Ion mobility-mass spectrometry for structural proteomics.

Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility-mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility-mass spectrometry data with more classical (e.

Repeated freeze-thawing of bone tissue affects Raman bone quality measurements.

The ability to probe fresh tissue is a key feature to biomedical Raman spectroscopy. However, it is unclear how Raman spectra of calcified tissues are affected by freezing. In this study, six transverse sections of femoral cortical bone were subjected to multiple freeze∕thaw cycles and probed using a custom Raman microscope.

Push-pull perfusion sampling with segmented flow for high temporal and spatial resolution in vivo chemical monitoring.

Low-flow push-pull perfusion is a sampling method that yields better spatial resolution than competitive methods like microdialysis. Because of the low flow rates used (50 nL/min), it is challenging to use this technique at high temporal resolution which requires methods of collecting, manipulating, and analyzing nanoliter samples. High temporal resolution also requires control of Taylor dispersion during sampling.

Peering at a buried polymer-crystal interface: probing heterogeneous nucleation by sum frequency generation vibrational spectroscopy.

Sum frequency generation vibrational spectroscopy (SFG-VS) has been applied to investigate the selective crystallization of two forms of acetaminophen (ACM) on polymer surfaces. To our knowledge, this is the first account of SFG-VS being applied to study a polymer-crystal interface. SFG elucidates the molecular-level interactions governing phase selection at this buried interface, providing insight into the process of polymer-induced heteronucleation (PIHn) in solution as well as from the vapor phase.

Palladium-catalyzed alkene carboamination reactions for the synthesis of substituted piperazines.

A strategy for the stereoselective preparation of enantiomerically enriched cis-2,6-disubstituted piperazines from amino acid precursors is described. The target compounds are generated in 95-99% ee with good to excellent levels of diastereoselectivity (usually 14:1 to >20:1) using Pd-catalyzed carboamination reactions between aryl or alkenyl halides and substituted ethylenediamine derivatives to form the heterocyclic rings. The synthesis requires only 4-5 steps from commercially available amino acids, and allows for the modular construction of piperazines bearing different substituents at N(1), N(4), C(2), and C(6).

Diastereoselective Nickel-Catalyzed Reductive Couplings of Aminoaldehydes and Alkynylsilanes: Application to the Synthesis of D-erythro-Sphingosine.

A strategy for the nickel-catalyzed reductive coupling of α-aminoaldehydes with silyl alkynes has been developed. The process proceeds with exceptional regiocontrol and diastereoselectivity. A variety of protected serinal derivatives were examined, and Garner aldehyde afforded the highest chemical yields of an easily deprotected coupling product.

Pd-catalyzed carboamination of oxazolidin-2-ones: a stereoselective route to trans-2,5-disubstituted pyrrolidines.

Palladium-catalyzed carboamination reactions between aryl bromides and 4-(but-3-enyl)-substituted oxazolidin-2-ones are described. These transformations afford bicyclic oxazolidin-2-one derivatives that can be converted to trans-2,5-disubstituted pyrrolidines in one step. The starting materials are easily prepared from amino acid precursors, and products that contain up to three stereocenters are generated with >20:1 dr.

Distribution of type I collagen morphologies in bone: relation to estrogen depletion.

Bone is an amazing material evolved by nature to elegantly balance structural and metabolic needs in the body. Bone health is an integral part of overall health, but our lack of understanding of the ultrastructure of healthy bone precludes us from knowing how disease may impact nanoscale properties in this biological material. Here, we show that quantitative assessments of a distribution of Type I collagen fibril morphologies can be made using atomic force microscopy (AFM).

Protein proton-proton dynamics from amide proton spin flip rates.

Residue-specific amide proton spin-flip rates K were measured for peptide-free and peptide-bound calmodulin. K approximates the sum of NOE build-up rates between the amide proton and all other protons. This work outlines the theory of multi-proton relaxation, cross relaxation and cross correlation, and how to approximate it with a simple model based on a variable number of equidistant protons.

Conformation dependence of the C(alpha)D(alpha) stretch mode in peptides. II. explicitly hydrated alanine peptide structures.

Our previous studies of the potential utility of the C(alpha)D(alpha) stretch frequency, nu(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923-10924; 2007, 111, 5300-5303) dealt with the spectroscopic characteristics of isolated alanine peptides with alpha(R), beta, and polyproline II structures. We have now extended these ab initio calculations to include various explicit-water environments interacting with such conformers. We find that the structure-discriminating feature of this technique is in fact enhanced as a result of the conformation-specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C(alpha)--D(alpha).

1,1'-Dimethoxy-3,3'-dimethyl-3,3'-(hexane-1,6-diyl)bis(triazen-2-ium-2-olate): a nitric oxide donor.

The title compound, C(10)H(24)N(6)O(4), is the most stable type of nitric oxide (NO) donor among the broad category of discrete N-diazeniumdiolates (NO adducts of nucleophilic small molecule amines). Sitting astride a crystallographic inversion center, the molecule contains a symmetric dimethylhexane-1,6-diamine structure bearing two planar O(2)-methylated N-diazeniumdiolate functional groups [N(O)=NOMe]. These two groups are parallel to each other and have the potential to release four molecules of NO.

