoresis

The class of equilibrium gradient methods utilizes the opposition of two forces, at least one of which changes in magnitude with position, to separate and concentrate analytes. The drawback of many methods of this type is that the production of two opposing forces requires in comparison to standard methods, such as capillary electrophoresis, a relatively complex apparatus. In addition, for techniques such as electric field gradient focusing, hydrodynamic flow leads to Taylor dispersion, which limits the attainable concentration factor. We propose a new method, gradient field electrophoresis, which achieves analyte separation and focusing with only one spatially varying force, an electric field gradient. A model for the method is developed and used to analyze peak capacity. Experimental results for a protein (R-phycoerythrin) are given and compared to the model.