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DOE OSTI2023

A novel statistical methodology for quantifying the spatial arrangements of axons in peripheral nerves

A thorough understanding of the neuroanatomy of peripheral nerves is required for a better insight into their function and the development of neuromodulation tools and strategies. In biophysical modeling, it is commonly assumed that the complex spatial arrangement of myelinated and unmyelinated axons in peripheral nerves is random, however, in reality the axonal organization is inhomogeneous and anisotropic. Present quantitative neuroanatomy methods analyze peripheral nerves in terms of the number of axons and the morphometric characteristics of the axons, such as area and diameter. In this study, we employed spatial statistics and point process models to describe the spatial arrangement of axons and Sinkhorn distances to compute the similarities between these arrangements (in terms of first- and second-order statistics) in various vagus and pelvic nerve cross-sections. We utilized high-resolution transmission electron microscopy (TEM) images that have been segmented using a custom-built high-throughput deep learning system based on a highly modified U-Net architecture. Our findings show a novel and innovative approach to quantifying similarities between spatial point patterns using metrics derived from the solution to the optimal transport problem. We also present a generalizable pipeline for quantitative analysis of peripheral nerve architecture. Our data demonstrate differences between male- and female-originating samples and similarities between the pelvic and abdominal vagus nerves.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1985

Estimation of biophysical properties of forest canopies through inversion of microwave scatterometer data

A method for estimating the biophysical properties of a forest canopy through inversion of microwave scatterometer data is discussed. A C-band scatterometer flown over an aspen site in northern Minnesota during 19 days from May 2 to October 20, 1984, was modified to enable continuous recording of the range of the target. This provided the backscatter cross section as a function of range and was used to study scattering processes within the canopy. The remote estimates of HH, VV, and HV extinction coefficient values agreed well with the estimates obtained with the use of an active radar calibrator.

Pitts, D. E.↗

NASA NTRS1991

The role of the EOS SAR in Mission to Planet Earth

The Earth Observing System (EOS) synthetic aperture radar (SAR) is a multifrequency, multipolarization radar which will be capable of the global monitoring of key quantitative measurements of geophysical and biophysical parameters. Scheduled to fly on its own dedicated spacecraft, it is one of three platforms that will make up the space-based component to EOS. The role of the SAR in the EOS mission is discussed, wtih emphasis on the geophysical product variables which will be generated with the SAR and used in global hydrologic, biogeochemical and energy cycle models. The latest concepts for processing the data, including calibration and geophysical processing strategies, are presented.

Holt, Benjamin↗

DOE OSTI2020

Modeling Functional Organic Chemistry in Arctic Rivers: An Idealized Siberian System

Rivers of the Arctic will become ever more important for the global climate, since they carry a majority of continental dissolved organic carbon flux into the rapidly changing polar ocean. Aqueous organics comprise a wide array of functional groups, several of which are likely to impact coastal and open water biophysical properties. Light attenuation, interfacial films, aerosol formation, gas release and momentum exchange can all be cited. We performed Lagrangian kinetic modeling for the evolution of riverine organic chemistry as the molecules in question make their way from the highlands to Arctic outlets. Classes as diverse as the proteins, sugars, lipids, re-condensates, humics, bio-tracers and small volatiles are all included. Our reduced framework constitutes an idealized northward flow driving a major hydrological discharge rate and primarily representing the Russian Lena. Mountainous, high solute and tundra sources are all simulated, and they meet up at several points between soil and delta process reactors. Turnover rates are parameterized beginning with extrapolated coastal values imposed along a limited tributary network, with connections between different terrestrial sub-ecologies. Temporal variation of our total dissolved matter most closely resembles the observations when we focus on the restricted removal and low initial carbon loads, suggesting relatively slow transformation along the water course. Thus, channel combinations and mixing must play a dominant role. Nevertheless, microbial and photochemical losses help determine the final concentrations for most species. Chemical evolution is distinct for the various functionalities, with special contributions from pre- and post-reactivity in soil and delta waters. Several functions are combined linearly to represent the collective chromophoric dissolved matter, characterized here by its absorption. Tributaries carry the signature of lignin phenols to segregate tundra versus taiga sources, and special attention is paid to the early then marine behaviors of low molecular weight volatiles. Heteropolycondensates comprise the largest percentage of reactive carbon in our simulations due to recombination/accumulation, and they tend to be preeminent at the mouth. Outlet concentrations of individual structures such as amino acids and absorbers lie above threshold values for biophysical influence, on the monolayer and light attenuation. The extent of coastal spreading is examined through targeted regional box modeling, relying on salinity and color for calibration. In some cases, plumes reach the scale of peripheral arctic seas, and amplification is expected during upcoming decades. Conclusions are mapped from the Lena to other boreal discharges, and future research questions are outlined regarding the bonding type versus mass release as permafrost degrades. Dynamic aqueous organic coupling is recommended for polar system models, from headwaters to coastal diluent.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2000

