Search NASA⌕ Search

SEARCH · Search NASA

Results for “Stem specific”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
NASA NTRS2009

Reflectance Spectra Comparison of Orbital Debris, Intact Spacecraft, and Intact Rocket Bodies in the GEO Regime

A key objective of NASA s Orbital Debris program office at Johnson Space Center (JSC) is to characterize the debris environment by way of assessing the physical properties (type, mass, density, and size) of objects in orbit. Knowledge of the geosynchronous orbit (GEO) debris environment in particular can be used to determine the hazard probability at specific GEO altitudes and aid predictions of the future environment. To calculate an optical size from an intensity measurement of an object in the GEO regime, a 0.175 albedo is assumed currently. However, identification of specific material type or types could improve albedo accuracy and yield a more accurate size estimate for the debris piece. Using spectroscopy, it is possible to determine the surface materials of space objects. The study described herein used the NASA Infrared Telescope Facility (IRTF) to record spectral data in the 0.6 to 2.5 micron regime on eight catalogued space objects. For comparison, all of the objects observed were in GEO or near-GEO. The eight objects consisted of two intact spacecraft, three rocket bodies, and three catalogued debris pieces. Two of the debris pieces stemmed from Titan 3C transtage breakup and the third is from COSMOS 2054. The reflectance spectra of the Titan 3C pieces share similar slopes (increasing with wavelength) and lack any strong absorption features. The COSMOS debris spectra is flat and has no absorption features. In contrast, the intact spacecraft show classic absorption features due to solar panels with a strong band gap feature near 1 micron. The two spacecraft are spin-stabilized objects and therefore have solar panels surrounding the outer surface. Two of the three rocket bodies are inertial upper stage (IUS) rocket bodies and have similar looking spectra. The slopes flatten out near 1.5 microns with absorption features in the near-infrared that are similar to that of white paint. The third rocket body has a similar flattening of slope but with fewer features of white paint - indicating that the surface paint on the SL-12 may be different than the IUS. This study shows that the surface materials of debris appear different spectrally than intact rocket bodies and spacecraft and therefore are not believed to be solar panel material or pristine white paint. Further investigation is necessary in order to eliminate materials as possible choices for the debris pieces.

Barker, Ed↗
DOE OSTI2025

Measuring the Muon Neutrino Magnetic Moment in the NOvA Near Detector

Measuring an enhanced neutrino magnetic moment would be a clear indication of physics beyond the Standard Model, shedding light on the correct beyond Standard Model theory or the potential Majorana nature of neutrinos. It would manifest in the NOvA near detector as an excess of neutrino-on-electron elastic scattering interactions at low electron recoil energies. Leveraging an intense and highly pure muon neutrino beam, along with a finely segmented liquid scintillator detector technology specifically designed for electromagnetic shower separation, enables NOvA to achieve a potentially world-leading sensitivity in probing the effective muon neutrino magnetic moment. This analysis, based on neutrino data collected between 2014 and 2021, corresponding to an exposure of $13.8\times10^{20}$ protons-on-target, yields a result consistent with the Standard Model-only hypothesis with a p-value of 0.31. An upper limit on the effective muon neutrino magnetic moment is set at $\mu_{\nu_\mu}<19.1\times 10^{-10}\mu_B$ at $90\%$ confidence level. Despite facing statistical limitations stemming from low cross section of the signal process, systematic uncertainties have a significant impact on this result. To address these challenges, the NOvA Test Beam experiment focuses on mitigating some of the largest systematic uncertainties within NOvA by investigating particle interactions and energy deposition in a small-scale replica NOvA detector. This thesis describes the calibration of the NOvA Test Beam detector, which is a crucial step in analysing the Test Beam data before they can be utilised to reduce NOvA systematic uncertainties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2015

