Structural complexity and functional diversity of plant NADPH oxidases.

Plant NADPH oxidases also known as respiratory burst oxidase homologs (Rbohs) are a family of membrane-bound enzymes that play diverse roles in the defense response and morphogenetic processes via regulated generation of reactive oxygen species. Rbohs are associated with a variety of functions, although the reason for this is not clear. To evaluate using bioinformatics, the possible mechanisms for the observed functional diversity within the plant kingdom, 127 Rboh protein sequences representing 26 plant species were analyzed. Multiple clusters were identified with gene duplications that were both dicot as well as monocot-specific. The N-terminal sequences were observed to be highly variable. The conserved cysteine (equivalent of Cys890) in C-terminal of AtRbohD suggested that the redox-based modification like S-nitrosylation may regulate the activity of other Rbohs. Three-dimensional models corresponding to the N-terminal domain for Rbohs from Arabidopsis thaliana and Oryza sativa were constructed and molecular dynamics studies were carried out to study the role of Ca2+ in the folding of Rboh proteins. Certain mutations indicated possibly affect the structure and function of the plant NADPH oxidases, thereby providing the rationale for further experimental validation.

Engineering extrinsic disorder to control protein activity in living cells.

Optogenetic and chemogenetic control of proteins has revealed otherwise inaccessible facets of signaling dynamics. Here, we use light- or ligand-sensitive domains to modulate the structural disorder of diverse proteins, thereby generating robust allosteric switches. Sensory domains were inserted into nonconserved, surface-exposed loops that were tight and identified computationally as allosterically coupled to active sites. Allosteric switches introduced into motility signaling proteins (kinases, guanosine triphosphatases, and guanine exchange factors) controlled conversion between conformations closely resembling natural active and inactive states, as well as modulated the morphodynamics of living cells. Our results illustrate a broadly applicable approach to design physiological protein switches.

Single-Step Fabrication of Computationally Designed Microneedles by Continuous Liquid Interface Production.

Microneedles, arrays of micron-sized needles that painlessly puncture the skin, enable transdermal delivery of medications that are difficult to deliver using more traditional routes. Many important design parameters, such as microneedle size, shape, spacing, and composition, are known to influence efficacy, but are notoriously difficult to alter due to the complex nature of microfabrication techniques. Herein, we utilize a novel additive manufacturing ("3D printing") technique called Continuous Liquid Interface Production (CLIP) to rapidly prototype sharp microneedles with tuneable geometries (size, shape, aspect ratio, spacing). This technology allows for mold-independent, one-step manufacturing of microneedle arrays of virtually any design in less than 10 minutes per patch. Square pyramidal CLIP microneedles composed of trimethylolpropane triacrylate, polyacrylic acid and photopolymerizable derivatives of polyethylene glycol and polycaprolactone were fabricated to demonstrate the range of materials that can be utilized within this platform for encapsulating and controlling the release of therapeutics. These CLIP microneedles effectively pierced murine skin ex vivo and released the fluorescent drug surrogate rhodamine.

Additive manufacturing. Continuous liquid interface production of 3D objects.

Additive manufacturing processes such as 3D printing use time-consuming, stepwise layer-by-layer approaches to object fabrication. We demonstrate the continuous generation of monolithic polymeric parts up to tens of centimeters in size with feature resolution below 100 micrometers. Continuous liquid interface production is achieved with an oxygen-permeable window below the ultraviolet image projection plane, which creates a "dead zone" (persistent liquid interface) where photopolymerization is inhibited between the window and the polymerizing part. We delineate critical control parameters and show that complex solid parts can be drawn out of the resin at rates of hundreds of millimeters per hour. These print speeds allow parts to be produced in minutes instead of hours.

Light-cleavable rapamycin dimer as an optical trigger for protein dimerization.

Rapamycin-induced protein heterodimerization of FKBP12 and FRB is one of the most commonly employed switches to conditionally control biological processes. We developed an optically activated rapamycin dimer that does not induce FKBP12-FRB dimerization until exposed to light, and applied it to control kinase, protease, and recombinase function.

Pore dynamics and conductance of RyR1 transmembrane domain.