Section on Observed Impacts on El Nino

Agricultural applications of El Nino forecasts are already underway in some countries and need to be evaluated or re-evaluated. For example, in Peru, El Nino forecasts have been incorporated into national planning for the agricultural sector, and areas planted with rice and cotton (cotton being the more drought-tolerant crop) are adjusted accordingly. How well are this and other such programs working? Such evaluations will contribute to the governmental and intergovernmental institutions, including the Inter-American Institute for Global Change Research and the US National Ocean and Atmospheric Agency that are fostering programs to aid the effective use of forecasts. As El Nino climate forecasting grows out of the research mode into operational mode, the research focus shifts to include the design of appropriate modes of utilization. Awareness of and sensitivity to the costs of prediction errors also grow. For example, one major forecasting model failed to predict the very large El Nino event of 1997, when Pacific sea-surface temperatures were the highest on record. Although simple correlations between El Nino events and crop yields may be suggestive, more sophisticated work is needed to understand the subtleties of the interplay among the global climate system, regional climate patterns, and local agricultural systems. Honesty about the limitations of an forecast is essential, especially when human livelihoods are at stake. An end-to-end analysis links tools and expertise from the full sequence of ENSO cause-and-effect processes. Representatives from many disciplines are needed to achieve insights, e.g, oceanographers and atmospheric scientists who predict El Nino events, climatologists who drive global climate models with sea-surface temperature predictions, agronomists who translate regional climate connections in to crop yield forecasts, and economists who analyze market adjustments to the vagaries of climate and determine the value of climate forecasts. Methods include historical studies to understand past patterns and to test hindcasts of the prediction tools, crop modeling, spatial analysis and remote sensing. This research involves expanding, deepening, and applying the understanding of physical climate to the fields of agronomy and social science; and the reciprocal understanding of crop growth and farm economics to climatology. Delivery of a regional climate forecast with no information about how the climate forecast was derived limits its effectiveness. Explanation of a region's major climate driving forces helps to place a seasonal forecast in context. Then, a useful approach is to show historical responses to previous El Nino events, and projections, with uncertainty intervals, of crop response from dynamic process crop growth models. Regional ID forecasts should be updated with real-time weather conditions. Since every El Nino event is different, it is important to track, report and advise on each new event as it unfolds. The stability of human enterprises depends on understanding both the potentialities and the limits of predictability. Farmers rely on past experience to anticipate and respond to fluctuations in the biophysical systems on which their livelihoods depend. Now scientists are improving their ability to predict some major elements of climate variability. The improvements in the reliability of El Nino forecasts are encouraging, but seasonal forecasts for agriculture are not, and will probably never be completely infallible, due to the chaotic nature of the climate system. Uncertainties proliferate as we extend beyond Pacific sea-surface temperatures to climate teleconnections and agricultural outcomes. The goal of this research is to shed as a clear light as possible on these inherent uncertainties and thus to contribute to the development of appropriate responses to El Nino and other seasonal forecasts for a range of stakeholders, which, ultimately, includes food consumers everywhere.

Rosenzweig, Cynthia↗

NASA NTRS2008

Modeling Bird Migration in Changing Habitats: Space-based Ornithology using Satellites and GIS

Understanding bird migration and avian biodiversity is one of the most compelling and challenging problems of modern biology with major implications for human health and conservation biology. Migration and conservation efforts cross national boundaries and are subject to numerous international agreements and treaties presenting challenges in both geographic space and time. Space based technology, coupled with geographic information systems, yields new opportunities to shed light on the distribution and movement of organisms on the planet and their sensitivity to human disturbances and environmental changes. At NASA, we are creating ecological forecasting tools for science and application users to address the consequences of loss of wetlands, flooding, drought or other natural disasters such as hurricanes on avian biodiversity and bird migration. In our work, we use individual organism biophysical models and drive these models with satellite observations and numerical weather predictions of the spatio-temporal gradients in climate and habitat. Geographic information system technology comprises one component of our overall simulation framework, especially for characterizing the changing habitats and conditions encountered by en-route migratory birds. Simulation provides a tool for studying bird migration across multiple scales and can be linked to mechanistic processes describing the time and energy budget states of migrating birds. Such models yield an understanding of how a migratory flyway and its component habitats function as a whole and link stop-over ecology with biological conservation and management. We present examples of our simulation of shorebirds, principally, pectoral sandpipers, along the central flyways of the United States and Canada from the Gulf of Mexico to Alaska.

