SEARCH · Search NASA

Results for “Origins of Life”

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.

SourceResearch connectionFrom yearThrough year

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

At least 379 records · Page 21

All sources NASA NTRS DOE OSTI

NASA NTRS2001

Human Exploration and Development of Space: Strategic Plan

In order to make possible the permanent extension of human presence beyond the bounds of Earth and enable historic improvements in our understanding of our solar system and the universe, and the quality of life, NASA must: (1) Undertake, in partnership with the scientific community, sustained international explorations throughout the inner solar system by integrated human/robotic expeditions; (2) Achieve breakthrough discoveries and technology developments through basic, applied, and commercial research in the unique venue of space--exploiting characteristics such as microgravity, vacuum, radiation, and location; (3) Establish safe and routine access to space in support of permanent commercial human operations in low-Earth orbit and ongoing exploration activities at one or more sites beyond Earth orbit; (4) Engage the private sector in the commercial development of space and enable the creation of new space industries generating new wealth for the US economy; and (5) Communicate the excitement and importance of the discovery of new worlds and the profound insights we will gain into the origins of life and the universe. In order to guide planning, the Human Exploration and Development of Space (HEDS) Enterprise has identified some potential future targets and goals (e.g. 'Design Reference Points') beginning with the near-term and extending to the far-term and beyond.

Branscome, Darrell↗

NASA NTRS2023

Peptide conjugates with polyaromatic hydrocarbons can benefit the activity of catalytic RNAs

Early stages of life likely employed catalytic RNAs (ribozymes) in many functions that are today filled by proteins. However, the earliest life forms must have emerged from heterogenous chemical mixtures, which included amino acids, short peptides, and many other compounds. Here we explored whether the presence of short peptides can help the emergence of catalytic RNAs. To do this, we conducted an in vitro selection for catalytic RNAs from randomized sequence in the presence of ten different peptides with a prebiotically plausible length of eight amino acids. This in vitro selection generated dozens of ribozymes, one of them with ∼900-fold higher activity in the presence of one specific peptide. Unexpectedly, the beneficial peptide had retained its N-terminal Fmoc protection group, and this group was required to benefit ribozyme activity. The same, or higher benefit resulted from peptide conjugates with prebiotically plausible polyaromatic hydrocarbons (PAHs) such as fluorene and naphthalene. This shows that PAH-peptide conjugates can act as potent cofactors to enhance ribozyme activity. The results are discussed in the context of the origin of life.

Kevin J. Sweeney↗

NASA NTRS2013

Extraterrestrial Amino Acids Identified in Metal-Rich CH and CB Carbonaceous Chondrites from Antarctica

Carbonaceous chondrites contain numerous indigenous organic compounds and could have been an important source of prebiotic compounds required for the origin of life on Earth or elsewhere. Extraterrestrial amino acids have been reported in five of the eight groups of carbonaceous chondrites and are most abundant in CI, CM, and CR chondritesbut are also present in the more thermally altered CV and CO chondrites. We report the abundance, distribution, and enantiomeric and isotopic compositions of simple primary amino acids in six metal-rich CH and CB carbonaceous chondrites that have not previously been investigated for amino acids: Allan Hills (ALH) 85085 (CH3), Pecora Escarpment(PCA) 91467 (CH3), Patuxent Range (PAT) 91546 (CH3), MacAlpine Hills (MAC) 02675(CBb), Miller Range (MIL) 05082 (CB), and Miller Range (MIL) 07411 (CB). Amino acid abundances and carbon isotopic values were obtained by using both liquid chromatography time-of-flight mass spectrometry and fluorescence, and gas chromatography isotope ratiomass spectrometry. The (delta D, delta C-13, delta N-15) ratios of multiple amino acids fall outside of the terrestrial range and support their extraterrestrial origin. Extracts of CH chondrites were found to be particularly rich in amino acids (1316 parts per million, ppm) while CB chondrite extracts had much lower abundances (0.22 ppm). The amino acid distributions of the CH and CB chondrites were distinct from the distributions observed in type 2 and 3 CM and CR chondrites and contained elevated levels of beta-, gamma-, and delta-amino acids compared to the corresponding alpha-amino acids, providing evidence that multiple amino acid formation mechanisms were important in CH and CB chondrites.

Burton, Aaron S.↗

NASA NTRS2017

Exploring Connectivity in Sequence Space of Functional RNA

Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.