An Approach for Performance Based Glove Mobility Requirements

The Space Suit Assembly (SSA) Development Team at NASA Johnson Space Center has invested heavily in the advancement of rear‐entry planetary exploration suit design but largely deferred development of extravehicular activity (EVA) glove designs, and accepted the risk of using the current flight gloves, Phase VI, for exploration missions. However, as design reference missions mature, the risks of using heritage hardware have highlighted the need for developing robust new glove technologies. To address the technology gap, the NASA Space Technology Mission Directorate's Game‐Changing Development Program provided start‐up funding for the High Performance EVA Glove (HPEG) Element as part of the Next Generation Life Support (NGLS) Project in the fall of 2013. The overarching goal of the HPEG Element is to develop a robust glove design that increases human performance during EVA and creates pathway for implementation of emergent technologies, with specific aims of increasing pressurized mobility to 60% of barehanded capability, increasing the durability in on‐pristine environments, and decreasing the potential of gloves to cause injury during use. The HPEG Element focused initial efforts on developing quantifiable and repeatable methodologies for assessing glove performance with respect to mobility, injury potential, thermal conductivity, and abrasion resistance. The team used these methodologies to establish requirements against which emerging technologies and glove designs can be assessed at both the component and assembly levels. The mobility performance testing methodology was an early focus for the HPEG team as it stems from collaborations between the SSA Development team and the JSC Anthropometry and Biomechanics Facility (ABF) that began investigating new methods for suited mobility and fit early in the Constellation Program. The combined HPEG and ABF team used lessons learned from the previous efforts as well as additional reviews of methodologies in physical and occupational therapy arenas to develop a protocol that assesses gloved range of motion, strength, dexterity, tactility, and fit in comparative quantitative terms and also provides qualitative insight to direct hardware design iterations. The protocol was evaluated using five experienced test subjects wearing the EMU pressurized to 4.3psid with three different glove configurations. The results of the testing are presented to illustrate where the protocol is and is not valid for benchmark comparisons. The process for requirements development based upon the results is also presented along with suggested performance values for the High Performance EVA Gloves to be procured in fiscal year 2015.

Aitchison, Lindsay↗
DOE OSTI2022

Cas9-induced large deletions and small indels are controlled in a convergent fashion

Repair of Cas9-induced double-stranded breaks results primarily in formation of small insertions and deletions (indels), but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a library of clonal NGS-validated mouse embryonic stem cells deficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection gene Nbn and the microhomology-mediated end joining gene Polq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

A Framework for Modeling Human-Machine Interactions

Modern automated flight-control systems employ a variety of different behaviors, or modes, for managing the flight. While developments in cockpit automation have resulted in workload reduction and economical advantages, they have also given rise to an ill-defined class of human-machine problems, sometimes referred to as 'automation surprises'. Our interest in applying formal methods for describing human-computer interaction stems from our ongoing research on cockpit automation. In this area of aeronautical human factors, there is much concern about how flight crews interact with automated flight-control systems, so that the likelihood of making errors, in particular mode-errors, is minimized and the consequences of such errors are contained. The goal of the ongoing research on formal methods in this context is: (1) to develop a framework for describing human interaction with control systems; (2) to formally categorize such automation surprises; and (3) to develop tests for identification of these categories early in the specification phase of a new human-machine system.

Shafto, Michael G.↗
NASA NTRS2016

An Approach for Performance Based Glove Mobility Requirements

The Space Suit Assembly (SSA) Development Team at NASA Johnson Space Center has invested heavily in the advancement of rear-entry planetary exploration suit design but largely deferred development of extravehicular activity (EVA) glove designs, and accepted the risk of using the current flight gloves, Phase VI, for exploration missions. However, as design reference missions mature, the risks of using heritage hardware have highlighted the need for developing robust new glove technologies. To address the technology gap, the NASA Space Technology Mission Directorate's Game-Changing Development Program provided start-up funding for the High Performance EVA Glove (HPEG) Element as part of the Next Generation Life Support (NGLS) Project in the fall of 2013. The overarching goal of the HPEG Element is to develop a robust glove design that increases human performance during EVA and creates pathway for implementation of emergent technologies, with specific aims of increasing pressurized mobility to 60% of barehanded capability, increasing the durability in on-pristine environments, and decreasing the potential of gloves to cause injury during use. The HPEG Element focused initial efforts on developing quantifiable and repeatable methodologies for assessing glove performance with respect to mobility, injury potential, thermal conductivity, and abrasion resistance. The team used these methodologies to establish requirements against which emerging technologies and glove designs can be assessed at both the component and assembly levels. The mobility performance testing methodology was an early focus for the HPEG team as it stems from collaborations between the SSA Development team and the JSC Anthropometry and Biomechanics Facility (ABF) that began investigating new methods for suited mobility and fit early in the Constellation Program. The combined HPEG and ABF team used lessons learned from the previous efforts as well as additional reviews of methodologies in physical and occupational therapy arenas to develop a protocol that assesses gloved range of motion, strength, dexterity, tactility, and fit in comparative quantitative terms and also provides qualitative insight to direct hardware design iterations. The protocol was evaluated using five experienced test subjects wearing the EMU pressurized to 4.3psid with three different glove configurations. The results of the testing are presented to illustrate where the protocol is and is not valid for benchmark comparisons. The process for requirements development based upon the results is also presented along with suggested performance values for the High Performance EVA Gloves currently in development.

