A Structurally Divergent Class Ia Ribonucleotide Reductase from a Tick-Borne Pathogen.

Ribonucleotide reductases (RNRs) generate 2'-deoxynucleotides for DNA biosynthesis, a reaction essential to all life. Class I RNRs have two subunits, α and β. α binds and reduces the substrate, whereas β oxidizes one of the cysteines in α to a C3'-H-bond-cleaving thiyl radical to begin the reaction.

Self-Assembly of Topologically Networked Protein-TiCT MXene Composites.

Hierarchical organization plays an important role in the stunning physical properties of natural and synthetic composites. Limits on the physical properties of such composites are generally defined by percolation theory and can be systematically altered using the volumetric filler fraction of the inorganic/organic phase. In natural composites, organic materials such as proteins that interact with inorganic filler materials can further alter the hierarchical order and organization of the composite topological interactions, expanding the limits of the physical properties defined by percolation theory.

Evidence for Modulation of Oxygen Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases.

Iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases generate iron(IV)-oxo (ferryl) intermediates that can abstract hydrogen from aliphatic carbons (R-H). Hydroxylation proceeds by coupling of the resultant substrate radical (R•) and oxygen of the Fe(III)-OH complex ("oxygen rebound"). Nonhydroxylation outcomes result from different fates of the Fe(III)-OH/R• state; for example, halogenation results from R• coupling to a halogen ligand cis to the hydroxide.

Hydrogen Donation but not Abstraction by a Tyrosine (Y68) during Endoperoxide Installation by Verruculogen Synthase (FtmOx1).

Hydrogen-atom transfer (HAT) from a substrate carbon to an iron(IV)-oxo (ferryl) intermediate initiates a diverse array of enzymatic transformations. For outcomes other than hydroxylation, coupling of the resultant carbon radical and hydroxo ligand (oxygen rebound) must generally be averted. A recent study of FtmOx1, a fungal iron(II)- and 2-(oxo)glutarate-dependent oxygenase that installs the endoperoxide of verruculogen by adding O between carbons 21 and 27 of fumitremorgin B, posited that tyrosine (Tyr or Y) 224 serves as HAT intermediary to separate the C21 radical (C21•) and Fe(III)-OH HAT products and prevent rebound.

Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.

All cells obtain 2'-deoxyribonucleotides for DNA synthesis through the activity of a ribonucleotide reductase (RNR). The class I RNRs found in humans and pathogenic bacteria differ in () use of Fe(II), Mn(II), or both for activation of the dinuclear-metallocofactor subunit, β; () reaction of the reduced dimetal center with dioxygen or superoxide for this activation; () requirement (or lack thereof) for a flavoprotein activase, NrdI, to provide the superoxide from O; and () use of either a stable tyrosyl radical or a high-valent dimetal cluster to initiate each turnover by oxidizing a cysteine residue in the α subunit to a radical (Cys•). The use of manganese by bacterial class I, subclass b-d RNRs, which contrasts with the exclusive use of iron by the eukaryotic Ia enzymes, appears to be a countermeasure of certain pathogens against iron deprivation imposed by their hosts.

Tunable thermal transport and reversible thermal conductivity switching in topologically networked bio-inspired materials.

The dynamic control of thermal transport properties in solids must contend with the fact that phonons are inherently broadband. Thus, efforts to create reversible thermal conductivity switches have resulted in only modest on/off ratios, since only a relatively narrow portion of the phononic spectrum is impacted. Here, we report on the ability to modulate the thermal conductivity of topologically networked materials by nearly a factor of four following hydration, through manipulation of the displacement amplitude of atomic vibrations.

ProtaBank: A repository for protein design and engineering data.

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries.

Mechanical Properties of Tandem-Repeat Proteins Are Governed by Network Defects.

Topological defects in highly repetitive structural proteins strongly affect their mechanical properties. However, there are no universal rules for structure-property prediction in structural proteins due to high diversity in their repetitive modules. Here, we studied the mechanical properties of tandem-repeat proteins inspired by squid ring teeth proteins using rheology and tensile experiments as well as spectroscopic and X-ray techniques.

Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase.

