AAAS Science & Technology Policy Fellow (Big Data/Analytics)
AAAS Science & Technology Policy Fellow at USAID
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AAAS Science & Technology Policy Fellow (Big Data/Analytics)
I'm just starting on the Data/Analytics team at USAID's Global Development Lab. I'll be identifying IT resources that can help make development activities more efficient and effective, designing and developing new data visualization tools, and identifying pilot opportunities for new technologies.
Watch this space for future updates!
* Mathematical modeling of post-translational biochemical oscillations
* Data-based parameterization of models of the mammalian circadian clock
* Modeling of intracellular signaling and synchronization in the suprachiasmatic nucleus
* Synthesis and structural characterization of protein-templated inorganic nanoparticles
* Molecular dynamics simulations of proteins and metal-organic coordination polymers
* DFT calculations on metal-organic complexes
* Network-theoretical analysis of complex chemical networks from biology and astrochemistry
* Computational studies of protein dynamics using constrained geometric simulations, with applications in protein complex assembly and flexible cryo-EM fitting.
* Ultrafast optical spectroscopy of photosynthetic membrane proteins from T. elongatus, C. reinhardtii, and G. sulphuraria.
* Homology modeling of photosynthetic membrane proteins.
I studied at ASU on an NSF IGERT fellowship as part of an interdisciplinary program involving students from biology, chemistry, physics, and engineering, focused on the development of "biomolecular devices" -- a meeting of molecular biology and engineering at the nanoscale.
My thesis title was "Structure and Dynamics in Photosystem I"
Multisite phosphorylation plays an important role in biological oscillators such as the circadian clock. Its general role, however, has been elusive. In this theoretical study, we show that a simple substrate with two modification sites acted upon by two opposing enzymes (e.g., a kinase and a phosphatase) can show oscillations in its modification state. An unbiased computational analysis of this oscillator reveals two common characteristics: a unidirectional modification cycle and sequestering of an enzyme by a specific modification state. These two motifs cause a substrate to act as a coupled system in which a unidirectional cycle generates single-molecule oscillators, whereas sequestration synchronizes the population by limiting the available enzyme under conditions in which substrate is in excess. We also demonstrate the conditions under which the oscillation period is temperature compensated, an important feature of the circadian clock. This theoretical model will provide a framework for analyzing and synthesizing posttranslational oscillators.
Protein cage nanoparticles (PCNs) are attractive platforms for developing functional nanomaterials using biomimetic approaches for functionalization and cargo encapsulation. Many strategies have been employed to direct the loading of molecular cargos inside a wide range of PCN architectures. Here we demonstrate the exploitation of a metal-ligand coordination bond with respect to the direct packing of guest molecules on the interior interface of a virus-like PCN derived from Salmonella typhimurium bacteriophage P22. The incorporation of these guest species was assessed using mass spectrometry, multiangle laser light scattering, and analytical ultracentrifugation. In addition to small-molecule encapsulation, this approach was also effective for the directed synthesis of a large macromolecular coordination polymer packed inside of the P22 capsid and initiated on the interior surface. A wide range of metals and ligands with different thermodynamic affinities and kinetic stabilities are potentially available for this approach, highlighting the potential for metal-ligand coordination chemistry to direct the site-specific incorporation of cargo molecules for a variety of applications.
Iron is an essential micronutrient for all organisms because it is a component of enzyme cofactors that catalyze redox reactions in fundamental metabolic processes. Even though iron is abundant on earth, it is often present in the insoluble ferric [Fe (III)] state, leaving many surface environments Fe-limited. The haploid green alga Chlamydomonas reinhardtii is used as a model organism for studying eukaryotic photosynthesis. This study explores structural and functional changes in PSI-LHCI supercomplexes under Fe deficiency as the eukaryotic photosynthetic apparatus adapts to Fe deficiency.