Wei, Chenyu↗

NASA NTRS2003

Isolation of Purines and Pyrimidines from the Murchison Meteorite

The origin of life on Earth, and possibly on other planets such as Mars, would have required the presence of liquid water and a continuous supply of prebiotic organic compounds. The delivery of organic matter by asteroids, comets, and carbonaceous meteorites could have contributed to the early Earth's prebiotic inventory by seeding the planet with biologically important organic compounds. A wide variety of prebiotic organic compounds have previously been detected in the Murchison CM type carbonaceous chondrite including amino acids, purines and pyrimidines'. These compounds play a major role in terrestrial biochemistry and are integral components of proteins, DNA and RNA. In this study we developed a new extraction technique using sublimation in order to isolate purines and pyrimidines from Murchison2, which is cleaner and more time efficient that traditional methods3. Several purines including adenine, guanine, hypoxanthine and xanthine were positively identified by high performance liquid chromatography and ultraviolet absorption detection in our Murchison extracts. The purines detected in Murchison do not correlate with the distribution of nucleobases found in geological environments on Earth4. Moreover, the abundance of extraterrestrial amino acids and the low level of terrestrial amino acid contaminants found in Murchison', support the idea that the purines in t h s meteorite are extraterrestrial in origin.

Glavin, D. P.↗

NASA NTRS2002

The origin and evolution of model organisms

The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.

Review, Academic↗

NASA NTRS1992

Evolution of catalytic RNA in the laboratory

We are interested in the biochemistry of existing RNA enzymes and in the development of RNA enzymes with novel catalytic function. The focal point of our research program has been the design and operation of a laboratory system for the controlled evolution of catalytic RNA. This system serves as working model of RNA-based life and can be used to explore the catalytic potential of RNA. Evolution requires the integration of three chemical processes: amplification, mutation, and selection. Amplification results in additional copies of the genetic material. Mutation operates at the level of genotype to introduce variability, this variability in turn being expressed as a range of phenotypes. Selection operates at the level of phenotype to reduce variability by excluding those individuals that do not conform to the prevailing fitness criteria. These three processes must be linked so that only the selected individuals are amplified, subject to mutational error, to produce a progeny distribution of mutant individuals. We devised techniques for the amplification, mutation, and selection of catalytic RNA, all of which can be performed rapidly in vitro within a single reaction vessel. We integrated these techniques in such a way that they can be performed iteratively and routinely. This allowed us to conduct evolution experiments in response to artificially-imposed selection constraints. Our objective was to develop novel RNA enzymes by altering the selection constraints in a controlled manner. In this way we were able to expand the catalytic repertoire of RNA. Our long-range objective is to develop an RNA enzyme with RNA replicase activity. If such an enzyme had the ability to produce additional copies of itself, then RNA evolution would operate autonomously and the origin of life will have been realized in the laboratory.

Joyce, Gerald F.↗

DOE OSTI2024

Emergence of catalytic function in prebiotic information-coding polymers

Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Emergence of catalytic function in prebiotic information-coding polymers

Tkachenko, Alexei V. (ORCID:000000031291243X)↗

NASA NTRS2014

Assessing the Origins of Aliphatic Amines in the Murchison Meteorite from their Compound-Specific Carbon Isotopic Ratios and Enantiomeric Composition

The study of meteoritic organic compounds provides a unique window into the chemical inventory of the early Solar System and prebiotic chemistry that may have been important for the origin of life on Earth. Multiple families of organic compounds have been extracted from the Murchison meteorite, which is one of the most thoroughly studied carbonaceous chondrites. The amino acids extracted from Murchison have been extensively analyzed, including measurements of non-terrestrial stable isotopic ratios and discoveries of L-enantiomeric excesses for alpha-dialkyl amino acids, notably isovaline. However, although the isotopic signatures of bulk amine-containing fractions have been measured, the isotopic ratios and enantiomeric composition of individual aliphatic amines, compounds that are chemically related to amino acids, remain unknown. Here, we report a novel method for the extraction, separation, identification and quantitation of aliphatic monoamines extracted from the Murchison meteorite. Our results show a complete suite of structural isomers, with a larger concentration of methylamine and ethylamine and decreasing amine concentrations with increasing carbon number. The carbon isotopic compositions of fourteen meteoritic aliphatic monoamines were measured, with delta C-13 values ranging from +21% to +129%, showing a decrease in C-13 with increasing carbon number, a relationship that may be consistent with the chain elongation mechanism under kinetic control previously proposed for meteoritic amino acids. We also found the enantiomeric composition of sec-butylamine, a structural analog to isovaline, was racemic within error, while the isovaline extracted from the same Murchison piece showed an L-enantiomeric excess of 9.7; this result suggested that processes leading to enantiomeric excess in the amino acid did not affect the amine. We used these collective data to assess the primordial synthetic origins of these meteoritic aliphatic amines and their potential linkage to meteoritic amino acids.