Iron(II)- and 2-(oxo)-glutarate-dependent oxygenases catalyze diverse oxidative transformations that are often initiated by abstraction of hydrogen from carbon by iron(IV)-oxo (ferryl) complexes. Control of the relative orientation of the substrate C-H and ferryl Fe-O bonds, primarily by direction of the oxo group into one of two cis-related coordination sites (termed inline and offline), may be generally important for control of the reaction outcome. Neither the ferryl complexes nor their fleeting precursors have been crystallographically characterized, hindering direct experimental validation of the offline hypothesis and elucidation of the means by which the protein might dictate an alternative oxo position.

A Pd-Catalyzed Synthesis of Functionalized Piperidines.

A readily available cyclic carbamate 1 functions as a general precursor to a range of functionalized piperidine products via a new Pd-catalyzed annulation strategy. An asymmetric catalytic variant provides a rapid and efficient means to access these heterocycles with high to excellent levels of enantiocontrol. Finally, these richly functionalized compounds are amenable to further chemoselective elaboration.

Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins.

Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions.

Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries.

The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs.

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles.

The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design.

An efficient algorithm for multistate protein design based on FASTER.

Most of the methods that have been developed for computational protein design involve the selection of side-chain conformations in the context of a single, fixed main-chain structure. In contrast, multistate design (MSD) methods allow sequence selection to be driven by the energetic contributions of multiple structural or chemical states simultaneously. This methodology is expected to be useful when the design target is an ensemble of related states rather than a single structure, or when a protein sequence must assume several distinct conformations to function.

Conformational analysis of a covalently cross-linked Watson-Crick base pair model.

Low-temperature NMR experiments and molecular modeling have been used to characterize the conformational behavior of a covalently cross-linked DNA base pair model. The data suggest that Watson-Crick or reverse Watson-Crick hydrogen bonding geometries have similar energies and can interconvert at low temperatures. This low-temperature process involves rotation about the crosslink CH(2)C(5') (psi) carbon-carbon bond, which is energetically preferred over the alternate CH(2)N(3) (phi) carbon-nitrogen bond rotation.

Computational protein design promises to revolutionize protein engineering.

Natural evolution has produced an astounding array of proteins that perform the physical and chemical functions required for life on Earth. Although proteins can be reengineered to provide altered or novel functions, the utility of this approach is limited by the difficulty of identifying protein sequences that display the desired properties. Recently, advances in the field of computational protein design (CPD) have shown that molecular simulation can help to predict sequences with new and improved functions.

Combinatorial methods for small-molecule placement in computational enzyme design.

The incorporation of small-molecule transition state structures into protein design calculations poses special challenges because of the need to represent the added translational, rotational, and conformational freedoms within an already difficult optimization problem. Successful approaches to computational enzyme design have focused on catalytic side-chain contacts to guide placement of small molecules in active sites. We describe a process for modeling small molecules in enzyme design calculations that extends previously described methods, allowing favorable small-molecule positions and conformations to be explored simultaneously with sequence optimization.

Dramatic performance enhancements for the FASTER optimization algorithm.

FASTER is a combinatorial optimization algorithm useful for finding low-energy side-chain configurations in side-chain placement and protein design calculations. We present two simple enhancements to FASTER that together improve the computational efficiency of these calculations by as much as two orders of magnitude with no loss of accuracy. Our results highlight the importance of choosing appropriate initial configurations, and show that efficiency can be improved by stringently limiting the number of positions that are allowed to relax in response to a perturbation.

Flexor tenolysis using a free suture.

The authors present a simple technique to release flexor tendon adhesions. It utilizes a suture which "snares" the adhesion and divides them like a Gigli saw. This minimizes collateral damage.

An isosparteine derivative for stereochemical assignment of stereogenic (chiral) methyl groups using tritium NMR: theory and experiment.

(N-CHDT)-(alpha)-isosparteinium ditosylamide can be used in conjunction with tritium NMR spectroscopy to assign the configuration of an intact stereogenic (chiral) methyl group. The S-CHDT group has a (3)H chemical shift that is 49 ppb downfield of the R-CHDT resonance. The sign and magnitude of this chemical shift difference of these diastereotopic tritium nuclei are found to be in agreement with predictions made via a purely ab initio computational approach.

Fomenting proton anisochronicity in the CH2D group.

A novel C-D...