Iron (Fe) availability is a major limiting factor for primary production in aquatic environments. Cyanobacteria respond to Fe deficiency by derepressing the isiAB operon, which encodes the antenna protein IsiA and flavodoxin. At nanomolar Fe concentrations, a PSI-IsiA supercomplex forms, comprising a PSI trimer encircled by two complete IsiA rings. This PSI-IsiA supercomplex is the largest photosynthetic membrane protein complex yet isolated. This study presents a detailed characterization of this complex using transmission electron microscopy and ultrafast fluorescence spectroscopy. Excitation trapping and electron transfer are highly efficient, allowing cyanobacteria to avoid oxidative stress. This mechanism may be a major factor used by cyanobacteria to successfully adapt to modern low-Fe environments.
Photosystem l-light harvesting complex I (PSI-LHCI) was isolated from the thermoacidophilic red alga Galdieria sulphuraria, and its structure, composition, and light-harvesting function were characterized by electron microscopy, mass spectrometry, and ultrafast optical spectroscopy. The results show that Galdieria PSI is a monomer with core features similar to those of PSI from green algae, but with significant differences in shape and size. A comparison with the crystal structure of higher plant (pea) PSI-LHCI indicates that Galdieria PSI binds seven to nine light-harvesting proteins. Results from ultrafast optical spectroscopy show that the functional coupling of the LHCI proteins to the PSI core is tighter than in other eukaryotic PSI-LHCI systems reported thus far. This tight coupling helps Galdieria perform efficient light harvesting under the low-light conditions present in its natural endolithic habitat.
Metal-organic coordination polymers are a growing class of technologically-important materials in which transition metal ions are connected by multitopic organic chelators to form a 3-D network structure. While the structures of many highly-ordered metal-organic frameworks have been determined, far less structural information is available about the more common disordered materials. Our study combines pair distribution function analysis from total X-ray scattering, ab initio quantum mechanical calculations, and all-atom molecular dynamics to explore the structure and dynamics of a poorly-ordered branched coordination polymer. The polymer structure is highly flexible and dynamic, and is dramatically affected by its solvation state, a finding with far-reaching implications for the incorporation of coordination polymers into nanocomposite materials.
Many pathogenic bacteria are able to survive attack by the host's immune system because of antioxidant systems that mitigate the effects of reactive oxygen species. Dps is a hollow 12-subunit protein nanocage that prevents oxidative damage by oxidizing and sequestering intracellular Fe2+; the resulting Fe3+ forms an iron oxyhydroxide nanoparticle in the cage interior. Charged sites on the protein nanocage create an electrostatic gradient that guides ions through well-defined pores that connect the cage interior with the surrounding solution and toward nucleation sites on the cage interior. In this study, we use all-atom molecular dynamics to simulate the motion of simple cations into the dodecameric cage formed by the Dps protein from Listeria monocytogenes. Ion trajectories are analyzed by using a novel, to our knowledge, genetic algorithm to determine the temporal sequence of ion-protein interactions. Ions enter Dps through well-defined pores at the ferritinlike C-3 axes, with negatively-charged residues on the outside of the cage forming a fairly well-defined entrance pathway. This method of trajectory analysis may be broadly applicable in situations where the spatial localization of ions or other small molecules is electrostatically driven by a biomolecule.
Recent years have seen dramatic advances in computational models of chemical processes in the interstellar medium (ISM). Typically, these models have been used to calculate changes in chemical abundances with time; the calculated abundances can then be compared with chemical abundances derived from observations. In this study, the output from an astrochemical simulation has been used to generate directed graphs with weighted edges; these have been analyzed with the tools of network theory to uncover whole-network properties of reaction systems in dark molecular clouds. The results allow the development of a model in which global network properties can be rationalized in terms of the basic physical properties of the reaction system. The ISM network exhibits an exponential degree distribution, which is likely to be a generic feature of chemical networks involving a broad range of reaction rate constants. While species abundances span several orders of magnitude, the formation and destruction rates for most species are approximately balanced-departures from this rule indicate species (such as CO) that play a critical role in shaping the dynamics of the system. Future theoretical or observational studies focusing on individual molecular species will be able to situate them in terms of their role in the complete system or quantify the degree to which they deviate from the typical system behavior.
