29 research outputs found
A Spectroscopic Survey of Substituted Indoles Reveals Effects of 1LB Transition Stabilization
Correlation of TrpGly and GlyTrp Rotamer Structure with W7 and W10 UV Resonance Raman Modes and Fluorescence Emission Shifts
Tryptophyl glycine (TrpGly) and glycyl tryptophan (GlyTrp) dipeptides at pH 5.5 and pH 9.3 show a pattern of fluorescence emission shifts with the TrpGly zwitterion emission solely blue shifted. This pattern is matched by shifts in the UV resonance Raman (UVRR) W10 band position and the W7 Fermi doublet band ratio. Ab initio calculations show that the 1340âcmâ1 band of the W7 doublet is composed of three modes, two of which determine the W7 band ratios for the dipeptides. Molecular dynamics simulations show that the dipeptides take on two conformations: one with the peptide backbone extended; one with the backbone curled over the indole. The dihedral angle critical to these conformations is Ï1 and takes on three discrete values. Only the TrpGly zwitterion spends an appreciable amount of time in the extended backbone conformation as this is stabilized by two hydrogen bonds with the terminal amine cation. According to a Stark effect model, a positive charge near the pyrrole keeps the 1La transition at high energy, limiting fluorescence emission red shift, as observed for the TrpGly zwitterion. The hydrogen bond stabilized backbone provides a rationale for the Cmethylene-Cα-Ccarbonyl W10 symmetric stretch that is unique to the TrpGly zwitterion
Global maps of soil temperature
Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0â5 and 5â15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (â0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications
Global maps of soil temperature
Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-kmÂČ resolution for 0â5 and 5â15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-kmÂČ pixels (summarized from 8500 unique temperature sensors) across all the worldâs major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications
Global maps of soil temperature.
Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications
The Color of CationâÏ Interactions: Subtleties of Amine-Tryptophan Interaction Energetics Allow for Radical-like Visible Absorbance and Fluorescence
Several peptides and a protein with
an inter- or intramolecular
cation-Ï interaction between tryptophan (Trp) and an amine cation
are shown to absorb and fluoresce in the visible region of the spectrum.
Titration of indole with sodium hydroxide or ammonium hydroxide yields
an increasing visible fluorescence as well. Visible absorption and
multipeaked fluorescence excitation spectra correlate with experimental
absorption spectra and the vibrational modes of calculated absorption
spectra for the neutral Trp radical. The radical character of the
cationâindole interaction is predicted to stem from the electrostatic
dislocation of indole highest occupied molecular orbital (HOMO) charge
density toward the cation with a subsequent electronic transition
from the HOMOâ2 to the HOMO. Because this is a vertical transition,
fluorescence is possible. Hydrogen bonding at the indole amine most
likely stabilizes the radical-like state. These results provide new
spectroscopic tools for the investigation of cation-Ï interactions
in numerous biological systems, among them, proteins and their myriad
ligands, and show that one, or at most, two, point mutations with
natural amino acids are all that is required to impart visible fluorescence
to proteins
Backbone âStretched;â Backbone âCurledâ: Conformational Similarity for Trp Dipeptides Parallels Fluorescence Emission and UVRR W10 Shifts
PHOXI: A High Quantum Yield, Solvent-Sensitive Blue Fluorescent 5âHydroxytryptophan Derivative Synthesized within Ten Minutes under Aqueous, Ambient Conditions
Multiple
tryptophan (Trp) proteins are not amenable to fluorescence
study because individual residue emission is not resolvable. Biosynthetic
incorporation of an indole analogue such as 5-hydroxyindole has not
provided sufficient spectroscopic resolution because of low quantum
yield and small emission shift. Here, 5-hydroxyindole is used as the
starting framework for building a blue emitting fluorophore of high
quantum yield, 2-phenyl-6<i>H</i>-oxazoloÂ[4,5-<i>e</i>]Âindole (PHOXI). This is a three reagent reaction completed in 10
min under ambient conditions in borate buffer at pH 8. Reaction conditions
have been optimized using 5-hydroxyindole. Derivatization is demonstrated
on tryptophanyl 5-hydroxytryptophan (5-HTP) and a stable ÎČ-hairpin
âzipperâ peptide with four tryptophan residues, TrpZip2,
where Trp 4 has been replaced with 5-HTP, W4 â 5-HTP. Reaction
optimization yields a PHOXI fluorophore that is essentially free of
byproducts. Reaction specificity is demonstrated by the lack of reaction
with <i>N</i>-acetyl-cysteine and amyloid ÎČ-40, a
peptide containing all amino acids except tryptophan, proline, and
cysteine and lacking 5-HTP. Fluorescence study of PHOXI-derivatized
5-hydroxyindole in different solvents reveals the sensitivity of PHOXI
to solvent polarity with a remarkable 87 nm red-shift in water relative
to cyclohexane while maintaining high quantum yield. Thus, PHOXI joins
the ranks of solvatochromic fluorophores such as PRODAN. Surprisingly,
DFT calculations reveal coplanarity of the oxazolo/indole extended
ring system and the phenyl substituent for both the HOMO and LUMO
orbitals. Despite the crowded environment of three additional Trps
in TrpZip2, CD spectroscopy shows that the TrpZip2 ÎČ-hairpin
structure is partially retained upon PHOXI incorporation. In an environment
of smaller residues, PHOXI incorporation can be less disruptive of
protein secondary structure, especially at molecular interfaces and
other environments where there is typically less steric hindrance