prebiotic chemistry↗

NASA NTRS2016

Aliphatic Amines in Antarctic CR2, CM2, and CM1/2 Carbonaceous Chondrites

Meteoritic water-soluble organic compounds provide a unique record of the processes that occurred during the formation of the solar system and the chemistry preceding the origins of life on Earth. We have investigated the molecular distribution, compound-specific delta13C isotopic ratios and enantiomeric compositions of aliphatic monoamines present in the hot acid-water extracts of the carbonaceous chondrites LAP 02342 (CR2), GRA 95229 (CR2), LON 94101 (CM2), LEW 90500 (CM2), and ALH 83100 (CM1/2). Analyses of the concentration of monoamines in these meteorites revealed: (a) the CR2 chondrites studied here contain higher concentrations of monoamines relative to the analyzed CM2 chondrites; (b) the concentration of monoamines decreases with increasing carbon number; and (c) isopropylamine is the most abundant monoamine in these CR2 chondrites, while methylamine is the most abundant amine species in these CM2 and CM1/2 chondrites. The delta13C values of monoamines in CR2 chondrite do not correlate with the number of carbon atoms; however, in CM2 and CM1/2 chondrites, the 13C enrichment decreases with increasing monoamine carbon number. The delta13C values of methylamine in CR2 chondrites ranged from −1 to +10per mille, while in CM2 and CM1/2 chondrites the delta13C values of methylamine ranged from +41 to +59per mille. We also observed racemic compositions of sec-butylamine, 3-methyl-2-butylamine, and sec-pentylamine in the studied carbonaceous chondrites. Additionally, we compared the abundance and delta13C isotopic composition of monoamines to those of their structurally related amino acids. We found that monoamines are less abundant than amino acids in CR2 chondrites, with the opposite being true in CM2 and CM1/2 chondrites. We used these collective data to evaluate different primordial synthetic pathways for monoamines in carbonaceous chondrites and to understand the potential common origins these molecules may share with meteoritic amino acids.

Meteoritic water-soluble organic compounds↗

NASA NTRS1999

A Mossbauer investigation of iron-rich terrestrial hydrothermal vent systems: lessons for Mars exploration

Hydrothermal spring systems may well have been present on early Mars and could have served as a habitat for primitive life. The integrated instrument suite of the Athena Rover has, as a component on the robotic arm, a Mossbauer spectrometer. In the context of future Mars exploration we present results of Mossbauer analysis of a suite of samples from an iron-rich thermal spring in the Chocolate Pots area of Yellowstone National Park (YNP) and from Obsidian Pool (YNP) and Manitou Springs, Colorado. We have found that Mossbauer spectroscopy can discriminate among the iron-bearing minerals in our samples. Those near the vent and on the surface are identified as ferrihydrite, an amorphous ferric mineraloid. Subsurface samples, collected from cores, which are likely to have undergone inorganic and/or biologically mediated alteration (diagenesis), exhibit spectral signatures that include nontronite (a smectite clay), hematite (alpha-Fe2O3), small-particle/nanophase goethite (alpha-FeOOH), and siderite (FeCO3). We find for iron minerals that Mossbauer spectroscopy is at least as efficient in identification as X-ray diffraction. This observation is important from an exploration standpoint. As a planetary surface instrument, Mossbauer spectroscopy can yield high-quality spectral data without sample preparation (backscatter mode). We have also used field emission scanning electron microscopy (FESEM), in conjunction with energy-dispersive X ray (EDX) fluorescence spectroscopy, to characterize the microbiological component of surface sinters and the relation between the microbiological and the mineralogical framework. Evidence is presented that the minerals found in these deposits can have multi-billion-year residence times and thus may have survived their possible production in a putative early Martian hot spring up to the present day. Examples include the nanophase property and the Mossbauer signature for siderite, which has been identified in a 2.09-billion-year old hematite-rich chert stromatolite. Our research demonstrates that in situ Mossbauer spectroscopy can help determine whether hydrothermal mineral deposits exist on Mars, which is significant for exobiology because of the issue of whether that world ever had conditions conductive to the origin of life. As a useful tool for selection of samples suitable for transport to Earth, Mossbauer spectroscopy will not only serve geological interests but will also have potential for exopaleontology.