Protein cages such as ferritins and virus capsids have been used as containers to synthesize a wide variety of protein-templated inorganic nanoparticles. While identification of the inorganic crystal phase has been successful in some cases, very little is known about the detailed nanoscale structure of the inorganic component. We have used pair distribution function analysis of total X-ray scattering to measure the crystalline domain size in nanoparticles of ferrihydrite, gamma-Fe(2)O(3), Mn(3)O(4), CoPt, and FePt grown inside 24-meric ferritin cages from H. sapiens and P. furiosus. The material properties of these protein-templated nanoparticles are influenced by processes at a variety of length scales: the chemistry of the material determines the precise arrangement of atoms at very short distances, while the interior volume of the protein cage constrains the maximum nanoparticle size attainable. At intermediate length scales, the size of coherent crystalline domains appears to be constrained by the arrangement of crystal nucleation sites on the interior of the cage. On the basis of these observations, some potential synthetic strategies for the control of crystalline domain size in protein-templated nanoparticles are suggested.
A branched iron-phenanthroline based coordination polymer has been constructed in a water based system using a click chemistry approach to link monomeric coordination complexes together within a protein cage nanoarchitecture, which acts both as a template and a sized constrained reaction environment.
Mass measurements of metal-mineralized protein cages allowed quantitative examination of the effects of metal-ion concentration on the final nanoparticle size. Modeling using a kinetic master equation suggests that particle growth involves both a binding phase and a growth phase.
The influence of the protein environment on the primary electron donor, P, a bacteriochlorophyll a dimer, of reaction centers from Rhodobacter sphaeroides, has been investigated using electron paramagnetic resonance and electron nuclear double resonance spectroscopy. These techniques were used to probe the effects on P that are due to alteration of three amino acid residues, His L168, Asn L170, and Asn M199. The introduction of Glu at L168, Asp at L170, or Asp at M199 changes the oxidation/reduction midpoint potential of P in a pH-dependent manner (Williams et al. (2001) Biochemistry 40, 15403–15407). For the double mutant His L168 to Glu and Asn at L170 to Asp, excitation results in electron transfer along the A-side branch of cofactors at pH 7.2, but at pH 9.5, a long-lived state involving B-side cofactors is produced (Haffa et al. (2004) J Phys Chem B 108, 4–7). Using electron paramagnetic resonance spectroscopy, the mutants with alterations of each of the three individual residues and a double mutant, with changes at L168 and L170, were found to have increased linewidths of 10.1–11.0 G compared to the linewidth of 9.6 G for wild type. The Special TRIPLE spectra were pH dependent, and at pH 8, the introduction of aspartate at L170 increased the spin density ratio, ρ L/ρ M, to 6.1 while an aspartate at the symmetry related position, M199, decreased the ratio to 0.7 compared to the value of 2.1 for wild type. These results indicate that the energy of the two halves of P changes by about 100 meV due to the mutations and are consistent with the interpretation that electrostatic interactions involving these amino acid residues contribute to the switch in pathway of electron transfer.
Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are consistent with the data and that preserve all the local stereochemistry associated with the biomolecule. We develop a new technique that maintains the local geometry and chemistry at each stage of the fitting procedure. A geometric simulation is used to drive the structure from some appropriate starting point (a nearby experimental structure or a modeled structure) toward the experimental density, via a set of small incremental motions. Structural motifs such as α-helices can be held rigid during the fitting procedure as the starting structure is brought into alignment with the experimental density. After validating this procedure on simulated data for adenylate kinase and lactoferrin, we show how cryo-EM data for two different GroEL structures can be fit using a starting x-ray crystal structure. We show that by incorporating the correct local stereochemistry in the modeling, structures can be obtained with effective resolution that is significantly higher than might be expected from the nominal cryo-EM resolution.
The elucidation of assembly pathways of multi-subunit protein complexes is a problem of great interest in structural biology and biomolecular modeling. In this study, we use a new computer algorithm for the simulation of large-scale motion in proteins to dock the subunit PsaC onto Photosystem I. We find that a complicated docking pathway involving multiple conformational changes can be quickly simulated by actively targeting only a few residues at a time to their target positions. Simulations for two possible docking scenarios are explored, and experimental approaches to distinguish between them are discussed.