Ryanodine receptors (RyR) are calcium release channels, playing a major role in the regulation of muscular contraction. Mutations in skeletal muscle RyR (RyR1) are associated with congenital diseases such as malignant hyperthermia and central core disease (CCD). The absence of high-resolution structures of RyR1 has limited our understanding of channel function and disease mechanisms at the molecular level. Previously, we have reported a hypothetical structure of the RyR1 pore-forming region, obtained by homology modeling and supported by mutational scans, electrophysiological measurements, and cryo-electron microscopy. Here, we utilize the expanded model encompassing six transmembrane helices to calculate the RyR1 pore region conductance, to analyze its structural stability, and to hypothesize the mechanism of the Ile4897 CCD-associated mutation. The calculated conductance of the wild-type RyR1 suggests that the proposed pore structure can sustain ion currents measured in single-channel experiments. We observe a stable pore structure on timescales of 0.2 µs, with multiple cations occupying the selectivity filter and cytosolic vestibule, but not the inner chamber. We further suggest that stability of the selectivity filter critically depends on the interactions between the I4897 residue and several hydrophobic residues of the neighboring subunit. Loss of these interactions in the case of polar substitution I4897T results in destabilization of the selectivity filter, a possible cause of the CCD-specific reduced Ca(2+) conductance.

Computational approaches to understanding protein aggregation in neurodegeneration.

The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders.

Rational design of a ligand-controlled protein conformational switch.

Design of a regulatable multistate protein is a challenge for protein engineering. Here we design a protein with a unique topology, called uniRapR, whose conformation is controlled by the binding of a small molecule. We confirm switching and control ability of uniRapR in silico, in vitro, and in vivo. As a proof of concept, uniRapR is used as an artificial regulatory domain to control activity of kinases. By activating Src kinase using uniRapR in single cells and whole organism, we observe two unique phenotypes consistent with its role in metastasis. Activation of Src kinase leads to rapid induction of protrusion with polarized spreading in HeLa cells, and morphological changes with loss of cell-cell contacts in the epidermal tissue of zebrafish. The rational creation of uniRapR exemplifies the strength of computational protein design, and offers a powerful means for targeted activation of many pathways to study signaling in living organisms.

Hybrid dynamics simulation engine for metalloproteins.

Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins' structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca(2+) form of the enzyme catechol O-methyl transferase, which, unlike the native Mg(2+) form, is catalytically inactive. The Mg(2+) site is ochtahedral, but the Ca(2+) is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight.

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization.

Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics, and sample near-native states in ab initio folding of proteins of ∼100 residues.

Rigid substructure search.

MOTIVATION: Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions. AVAILABILITY AND IMPLEMENTATION: We provide this service through a web server at http://erebus.dokhlab.org.

Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP.

We developed a new system for light-induced protein dimerization in living cells using a photocaged analogue of rapamycin together with an engineered rapamycin binding domain. Using focal adhesion kinase as a target, we demonstrated successful light-mediated regulation of protein interaction and localization in living cells. Modification of this approach enabled light-triggered activation of a protein kinase and initiation of kinase-induced phenotypic changes in vivo.

Spontaneous and specific activation of chemical bonds in macromolecular fluids.

Mechanical activation of chemical bonds typically involves the application of external forces, which implies a broad distribution of bond tensions. We demonstrate that controlling the flow profile of a macromolecular fluid generates and delineates mechanical force concentration, enabling a hierarchical activation of chemical bonds on different length scales from the macroscopic to the molecular. Bond tension is spontaneously generated within brushlike macromolecules as they spread on a solid substrate. The molecular architecture creates an uneven distribution of tension in the covalent bonds, leading to spatially controlled bond scission. By controlling the flow rate and the gradient of the film pressure, one can sever the flowing macromolecules with high precision. Specific chemical bonds are activated within distinct macromolecules located in a defined area of a thin film. Furthermore, the flow-controlled loading rate enables quantitative analysis of the bond activation parameters.

Flory theorem for structurally asymmetric mixtures.

The generalization of the Flory theorem for structurally asymmetric mixtures was derived and tested by direct visualization of conformational transformations of brushlike macromolecules embedded in a melt of linear chains. Swelling of a brush molecule was shown to be controlled not only by the degree of polymerization (DP) of the surrounding linear chains, N(B), but also by the DP of the brush's side chains, N, which determines the structural asymmetry of the mixed species. The boundaries of the swelling region were established by scaling analysis as N(2) < N (B) < N (A)/N, where N (A) is the degree of polymerization of the brush backbone. Experiment and theory demonstrated good agreement.