NASA Discipline Exobiology↗

DOE OSTI2026

Surface heterogeneity propagation and homogenization for pouch cell-scale Li metal anodes

Li metal anode is a promising candidate for next-generation energy storage systems and is widely explored in Li-ion and solid-state batteries. Despite its potential, Li metal anodes face instabilities during long-term cycling, especially when paired with NMC or sulfur-based cathodes, where Li is cycled at high capacities of 6-8 mAh/cm2, equivalent to a thickness of 30-40 µm. During such extensive utilization, degradation mechanisms such as excessive solid electrolyte interphase (SEI), dendrites, and dead Li emerge, and ultimately lead to sudden failure and reduced cycle life. The origin of the degradation mechanisms stem from surface heterogeneities introduced during Li foil manufacturing and storage [1, 2]. As cycling progresses, the local heterogeneities propagate, resulting in uneven Li utilization and degradation-prone regions across the electrode [3], which consequently induce performance variations at the cell level. This heterogeneity propagation is particularly pronounced in large-format pouch cells in practical applications, where the surface effects are magnified. Without a clear understanding of the multi-scale heterogeneities and the development of surface homogenization methods, the performance consistency will be compromised, hindering the commercialization of Li metal batteries. In this presentation, we investigate the evolution of surface heterogeneity propagation on commercially available Li foils. We discover that inhomogeneous Li utilization appears as early as the first half-cycle of formation, manifesting as localized clusters and pits. In pouch cell configurations, these features exhibit areal density variations across the electrode on a scale of millimeters. To improve Li utilization homogeneity, a scalable mechanical brushing method is introduced to remove the chemically heterogeneous surface passivation layer. Furtherore, the influence of utilization homogeneity on cell-to-cell consistency is evaluated using 32 Li-NMC811 pouch cells divided into as-received and brushed Li groups. On the brushed Li, clusters and pits are no longer observable, and the cells exhibit significantly improved consistency in discharge capacity trajectories and cycle lifetime. Overall, this study highlights the role of Li surface utilization homogeneity on long-term cycling performance. Our research provides a pathway for improving large-area electrode uniformity and establishing evaluation methods for cell-to-cell consistency, both are key steps toward the commercialization of Li metal batteries and beyond. [1] Otto, Svenja-K., et al. "In-depth characterization of lithium-metal surfaces with XPS and ToF-SIMS: toward better understanding of the passivation layer." Chemistry of Materials 33.3 (2021): 859-867. [2] Hatzell, Kelsey, et al. "Aligning lithium metal battery research and development across academia and industry." Joule (2024). [3] Kim, Sangwook, et al. "Calendar life of lithium metal batteries: Accelerated aging and failure analysis." Energy Storage Materials 65 (2024): 103147.

25 - ENERGY STORAGE↗

NASA NTRS1996

The Chemistry of Early Self-Replicating Systems

The NASA Specialized Center of Research and Training (NSCORT) in Exobiology is a consortium of scientists at the University of California at San Diego (UCSD), The Salk Institute for Biological Studies (Salk) and The Scripps Research Institute (TSRI). All three institutions are located in close geographical proximity in La Jolla, California. The NSCORT/Exobiology is administered through the Scripps Institution of Oceanography. Since its inception in January 1992, the NSCORT in Exobiology has made major contributions with respect to the question of how life began on Earth. The Principal Investigators (PIs) and their associated Fellows have published numerous articles in peer reviewed journals on topics relevant to Exobiology. They have presented papers and sponsored symposia at several meetings of national and international scientific societies. A total of 30 undergraduate, 12 graduate and 15 postdoctoral Fellows have been supported by the NSCORT. The Fellows have met on their own at least once a month to discuss Exobiology topics and research progress. The NSCORT has arranged seminars and evening discussion meetings, and offered an undergraduate class on "Biochemical Evolution" as well as graduate courses dealing with topics in Exobiology. A visiting scientist program has allowed 11 scientists from the U.S. and 4 foreign countries to conduct cooperative research with the various PIs. An active outreach program has been initiated, which includes an Exobiology high school level teaching module and curriculum guide, and an elementary school level booklet about basic atomic structure and formation of the universe, Sun and Earth. A World Wide Web Homepage (http://www-chem.ucsd.edu/-nscort/ NSCORT.html) has been developed, which describes the NSCORT activities, research programs and Fellowship opportunities. The various activities of the NSCORT in Exobiology have received wide-spread coverage in both the scientific and public media. The major function of the NSCORT is the training of young scientists in the field of Exo- biology. Thus, the bulk of the $1,000,000 annual budget is used to support the research and training of undergraduate, graduate and post-doctoral Fellows who are selected on a competitive basis. About five Fellows at each level are supported each year. Our goal is to train scientists whose major research interest is Exobiology, but whose mastery in the classical fields of chemistry, biology and earth science is so strong that they outstanding candidates for either graduate school or academic tenure-track positions in departments at leading national and international Universities. Applicants for these Fellowships are solicited by advertisements in journals such as Science and Nature and in organizational newsletters such as the one published by the International Society for the Study of the Origin of Life (ISSOL), by contacting academic and NASA colleagues working in Exobiology or related fields and by recruiting students who have already been admitted into the various academic programs with which the PIs are affiliated.

