A5013803827- Protein Structure and Dynamics
- Enzyme Structure and Function
- Photosynthetic Processes and Mechanisms
- Lipid Membrane Structure and Behavior
- Methane Hydrates and Related Phenomena
- RNA and protein synthesis mechanisms
- Metabolomics and Mass Spectrometry Studies
- Bacteriophages and microbial interactions
- Monoclonal and Polyclonal Antibodies Research
- Mass Spectrometry Techniques and Applications
- Isotope Analysis in Ecology
- Genetics, Bioinformatics, and Biomedical Research
- Geochemistry and Elemental Analysis
- Microbial Metabolic Engineering and Bioproduction
- Groundwater and Isotope Geochemistry
- Chemical Reaction Mechanisms
- Electrohydrodynamics and Fluid Dynamics
- Computational Drug Discovery Methods
- Surface Roughness and Optical Measurements
- Biochemical effects in animals
- Iron oxide chemistry and applications
- Spectroscopy Techniques in Biomedical and Chemical Research
- Radioactive element chemistry and processing
- Chemical Reactions and Isotopes
- Crystallography and molecular interactions
Dartmouth College
2019-2025
University of Michigan
2020-2024
Wellesley College
2019
University of Waterloo
2017
Yale University
2010-2014
The pioneering work of Ramachandran and colleagues emphasized the dominance steric constraints in specifying structure polypeptides. ubiquitous plot backbone dihedral angles (ϕ ψ) defined allowed regions conformational space. These predictions were subsequently confirmed proteins known structure. also investigated influence angle τ on distribution ϕ/ψ combinations. "bridge region" ≤ 0° -20° ψ 40°) was predicted to be particularly sensitive value τ. Here we present an analysis 850...
ABSTRACT The stable hydrogen isotope composition (δ 2 H) of lipid biomarkers can track environmental processes and remain over geologically relevant time scales, enabling studies past climate, hydrology, ecology. Most research has focused on lipids from the domain Eukarya (e.g., plant waxes, long-chain alkanes), potential prokaryotic Archaea to offer unique insights into environments not captured by eukaryotic remains unclear. Here, we investigate H-isotope biphytanes in Sulfolobus...
Summary Microorganisms regulate the composition of their membranes in response to environmental cues. Many Archaea maintain fluidity and permeability by adjusting number cyclic moieties within cores glycerol dibiphytanyl tetraether (GDGT) lipids. Cyclized GDGTs increase membrane packing stability, which has been shown help cells survive shifts temperature pH. However, extent this cyclization also varies with growth phase electron acceptor or donor limitation. These observations indicate a...
The side-chain dihedral angle distributions of all amino acids have been measured from myriad high-resolution protein crystal structures. However, we do not yet know the dominant interactions that determine these distributions. Here, explore to what extent defining features different can be captured by a simple physical model. We find hard-sphere model for dipeptide mimetic includes only steric plus stereochemical constraints is able recapitulate key back-bone dependent observed acid Ser,...
With the advent of online social networks, there is an increasing demand for storage and processing graph-structured data. Social networking applications pose new challenges to data management systems due real-time querying manipulation graph structure. Recently, several specialized have been introduced. However, whether we should abandon mature RDBMS technology databases remains ongoing discussion. In this paper present database benchmarking architecture built on existing LDBC Network...
We elucidate mechanisms of electron-induced radiolysis in cosmic (interstellar, planetary, and cometary) ice analogs ammonia (NH3), likely the most abundant nitrogen-containing compound interstellar medium (ISM). Astrochemical processes were simulated under ultrahigh vacuum conditions by high-energy (1 keV) low-energy (7 eV) electron-irradiation nanoscale thin films deposited on cryogenically cooled metal substrates. Irradiated analyzed temperature-programmed desorption (TPD). Experiments...
Summary Adaptation of lipid membrane composition is an important component archaeal homeostatic response. Historically, the number cyclopentyl and cyclohexyl rings in glycerol dibiphytanyl tetraether (GDGT) Archaeal lipids has been linked to variation environmental temperature. However, recent work with GDGT‐making archaea highlight roles other factors, such as pH or energy availability, influencing degree GDGT cyclization. To better understand role multiple variables a consistent...