The chemical basis of life involves more than simply the presence of biological molecules; biochemical systems embody a complex network of reactions with characteristic topological features. At the same time, chemical complexity is also present in nonbiological contexts, inviting us to clarify the relationship between chemistry and life through comparative studies. This study examines chemical networks from biology (the metabolism of E. coli) and astronomy (gas-phase reactions in dark molecular clouds) to establish common topological features that may be generic for any complex chemical system, as well as clear differences that may be topological signatures of life. The biological and astrochemical networks exhibit different scaling behaviors, and the network motifs found in the two systems show similarities as well as significant differences. The PageRank algorithm was used to quantify the degree to which individual species act primarily as products or reactants; in the metabolic network, these two roles are nearly identical for most species, whereas the astrochemical network shows a clearer partitioning into reactants and products.
Encapsulation of inorganic nanoparticles within oligomeric protein cages can provide a multivalent approach for the synthesis of biocompatible nanomaterials by combining the nanoparticle-forming catalytic abilities of the cage interior with the biointeractive exterior surface of the cage. Protein cages provide more than simply a passive compartment for nanoparticle formation: protein-templated nanoparticles can exhibit structural and electronic properties that are dramatically different from materials synthesized without protein templating. Mixed Fe/Mn oxides formed under hydrothermal conditions form a structural series ranging from the γ-Fe2O3 (maghemite) to the Mn3O4 (hausmannite) spinel structure as the Mn fraction is increased from 0 to 100%, while similar materials formed inside of human ferritin transition instead from maghemite to a layered Mn oxide structure similar to chalcophanite. The electronic properties of the protein-templated nanoparticles, as determined from soft X-ray absorption spectroscopy, also differ from those of their protein-free counterparts, in agreement with the structural results. Protein-templated synthesis may provide the opportunity for powerful control over nanomaterial properties through nanoconfinement, but the ultimate physical basis for these effects remains to be determined.
Nanoparticles of (MnxFe1−x)3O4 with a concentration ranging from x = 0 to 1 and a crystallite size of 14–15 nm were measured using X-ray absorption spectroscopy and X-ray magnetic circular dichroism to determine the ratio of the orbital moment to the spin moment for Mn and Fe. At low Mn concentrations, the Mn substitutes into the host Fe3O4 spinel structure as Mn2+ in the tetrahedral A-site. The net Fe moment, as identified by the X-ray dichrosim intensity, is found to increase at the lowest Mn concentrations then rapidly decrease until no dichroism is observed at 20% Mn. The average Fe orbit/spin moment ratio is determined to initially be negative and small for pure Fe3O4 nanoparticles and quickly go to 0 by 5%–10% Mn addition. The average Mn moment is anti-aligned to the Fe moment with an orbit/spin moment ratio of 0.12 which gradually decreases with Mn concentration.
The use of protein templates to direct the formation of inorganic nanostructures offers a novel bio-inspired route to nanomaterial synthesis that avoids the use of harsh reaction conditions and offers unique functionalities including biocompatibility and hierarchical assembly. Pair distribution function (PDF) analysis from total X-ray scattering has been used to determine the structure of TiO2 nanoparticles grown within an icosahedral virus capsid. The protein–TiO2 composites are similar to nanocrystalline anatase and show photocatalytic activity. PDF analysis is ideally suited to the study of protein–inorganic nanocomposites, and may be able to provide information about the hard/soft interface.
Soft x-ray absorption spectroscopy, soft x-ray magnetic circular dichroism, and alternating current magnetic susceptibility were performed on 6.7 nm iron oxide nanoparticles doped with (5%–33%) Mn grown inside the horse-spleen ferritin protein cages and compared to similarly protein encapsulated pure Fe-oxide and Mn-oxide nanoparticles to determine the site of the Mn dopant and to quantify the magnetic behavior with varying Mn concentration. The Mn dopant is shown to substitute preferentially as Mn+2 and prefers the octahedral site in the defected spinel structure. The Mn multiplet structure for the nanoparticles is simpler than for the bulk standards, suggesting that the nanoparticle lattices are relaxed from the distortions present in the bulk. Addition of Mn is found to alter the host Fe-oxide lattice from a defected ferrimagnetic spinel structure similar to γ-Fe2O3 to a nonferromagnetic spinel structure with a local Fe environment similar to Fe3O4.