Smith, James A.↗

NASA NTRS2015

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗

DOE OSTI2025

Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human brain and hiPSC-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 493 synaptic candidates supported by proteomics. We further investigate three such proteins that are associated with neurodevelopmental disorders – the CUL3 E3 ubiquitin ligase, the DDX3X and YBX1 nucleic-acid binding proteins – by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to systematically and more comprehensively resolve the synaptic architecture.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1996

Rejoining and misrejoining of radiation-induced chromatin breaks. II. Biophysical Model

A biophysical model for the kinetics of the formation of radiation-induced chromosome aberrations is developed to account for the recent experimental results obtained with a combination of the premature chromosome condensation (PCC) and fluorescence in situ hybridization (FISH) techniques. In this model, we consider the broken ends of DNA double-strand breaks (DSBs) to be reactant and make use of the interaction distance hypothesis. The repair/misrepair process between broken ends is suggested to consist of two steps; the first step represents the two break ends approaching each other, and the second step represents the enzymatic processes leading to DNA end-to-end rejoining. Only the second step is reflected in the kinetics observed in experiments using PCC. The model appears to be able to fit existing data for human cells. It is shown that the kinetics of the formation of chromosome aberrations can be explained by a single rate that characterizes both rejoining and misrejoining of DSBs, suggesting that repair and misrepair share the same mechanism. Fast repair (completed in minutes) in a subset of DSBs is suggested as an explanation of the complete exchanges observed with PCC in human lymphocytes immediately after irradiation. The fast repair component seems to be absent in human fibroblasts.

NASA Center JSC↗

DOE OSTI2024

Additive Manufacturing with Cellulose-Based Composites: Materials, Modeling, and Applications

Recent advances in large-scale additive manufacturing (AM) with polymer-based composites have enabled efficient production of high-performance materials. Cellulose nanomaterials (CNMs) have emerged as bio-based feedstocks due to their exceptional strength and sustainability. However, challenges such as hornification and poor dispersion in polymer matrices still limit large-scale CNM–polymer composite manufacturing, requiring novel strategies. Here, this review outlines an approach starting with atomic-level simulations to link molecular composition to key parameters like bulk density, viscosity, and modulus. These simulations provide data for finite element analysis (FEA), which informs large-scale experiments and reduces the need for extensive trials. The strategy explores how atomic interactions impact the morphology, adhesion, and mechanical properties of CNM-based composites in AM processes. The review also discusses current developments in AM, along with predictions of mechanical and thermal properties for structural applications, packaging, flexible electronics, and hydrogel scaffolds. By integrating experimental findings with molecular dynamics (MD) simulations and finite element modeling (FEM), valuable insights for material design, process optimization, and performance enhancement in CNM-based AM are provided to address ongoing challenges.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

Correlated motions of proteins are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved X-ray methods hold promise for addressing this challenge, but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature jumps, through thermal excitation of the solvent, have been utilized to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform temperature-jump small- and wide-angle X-ray scattering measurements on a dynamic enzyme, cyclophilin A, demonstrating that these experiments are able to capture functional intramolecular protein dynamics on the microsecond timescale. We show that cyclophilin A displays rich dynamics following a temperature jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes. Furthermore, two relaxation processes are resolved: a fast process is related to surface loop motions, and a slower process is related to motions in the core of the protein that are critical for catalytic turnover.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Dissecting pigment architecture of individual photosynthetic antenna complexes in solution

Significance Energy from the sun is captured by the biosphere through photosynthetic antenna proteins, which function by integration of a set of pigments into a protein scaffold. Nature uses relatively similar pigment building blocks to achieve diverse functions, and the organizing principles behind this process are not fully understood. Using a single-molecule microfluidic trap and multiparameter fluorescence spectroscopy, we explore how the photophysical properties of individual pigment sites are modulated by the protein’s oligomerization states, using single proteins of a model antenna from cyanobacteria. Our measurements achieve a bottom-up dissection of the structural-function relation of the model pigment−protein complex with important implications for photosynthetic antenna biophysics.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1991