Aitchison, Lindsay↗
DOE OSTI2021

Xylan Is Critical for Proper Bundling and Alignment of Cellulose Microfibrils in Plant Secondary Cell Walls

Plant biomass represents an abundant and increasingly important natural resource and it mainly consists of a number of cell types that have undergone extensive secondary cell wall (SCW) formation. These cell types are abundant in the stems of Arabidopsis, a well-studied model system for hardwood, the wood of eudicot plants. The main constituents of hardwood include cellulose, lignin, and xylan, the latter in the form of glucuronoxylan (GX). The binding of GX to cellulose in the eudicot SCW represents one of the best-understood molecular interactions within plant cell walls. The evenly spaced acetylation and 4-O-methyl glucuronic acid (MeGlcA) substitutions of the xylan polymer backbone facilitates binding in a linear two-fold screw conformation to the hydrophilic side of cellulose and signifies a high level of molecular specificity. However, the wider implications of GX–cellulose interactions for cellulose network formation and SCW architecture have remained less explored. In this study, we seek to expand our knowledge on this by characterizing the cellulose microfibril organization in three well-characterized GX mutants. The selected mutants display a range of GX deficiency from mild to severe, with findings indicating even the weakest mutant having significant perturbations of the cellulose network, as visualized by both scanning electron microscopy (SEM) and atomic force microscopy (AFM). We show by image analysis that microfibril width is increased by as much as three times in the severe mutants compared to the wild type and that the degree of directional dispersion of the fibrils is approximately doubled in all the three mutants. Further, we find that these changes correlate with both altered nanomechanical properties of the SCW, as observed by AFM, and with increases in enzymatic hydrolysis. Results from this study indicate the critical role that normal GX composition has on cellulose bundle formation and cellulose organization as a whole within the SCWs.

09 BIOMASS FUELS↗
DOE OSTI2021

Sclerostin Depletion Induces Inflammation in the Bone Marrow of Mice

Romosozumab, a humanized monoclonal antibody specific for sclerostin (SOST), has been approved for treatment of postmenopausal women with osteoporosis at a high risk for fracture. Previous work in sclerostin global knockout (Sost-/- ) mice indicated alterations in immune cell development in the bone marrow (BM), which could be a possible side effect in romosozumab-treated patients. Here, we examined the effects of short-term sclerostin depletion in the BM on hematopoiesis in young mice receiving sclerostin antibody (Scl-Ab) treatment for 6 weeks, and the effects of long-term Sost deficiency on wild-type (WT) long-term hematopoietic stem cells transplanted into older cohorts of Sost-/- mice. Our analyses revealed an increased frequency of granulocytes in the BM of Scl-Ab-treated mice and WT→Sost -/- chimeras, indicating myeloid-biased differentiation in Sost-deficient BM microenvironments. This myeloid bias extended to extramedullary hematopoiesis in the spleen and was correlated with an increase in inflammatory cytokines TNFα, IL-1α, and MCP-1 in Sost-/- BM serum. Additionally, we observed alterations in erythrocyte differentiation in the BM and spleen of Sost-/- mice. Taken together, our current study indicates novel roles for Sost in the regulation of myelopoiesis and control of inflammation in the BM.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Modeled Microgravity Disrupts Collagen I/Integrin Signaling During Osteoblastic Differentiation of Human Mesenchymal Stem Cells