The effect of high salt concentration (100 mM NaCl) on the organization of photosystem I-light harvesting complex I supercomplexes (PSI-LHCI) of Chlamydomonas reinhardtii was studied. The electron transfer activity was reduced by 39% in isolated PSI-LHCI supercomplexes. The visible circular dichroism (CD) spectra associated with strongly coupled chlorophyll (Chl) dimers were reduced in intensity, indicating that pigment–pigment interactions were disrupted. This data is consistent with results from fluorescence streak camera spectroscopy, which suggest that red-shifted pigments in the PSI-LHCI antenna had been lost. Denaturing gel electrophoresis and immunoblot analysis reveals that levels of the PSI reaction center proteins PsaD, PsaE and PsaF were reduced due to salt stress. PsaE is almost completely absent under high salt conditions. It is known that the membrane-extrinsic subunits PsaD and E form the ferredoxin-docking site. Our results indicate that the PSI-LHCI supercomplex is damaged by reactive oxygen species at high salt concentration, with particular impact on the ferredoxin-docking site and the PSI-LHCI interface.
A novel supercomplex of Photosystem I (PSI) with light harvesting complex I (LHCI) was isolated from the green alga Chlamydomonas reinhardtii. This novel supercomplex is unique as it is the first stable supercomplex of PSI together with its external antenna. The supercomplex contains 256 chlorophylls per reaction center. The supercomplex was isolated under anaerobic conditions and may represent the State II form of the photosynthetic unit. In contrast to previously reported supercomplexes isolated in State I, which contain only 4 LHC I proteins, this supercomplex contains 10–11 LHC I proteins tightly bound to the PSI core. In contrast to plants, no LHC II is tightly bound to the PSI–LHCI supercomplex in State II. Investigation of the energy transfer from the antenna system to the reaction center core shows that the LHC supercomplexes are tightly coupled to the PSI core, not only structurally but also energetically. The excitation energy transfer kinetics are completely dominated by the fast phase, with a near-complete lack of long-lived fluorescence. This tight coupling is in contrast to all reports of energy transfer in PSI–LHCI supercomplexes (in State I), which have so far been described as weakly coupled supercomplexes with low efficiency for excitation energy transfer. These results indicate that there are large and dynamic changes of the PSI–LHCI supercomplex during the acclimation from aerobic (State I) to anaerobic (State II) conditions in Chlamydomonas.
With the availability of structural models for photosystem I (PSI) in cyanobacteria and plants it is possible to compare the excitation transfer networks in this ubiquitous photosystem from two domains of life separated by over one billion years of divergent evolution, thus providing an insight into the physical constraints that shape the networks’ evolution. Structure-based modeling methods are used to examine the excitation transfer kinetics of the plant PSI-LHCI supercomplex. For this purpose an effective Hamiltonian is constructed that combines an existing cyanobacterial model for structurally conserved chlorophylls with spectral information for chlorophylls in the Lhca subunits. The plant PSI excitation migration network thus characterized is compared to its cyanobacterial counterpart investigated earlier. In agreement with observations, an average excitation transfer lifetime of ∼49 ps is computed for the plant PSI-LHCI supercomplex with a corresponding quantum yield of 95%. The sensitivity of the results to chlorophyll site energy assignments is discussed. Lhca subunits are efficiently coupled to the PSI core via gap chlorophylls. In contrast to the chlorophylls in the vicinity of the reaction center, previously shown to optimize the quantum yield of the excitation transfer process, the orientational ordering of peripheral chlorophylls does not show such optimality. The finding suggests that after close packing of chlorophylls was achieved, constraints other than efficiency of the overall excitation transfer process precluded further evolution of pigment ordering.
Photosystem (PS) I is a large membrane protein complex vital for oxygenic photosynthesis, one of the most important biological processes on the planet. We present an “atomic” model of higher plant PSI, based on theoretical modeling using the recent 4.4 Å x-ray crystal structure of PSI from pea. Because of the lack of information on the amino acid side chains in the x-ray structural model and the high cofactor content in this system, novel modeling techniques were developed. Our model reveals some important structural features of plant PSI that were not visible in the crystal structure, and our model sheds light on the evolutionary relationship between plant and cyanobacterial PSI.
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