Stereoselective synthesis of imidazolidin-2-ones via Pd-catalyzed alkene carboamination. Scope and limitations.

A method for the synthesis of imidazolidin-2-ones from N-allylureas and aryl or alkenyl bromides via Pd-catalyzed carboamination reactions is described. The N-allylurea precursors are prepared in one step from readily available allylic amines and isocyanates, and the Pd-catalyzed reactions effect the formation of a C-C bond, a C-N bond, and up to two stereocenters in a single step. Good diastereoselectivities are obtained for the conversion of substrates bearing allylic substituents to 4,5-disubstituted imidazolidin-2-ones, and excellent selectivity for the generation of products resulting from syn-addition across the alkene is observed when substrates derived from cyclic alkenes or E-1,2-disubstituted alkenes are employed.

Mild conditions for Pd-catalyzed carboamination of N-protected hex-4-enylamines and 1-, 3-, and 4-substituted pent-4-enylamines. Scope, limitations, and mechanism of pyrrolidine formation.

The use of the weak base Cs2CO3 in Pd-catalyzed carboamination reactions of N-protected gamma-aminoalkenes with aryl bromides leads to greatly increased tolerance of functional groups and alkene substitution. Substrates derived from (E)- or (Z)-hex-4-enylamines are stereospecifically converted to 2,1'-disubstituted pyrrolidine products that result from suprafacial addition of the nitrogen atom and the aryl group across the alkene. Transformations of 4-substituted pent-4-enylamine derivatives proceed in high yield to afford 2,2-disubstituted products, and cis-2,5- or trans-2,3-disubstituted pyrrolidines are generated in good yield with excellent diastereoselectivity from N-protected pent-4-enylamines bearing substituents at C1 or C3.

Multiplexed detection and applications for separations on parallel microchips.

Much work has been performed since the development of the lab-on-a-chip concept that has brought microfabricated systems to the forefront of bioanalytical research. The success of using these microchips for performing complicated biological assays faster and cheaper than conventional methods has facilitated their emerging popularity among researchers. A recently exploited advantage of microfabricated technology has led to the creation of single wafers with multiple channel manifolds for high-throughput experiments.

The cytochromes P450 and b5 and their reductases--promising targets for structural studies by advanced solid-state NMR spectroscopy.

Members of the cytochrome P450 (cyt P450) superfamily of enzymes oxidize a wide array of endogenous and xenobiotic substances to prepare them for excretion. Most of the drugs in use today are metabolized in part by a small set of human cyt P450 isozymes. Consequently, cyt P450s have for a long time received a lot of attention in biochemical and pharmacological research.

Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis.

Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) complex that catalyzes the metal-dependent maturation of the 5' end of precursor tRNAs (pre-tRNAs) in all organisms. RNase P is comprised of a catalytic RNA (P RNA), and at least one essential protein (P protein). Although P RNA is the catalytic subunit of the enzyme and is active in the absence of P protein under high salt concentrations in vitro, the protein is still required for enzyme activity in vivo.

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.

The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of G76 is restricted by stacking with G76 of a neighboring molecule.

Mild conditions for the synthesis of functionalized pyrrolidines via Pd-catalyzed carboamination reactions.

[reaction: see text] The palladium-catalyzed carboamination of N-protected gamma-aminoalkenes with aryl bromides and triflates has been achieved under new, mild reaction conditions using the weak base Cs(2)CO(3) in dioxane solvent. These reactions tolerate a wide variety of functional groups, including enolizable ketones, nitro groups, methyl esters, and acetates, which are not compatible with previously described conditions.

Future of biomedical sciences: single molecule microscopy.

The behavior of single molecule defines whether a cell lives, dies, or responds to a specific drug treatment. Single molecule microscopies have begun to reveal the number, location, and functionalities of molecules outside and inside living cells. This issue of Biopolymers presents a first set of reviews that aim to highlight the accomplishments and future prospects of single molecule microscopies.

Stereoselective Synthesis of Saturated Heterocycles via Pd-Catalyzed Alkene Carboetherification and Carboamination Reactions.

The development of Pd-catalyzed carboetherification and carboamination reactions between aryl/alkenyl halides and alkenes bearing pendant heteroatoms is described. These transformations effect the stereoselective construction of useful heterocycles such as tetrahydrofurans, pyrrolidines, imidazolidin-2-ones, isoxazolidines, and piperazines. The scope, limitations, and applications of these reactions are presented, and current stereochemical models are described.

Under the microscope: single molecule symposium at the University of Michigan, 2006.

In recent years, a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biopolymers in unprecedented detail. A recent Gordon Research Conference style meeting, hosted by the University of Michigan, highlighted current status and future perspectives of this rising field as researchers begin to integrate it with mainstream biology and nanotechnology.

Molecular dynamics simulations of RNA: an in silico single molecule approach.

RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application.