Spaceflight leads to reduced bone mineral density in weight bearing bones that is primarily attributed to a reduction in bone formation. We have previously demonstrated severely reduced osteoblastogenesis of human mesenchymal stem cells (hMSC) following seven days culture in modeled microgravity. One potential mechanism for reduced osteoblastic differentiation is disruption of type I collagen-integrin interactions and reduced integrin signaling. Integrins are heterodimeric transmembrane receptors that bind extracellular matrix proteins and produce signals essential for proper cellular function, survival, and differentiation. Therefore, we investigated the effects of modeled microgravity on integrin expression and function in hMSC. We demonstrate that seven days of culture in modeled microgravity leads to reduced expression of the extracellular matrix protein, type I collagen (Col I). Conversely, modeled microgravity consistently increases Col I-specific alpha2 and beta1 integrin protein expression. Despite this increase in integrin sub-unit expression, autophosphorylation of adhesion-dependent kinases, focal adhesion kinase (FAK) and proline-rich tyrosine kinase 2 (PYK2), is significantly reduced. Activation of Akt is unaffected by the reduction in FAK activation. However, reduced downstream signaling via the Ras-MAPK pathway is evidenced by a reduction in Ras and ERK activation. Taken together, our findings indicate that modeled microgravity decreases integrin/MAPK signaling, which likely contributes to the observed reduction in osteoblastogenesis.

Meyers, Valerie E.↗
DOE OSTI2023

Real-space imaging of periodic nanotextures in thin films via phasing of diffraction data

New properties and exotic quantum phenomena can form due to periodic nanotextures, including Moire patterns, ferroic domains, and topologically protected magnetization and polarization textures. Despite the availability of powerful tools to characterize the atomic crystal structure, the visualization of nanoscale strain-modulated structural motifs remains challenging. Here, we develop nondestructive real-space imaging of periodic lattice distortions in thin epitaxial films and report an emergent periodic nanotexture in a Mott insulator. Specifically, we combine iterative phase retrieval with unsupervised machine learning to invert the diffuse scattering pattern from conventional X-ray reciprocal-space maps into real-space images of crystalline displacements. Our imaging in PbTiO 3 /SrTiO 3 superlattices exhibiting checkerboard strain modulation substantiates published phase-field model calculations. Furthermore, the imaging of biaxially strained Mott insulator Ca 2 RuO 4 reveals a strain-induced nanotexture comprised of nanometer-thin metallic-structure wires separated by nanometer-thin Mott-insulating-structure walls, as confirmed by cryogenic scanning transmission electron microscopy (cryo-STEM). The nanotexture in Ca 2 RuO 4 film is induced by the metal-to-insulator transition and has not been reported in bulk crystals. We expect the phasing of diffuse X-ray scattering from thin crystalline films in combination with cryo-STEM to open a powerful avenue for discovering, visualizing, and quantifying the periodic strain-modulated structures in quantum materials.

Science & Technology - Other Topics↗
NASA NTRS2001

Simple Thermal Environment Model (STEM) User's Guide

This report presents a Simple Thermal Environment Model (STEM) for determining appropriate engineering design values to specify the thermal environment of Earth-orbiting satellites. The thermal environment of a satellite, consists of three components: (1) direct solar radiation, (2) Earth-atmosphere reflected shortwave radiation, as characterized by Earth's albedo, and (3) Earth-atmosphere-emitted outgoing longwave radiation (OLR). This report, together with a companion "guidelines" report provides methodology and guidelines for selecting "design points" for thermal environment parameters for satellites and spacecraft systems. The methods and models reported here are outgrowths of Earth Radiation Budget Experiment (ERBE) satellite data analysis and thermal environment specifications discussed by Anderson and Smith (1994). In large part, this report is intended to update (and supersede) those results.