Combined fluorescence, reflectance, and ground measurements of a stressed Norway spruce forest for forest damage assessment

The detection and monitoring of stress and damage in forested areas is of utmost importance to forest managers for planning purposes. Remote sensing are the most suitable means to obtain this information. This requires that remote sensing data employed in a forest survey be properly chosen and utilized for their ability to measure canopy spectral features directly related to key tree and canopy properties that are indicators of forest health and vitality. Plant reflectance in the visible to short wave IR regions (400 to 2500 nm) provides information on its biochemical, biophysical, and morphological make up, whereas plant fluorescence in the 400 to 750 nm region is more indicative of the capacity and functioning of its photosynthetic apparatus. A measure of both these spectral properties can be used to provide an accurate assessment of stress and damage within the forest canopy. Foliar chlorophyll and nitrogen are essential biochemical constituents required for the proper functioning and maintenance of a plant's biological processes. Chlorophyll-a is the prime reactive center for photosynthesis, by which a plant converts CO2 and H2O into necessary plant products. Nitrogen forms an important component of the amino-acids, enzymes, proteins, alkaloids, and cyanogenic compounds that make up a plant, including its pigments. Both chlorophyll and nitrogen have characteristic absorption features in the visible to short wave IR region. By measuring the wavelength position and depth of these features and the fluorescence response of the foliage, the health and vitality of a canopy can be ascertained. Examples for a stressed Norway spruce forest in south-eastern Austria are presented.

Banninger, C.↗

NASA NTRS2008

Irrigation Requirement Estimation using MODIS Vegetation Indices and Inverse Biophysical Modeling; A Case Study for Oran, Algeria

Human demand for food influences the water cycle through diversion and extraction of fresh water needed to support agriculture. Future population growth and economic development alone will substantially increase water demand and much of it for agricultural uses. For many semi-arid lands, socio-economic shifts are likely to exacerbate changes in climate as a driver of future water supply and demand. For these areas in particular, where the balance between water supply and demand is fragile, variations in regional climate can have potentially predictable effect on agricultural production. Satellite data and biophysically-based models provide a powerful method to quantify the interactions between local climate, plant growth and water resource requirements. In irrigated agricultural lands, satellite observations indicate high vegetation density while the precipitation amount indicates otherwise. This inconsistency between the observed precipitation and the observed canopy leaf density triggers the possibility that the observed high leaf density is due to an alternate source of water, irrigation. We explore an inverse process approach using observations from the Moderate Resolution Imaging Spectroradiometer (MODIS), climatological data, and the NASA's Simple Biosphere model, SiB2, to quantitatively assess water demand in a semi-arid agricultural land by constraining the carbon and water cycles modeled under both equilibrium (balance between vegetation and prevailing local climate) and nonequilibrium (water added through irrigation) conditions. We postulate that the degree to which irrigated lands vary from equilibrium conditions is related to the amount of irrigation water used. We added water using two distribution methods: The first method adds water on top of the canopy and is a proxy for the traditional spray irrigation. The second method allows water to be applied directly into the soil layer and serves as proxy for drip irrigation. Our approach indicates that over the study site, for the month of July, spray irrigation resulted in an irrigation amount of about 1.4 mm per occurrence with an average frequency of occurrence of 24.6 hours. The simulated total monthly irrigation for July was 34.85 mm. In contrast, the drip irrigation resulted in less frequent irrigation events with an average water requirement about 57% less than that simulated during the spray irrigation case. The efficiency of the drip irrigation method rests on its reduction of the canopy interception loss compared to the spray irrigation method. When compared to a country-wide average estimate of irrigation water use, our numbers are quite low. We would have to revise the reported country level estimates downward to 17% or less

Bounoua, L.↗

DOE OSTI2016

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9

Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. In this paper, we report the discovery of an allosteric small-molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X-ray crystallographic screen was used to identify two distinct small-molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9–5.8 mm. Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand-induced rigidification of Ubc9 as a mechanism of inhibition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Modeling pulsed soil respiration in an African savanna ecosystem