The degree of cyclization, or ring index (RI), in archaeal glycerol dibiphytanyl tetraether (GDGT) lipids was long thought to reflect homeoviscous adaptation temperature. However, more recent experiments show that other factors (e.g., pH, growth phase, and energy flux) can also affect membrane composition. main objective this study investigate the effect carbon metabolism on cyclization. To do so, we cultivated
Web archiving initiatives around the world capture ephemeral content to preserve our collective digital memory. However, unlocking potential of archives for humanities scholars and social scientists requires a scalable analytics infrastructure support exploration captured content. We present Warcbase, an open-source platform that aims fill this need. Our takes advantage modern “big data” infrastructure, namely Hadoop, HBase, Spark, has been widely deployed in industry. Warcbase provides two...
A fundamental question in protein science is what the intrinsic propensity for an amino acid to be α-helix, β-sheet, or other backbone dihedral angle ( ϕ-ψ) conformation. This has been hotly debated many years because including all crystal structures from database, increases probabilities α-helical structures, while experiments on small peptides observe that β-sheet-like conformations predominate. We perform molecular dynamics (MD) simulations of a hard-sphere model Ala dipeptide mimetics...
To successfully design new proteins and understand the effects of mutations in natural proteins, we must geometric physicochemical principles underlying protein structure. The side chains amino acids peptides adopt specific dihedral angle combinations; however, still do not have a fundamental quantitative understanding why some side-chain combinations are highly populated others not. Here employ hard-sphere plus stereochemical constraint model dipeptide mimetics to enumerate angles leucine...
Abstract Chemical sedimentary deposits called Banded Iron Formations (BIFs) are one of the best surviving records ancient marine (bio)geochemistry. Many BIF precursor sediments precipitated from ferruginous, silica‐rich waters prior to Great Oxidation Event at ~2.43 Ga. Reconstructing mineralogy phases is key understanding coevolution seawater chemistry and early life. models deposition invoke activity Fe(II)‐oxidizing photoautotrophic bacteria as a mechanism for precipitating mixed‐valence...
The stable hydrogen isotope composition (δ 2 H) of lipid biomarkers can track environmental processes and remain over geologically relevant time scales, enabling studies past climate, hydrology, ecology. Most research has focused on lipids from the domain Eukarya (e.g., plant waxes, long-chain alkanes), potential prokaryotic Archaea to offer unique insights into environments not captured by eukaryotic remains unclear. Here, we investigate H-isotope biphytanes in Sulfolobus acidocaldarius, a...
The calcuated Ramachandran plot depends critically on the value of bond angle τ (between C′, Cα, and N). Specifically, as increases within range 100° ≤ 120°, configurations in “bridge region” with ϕ 0° −20° ψ 40° change from being disallowed at = to be allowed 115° above. In fact, this result dates back 1965,3 but most often plots are drawn for a single τ, typically 110°. dependence is generally not considered. We analyzed database4 high-resolution protein structures plotted backbone...
Abstract The degree of cyclization, or ring index (RI), in archaeal glycerol dibiphytanyl tetraether (GDGT) lipids was long thought to reflect homeoviscous adaptation temperature. However, more recent experiments show that other factors (e.g., pH, growth phase, and energy flux) can also affect membrane composition. main objective this study investigate the effect carbon metabolism on cyclization. To do so we cultivated Acidianus sp. DS80, a metabolically flexible thermoacidophilic archaeon,...
The stable hydrogen isotope composition of archaeal lipids is emerging as a potential paleoenvironmental proxy, adding to the well-established application plant leaf wax-derived n-alkanes in paleohydrological reconstruction. A handful studies reported relatively invariant and depleted compositions for despite range different organisms growth conditions explored. However, how modes metabolism physiological state (growth phase) affect signatures remains poorly understood, limiting our ability...