Justus, C.G.↗
NASA NTRS2016

The Effects of Spaceflight on Cellular Aging in Saccharomyces cerevisiae

The conditions encountered during spaceflight place unique stresses on physiological processes that oftentimes lead to deleterious effects. Identifying these effects and better understanding their molecular mechanisms will be essential in enabling long-duration space travel by humans. Studies in Saccharomyces cerevisiae suggest an aging model that involves the accumulation of toxic components, such as excess extrachromosomal rDNA and damaged mitochondria. This build-up then limits the replicative lifespan (the number of times a mother cell can form a new daughter cell). Remarkably, each new daughter cell emerges completely renewed from the senescing mother cell through an asymmetric distribution of aging determinants via mechanisms that are intricately linked to the budding process. When exposed to simulated microgravity, S. cerevisiae undergoes an altered budding process characterized by a breakdown in bud scar polarity. Because the budding process is critical to replicative aging, we hypothesize that the replicative lifespan may be affected by microgravity as well. To measure relative replicative aging rates, we will construct a strain of yeast in which daughter cells are inviable. In this strain, the Cre recombinase will be expressed under the control of the daughter cell specific promoter, pSCW11, and LoxP sites will be inserted at both flanks of two essential genes involved in the cell cycle, UBC9 and CDC20, using a CRISPRCas9 system. Thus, UBC9 and CDC20 will be excised from daughter cells, leading to cell-cycle arrest and eventual death. To mimic the low shear conditions encountered in microgravity, this strain will be grown in rotating wall vessels. The number of viable mother cells will be monitored over time, and this rate will be compared to cells growing in standard conditions. Because asymmetric division also occurs in mammalian cells (e.g. in neural stem cells), this study will provide insight into how cellular aging rates may change in mammals and will help empower humans to thrive in space for extended and even indefinite periods of time.

aging↗
DOE OSTI2025

BAMCensus (The Behavior and Advanced Mobility Census Dataset Aggregator) [SWR-25-120]

This software is a high-performance tool developed in Rust for downloading and processing large-scale geospatial datasets, specifically focusing on US Census data. It is designed to address scaling limitations found in existing tools, such as R's [tidycensus](https://walker-data.com/tidycensus/), by providing performant streaming dataset JOIN operations between various US Census datasets (like ACS and LEHD) and their corresponding geometries stored on the TIGER/Lines web server. The tool automates the process of joining these data sources, returning aggregated data to the user based on a specified census GEOID type. The tool automates the process of joining these data sources, returning aggregated data to the user based on a specified census GEOID type. Its primary motivation stems from the need for a high-performance solution to combine spatial datasets with graph traversals within the context of mobility analysis tooling being developed at NREL's Behavior and Advanced Mobility (BAM) group.

Fitzgerald, Robert [National Renewable Energy Labo↗
NASA NTRS1998

Protein Crystallization: Specific Phenomena and General Insights on Crystallization Kinetics

Experimental and simulation studies of the nucleation and growth kinetics of proteins have revealed phenomena that are specific for macromolecular crystallization, and others that provide a more detailed understanding of solution crystallization in general. The more specific phenomena, which include metastable liquid-liquid phase separations and gelation prior to solid nucleation, are due to the small ratio of the intermolecular interaction-range to the size of molecules involved. The apparently more generally applicable mechanisms include the cascade-like formation of macrosteps, as an intrinsic morphological instability that roots in the coupled bulk transport and nonlinear interface kinetics in systems with mixed growth rate control. Analyses of this nonlinear response provide (a) criteria for the choice of bulk transport conditions to minimize structural defect formation, and (b) indications that the "slow" protein crystallization kinetics stems from the mutual retardation of growth steps.