Savannas cover 60% of the African continent and play an important role in the global carbon (C) emissions from fire and land use. To better characterize the biophysical controls over soil respiration in these settings, half-hourly observations of volumetric soil-water content, temperature, and the concentration of carbon dioxide (CO2) at different soil depths were continually measured from 2005 to 2007 under trees ("sub-canopy") and between trees ("inter-canopy") in a savanna vegetation near Skukuza, Kruger National Park, South Africa. The measured soil climate and CO2 concentration data were assimilated into a process-based model that estimates the CO2 production and flux with coupled dynamics of dissolved organic C (DOC) and microbial biomass C. Our results show that temporal and spatial variations in CO2 flux were strongly influenced by precipitation and vegetation cover, with two times greater CO2 flux in the subcanopy plots (similar to 2421 g CO2 m(-2) yr(-1)) than in the inter-canopy plots (similar to 1290 g CO2 m(-2) yr(-1)). Precipitation influenced soil respiration by changing soil temperature and moisture; however, our modeling analysis suggests that the pulsed response of soil respiration to precipitation events (known as "Birch effect") is a key control on soil fluxes at this site. At this site, "Birch effect" contributed to approximately 50% and 65% of heterotrophic respiration or 20% and 39% of soil respiration in the sub-canopy and inter-canopy plots, respectively. These results suggest that pulsed response of respiration to precipitation events is an important component of the C cycle of savannas and should be considered in both measurement and modeling studies of carbon exchange in similar ecosystems. (C) 2014 Elsevier B.V. All rights reserved.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation

G-protein-coupled receptors (GPCRs) modulate many physiological processes by transducing a variety of extracellular cues into intracellular responses. Ligand binding to an extracellular orthosteric pocket propagates conformational change to the receptor cytosolic region to promote binding and activation of downstream signalling effectors such as G proteins and β-arrestins. It is well known that different agonists can share the same binding pocket but evoke unique receptor conformations leading to a wide range of downstream responses (‘efficacy’). Furthermore, increasing biophysical evidence, primarily using the β 2 -adrenergic receptor (β 2 AR) as a model system, supports the existence of multiple active and inactive conformational states. However, how agonists with varying efficacy modulate these receptor states to initiate cellular responses is not well understood. Here we report stabilization of two distinct β 2 AR conformations using single domain camelid antibodies (nanobodies)—a previously described positive allosteric nanobody (Nb80) and a newly identified negative allosteric nanobody (Nb60). We show that Nb60 stabilizes a previously unappreciated low-affinity receptor state which corresponds to one of two inactive receptor conformations as delineated by X-ray crystallography and NMR spectroscopy. Furthermore, we find that the agonist isoprenaline has a 15,000-fold higher affinity for β 2 AR in the presence of Nb80 compared to the affinity of isoprenaline for βA 2 R in the presence of Nb60, highlighting the full allosteric range of a GPCR. Assessing the binding of 17 ligands of varying efficacy to the β 2 AR in the absence and presence of Nb60 or Nb80 reveals large ligand-specific effects that can only be explained using an allosteric model which assumes equilibrium amongst at least three receptor states. Agonists generally exert efficacy by stabilizing the active Nb80-stabilized receptor state (R 80 ). In contrast, for a number of partial agonists, both stabilization of R80 and destabilization of the inactive, Nb60-bound state (R 60 ) contribute to their ability to modulate receptor activation. These data demonstrate that ligands can initiate a wide range of cellular responses by differentially stabilizing multiple receptor states.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Synchrotron X-ray footprinting as a method to visualize water in proteins

The vast majority of biomolecular processes are controlled or facilitated by water interactions. In enzymes, regulatory proteins, membrane-bound receptors and ion-channels, water bound to functionally important residues creates hydrogen-bonding networks that underlie the mechanism of action of the macromolecule. High-resolution X-ray structures are often difficult to obtain with many of these classes of proteins because sample conditions, such as the necessity of detergents, often impede crystallization. Other biophysical techniques such as neutron scattering, nuclear magnetic resonance and Fourier transform infrared spectroscopy are useful for studying internal water, though each has its own advantages and drawbacks, and often a hybrid approach is required to address important biological problems associated with protein–water interactions. One major area requiring more investigation is the study of bound water molecules which reside in cavities and channels and which are often involved in both the structural and functional aspects of receptor, transporter and ion channel proteins. Recently, significant progress has been made in synchrotron-based radiolytic labeling and mass spectroscopy techniques for both the identification of bound waters and for characterizing the role of water in protein conformational changes at a high degree of spatial and temporal resolution. Finally, here the latest developments and future capabilities of this method for investigating water–protein interactions and its synergy with other synchrotron-based methods are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