Adsorption-induced scission of carbon-carbon bonds.

Covalent carbon-carbon bonds are hard to break. Their strength is evident in the hardness of diamonds and tensile strength of polymeric fibres; on the single-molecule level, it manifests itself in the need for forces of several nanonewtons to extend and mechanically rupture one bond. Such forces have been generated using extensional flow, ultrasonic irradiation, receding meniscus and by directly stretching a single molecule with nanoprobes. Here we show that simple adsorption of brush-like macromolecules with long side chains on a substrate can induce not only conformational deformations, but also spontaneous rupture of covalent bonds in the macromolecular backbone. We attribute this behaviour to the fact that the attractive interaction between the side chains and the substrate is maximized by the spreading of the side chains, which in turn induces tension along the polymer backbone. Provided the side-chain densities and substrate interaction are sufficiently high, the tension generated will be strong enough to rupture covalent carbon-carbon bonds. We expect similar adsorption-induced backbone scission to occur for all macromolecules with highly branched architectures, such as brushes and dendrimers. This behaviour needs to be considered when designing surface-targeted macromolecules of this type-either to avoid undesired degradation, or to ensure rupture at predetermined macromolecular sites.

Flow-enhanced epitaxial ordering of brush-like macromolecules on graphite.

Long-range orientational order in monolayers of brush-like macromolecules was achieved during spreading of a polymer melt on the surface of highly oriented pyrolytic graphite. The combination of wetting-induced flow and epitaxial adsorption of poly(n-butylacrylate) side chains on graphite led to the formation of large domains of uniaxially oriented rodlike molecules. The domain size varied from ca. 1 to 10 microm which is noticeably larger than the submicrometer-sized mosaic domains typically observed upon adsorption from solution. The increase in the degree of order is attributed to the flow-enhanced diffusion of the macromolecules within spreading monolayers which facilitates the epitaxial alignment of the large macromolecules. The diffusion coefficient was shown to increase linearly with the spreading rate. Even though the ordering occurred during flow, no correlation was observed between the molecular orientation and the flow direction. Thus, the role of the flow was not to induce the molecular orientation but to facilitate the intrinsic ordering process. This finding can inspire and lead to new strategies for constructing large scale ordered structures on surfaces.

Molecular visualization of conformation-triggered flow instability.

A new type of flow fingering instability was observed in monolayer-thick polymer films as they spread on a solid substrate. Tracing the movement of individual molecules by atomic force microscopy enabled us to follow the development of the flow instability on the molecular level and to understand the underlying physical mechanism. The fingering instability was observed to be triggered by conformational changes of brushlike macromolecules in response to the pressure gradient driving the flow.

Molecular motion in a spreading precursor film.

Spreading of a polymer drop on a solid substrate was monitored with molecular resolution. Three characteristic rates, i.e., the spreading rate of the precursor film D(spread)=(3.9+/-0.2)x10(3) nm(2)/s, the flow-induced diffusion rate of molecules within the film D(induced)=1.3+/-0.1 nm(2)/s, and the thermal diffusion coefficient of single molecules D(therm)>D(induced), the plug flow of polymer chains was identified as the main mass-transport mechanism of spreading with an insignificant contribution from the molecular diffusion.

Multiarm molecular brushes: effect of the number of arms on the molecular weight polydispersity and surface ordering.

Individual molecules of multiarm starlike molecular brushes were visualized by atomic force microscopy. In the studied series of brushes, the number of arms varied from one for a linear chain to four, while the length of the side chains was kept approximately constant. Molecular visualization provided a unique opportunity for independent size characterization of the brush arms separately from that of the entire molecule. In agreement with the Schulz-Flory theory for chain coupling, the polydispersity of the total length was significantly lower than that of the arm length. The variation in polydispersity had an effect on molecular ordering. Lateral compression of the starlike brushes caused a transition from an extended dendritic-like conformation to a compact disklike conformation. In contrast to one-, two-, and three-arm brushes, the four-arm molecules with a lower polydispersity index of 1.04 demonstrated local hexagonal order.