Rosenberger, F.↗
NASA NTRSDate not supplied

Unbounded Learning Environments as an Approach to Preserving Design Flexibility Demonstrated With Nasa Stem Enhancement in Earth Science (SEES) Students

The Artemis Lunar program is providing opportunity for young scientists and engineers to contribute towards leading edge design concepts regarding early on-surface work areas that are aligned with major national initiatives. Therefore, it is imperative in any discovery process that those young scientists and engineers be provided the bandwidth or operating in a ‘greenfield’ technology environment that encourages new ideas, and perhaps the discovery of ideas that would not be realized within typical structured engineering constraints. To facilitate this concept, the use of unbounded teaching methods was utilized to provide a low-constraint environment from which students can design and discover the requirements that are bounded by the natural environment of the lunar surface, and then build up design requirements un-hindered by budgetary and/or logistics realizations of the moment funding capabilities. Specifically, this design exercise provided the students to operate with unlimited budgets, and unlimited up-mass lifts to the lunar surface to develop a preliminary feasible process for establishing a working lunar research based upon the near-area permanently shadowed regions within the lunar surface. In concept, working near PSRs will be advantageous as they receive near eternal shielding from solar radiation and may potentially host numerous volatile substances such as water ice, methane, hydrogen sulfide and helium-3 that will be the target of scientific investigation and in-situ resource utilization ISRU. The advantage of an upstream working area is that the quality of return materials could potentially be exponential when including an upstream analysis prior to earth-return missions. Furthermore, it’s well known within the scientific and engineering community that working with the base materials in front of human eyes elucidates new features and observations that may not survive when stored and shipped to Earth. Finally, it is theorized that these methods and techniques developing on the lunar surface would be applicable to other planets or cometary surfaces.

Education↗
NASA NTRS1993

Automatic partitioning of unstructured meshes for the parallel solution of problems in computational mechanics

Most of the recently proposed computational methods for solving partial differential equations on multiprocessor architectures stem from the 'divide and conquer' paradigm and involve some form of domain decomposition. For those methods which also require grids of points or patches of elements, it is often necessary to explicitly partition the underlying mesh, especially when working with local memory parallel processors. In this paper, a family of cost-effective algorithms for the automatic partitioning of arbitrary two- and three-dimensional finite element and finite difference meshes is presented and discussed in view of a domain decomposed solution procedure and parallel processing. The influence of the algorithmic aspects of a solution method (implicit/explicit computations), and the architectural specifics of a multiprocessor (SIMD/MIMD, startup/transmission time), on the design of a mesh partitioning algorithm are discussed. The impact of the partitioning strategy on load balancing, operation count, operator conditioning, rate of convergence and processor mapping is also addressed. Finally, the proposed mesh decomposition algorithms are demonstrated with realistic examples of finite element, finite volume, and finite difference meshes associated with the parallel solution of solid and fluid mechanics problems on the iPSC/2 and iPSC/860 multiprocessors.

Farhat, Charbel↗
DOE OSTI2025

Navigating the Noise: Bringing Clarity to ML Parameterization Design With O $\boldsymbol{\mathcal{O}}$(100) Ensembles

Abstract Machine‐learning (ML) parameterizations of subgrid processes (here of turbulence, convection, and radiation) may one day replace conventional parameterizations by emulating high‐resolution physics without the cost of explicit simulation. However, uncertainty about the relationship between offline and online performance (i.e., when integrated with a large‐scale general circulation model) hinders their development. Much of this uncertainty stems from limited sampling of the noisy, emergent effects of upstream ML design decisions on downstream online hybrid simulation. Our work rectifies the sampling issue via the construction of a semi‐automated, end‐to‐end pipeline for size ensembles of hybrid simulations, revealing important nuances in how systematic reductions in offline error manifest in changes to online error and online stability. For example, removing dropout and switching from a Mean Squared Error to a Mean Absolute Error loss both reduce offline error, but they have opposite effects on online error and online stability. Other design decisions, like incorporating memory, converting moisture input from specific humidity to relative humidity, using batch normalization, and training on multiple climates do not come with any such compromises. Finally, we show that ensemble sizes of may be necessary to reliably detect causally relevant differences online. By enabling rapid online experimentation at scale, we can empirically settle debates regarding subgrid ML parameterization design that would have otherwise remained unresolved in the noise.

Lin, Jerry [Department of Earth System Sciences Un↗
NASA NTRS2018

Marginal protein stability drives subcellular proteome isoelectric point

There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome—a highly acidic compartment in the cell—have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.

Kaiser Loell↗