Bada, Jeffrey L.↗

DOE OSTI2020

A Unified Mechanism on the Formation of Acenes, Helicenes, and Phenacenes in the Gas Phase

Abstract A unified low‐temperature reaction mechanism on the formation of acenes, phenacenes, and helicenes—polycyclic aromatic hydrocarbons (PAHs) that are distinct via the linear, zigzag, and ortho ‐condensed arrangements of fused benzene rings—is revealed. This mechanism is mediated through a barrierless, vinylacetylene mediated gas‐phase chemistry utilizing tetracene, [4]phenacene, and [4]helicene as benchmarks contesting established ideas that molecular mass growth processes to PAHs transpire at elevated temperatures. This mechanism opens up an isomer‐selective route to aromatic structures involving submerged reaction barriers, resonantly stabilized free‐radical intermediates, and systematic ring annulation potentially yielding molecular wires along with racemic mixtures of helicenes in deep space. Connecting helicene templates to the Origins of Life ultimately changes our hypothesis on interstellar carbon chemistry.

Zhao, Long↗

DOE OSTI2019

A Unified Mechanism on the Formation of Acenes, Helicenes, and Phenacenes in the Gas Phase

A unified low-temperature reaction mechanism on the formation of acenes, phenacenes, and helicenes—polycyclic aromatic hydrocarbons (PAHs) that are distinct via the linear, zigzag, and ortho-condensed arrangements of fused benzene rings—is illustrated. This mechanism is mediated through a barrierless, vinylacetylene mediated gas-phase chemistry utilizing tetracene, [4]phenacene, and [4]helicene as benchmarks contesting established ideas that molecular mass growth processes to PAHs transpire at elevated temperatures. This mechanism opens up an isomer-selective route to aromatic structures involving submerged reaction barriers, resonantly stabilized free-radical intermediates, and systematic ring annulation potentially yielding molecular wires along with racemic mixtures of helicenes in deep space. Thus, connecting helicene templates to the Origins of Life ultimately changes our hypothesis on interstellar carbon chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Investigations of water/oxide interfaces by molecular dynamics simulations

Water/oxide interfaces are ubiquitous on earth and show significant influence on many chemical processes. For example, understanding water and solute adsorption as well as catalytic water splitting can help build better fuel cells and solar cells to overcome our looming energy crisis; the interaction between biomolecules and water/oxide interfaces is one hypothesis to explain the origin of life. However, knowledge in this area is still limited due to the difficulty of studying water/solid interfaces. As a result, research using increasingly sophisticated experimental techniques and computational simulations has been carried out in recent years. Although it is difficult for experimental techniques to provide detailed microscopic structural information, molecular dynamics (MD) simulations have satisfactory performance. In this report, we discuss classical and ab initio MD simulations of water/oxide interfaces. Generally, we are interested in the following questions: How do solid surfaces perturb interfacial water structure? How do interfacial water molecules and adsorbed solutes affect solid surfaces and how do interfacial environments affect solvent and solute behavior? Finally, we discuss progress in the application of neural network potential based MD simulations, which offer a promising future because this approach has already enabled ab initio level accuracy for very large systems and long trajectories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Designing Peptide Fossils That Model the Evolution of the Bacterial Ferredoxin Fold

Electron transfer coupled to redox chemistry is at the heart of metabolism. The proteins responsible for moving electrons (protein electron carriers) must have emerged at the origin of life. The small iron–sulfur-binding bacterial ferredoxins were likely among these first proteins. Embedded within the ferredoxin sequence and structure is a symmetry that points to an ancient gene duplication event. Little is understood about the nature of ferredoxins prior to this duplication event or what environmental factors may have driven the selection for more complex forms. The deep-time molecular history of ferredoxins goes back billions of years and cannot be reconstructed by phylogenetic analyses based on amino acid sequences. Here, we use structure-guided protein design to model a fossil half-ferredoxin stage in the evolution of this fold, the semidoxins, and their symmetric full-length counterparts, the symdoxins. Semidoxin designs homodimerize, exhibiting structural, thermodynamic, and electrochemical behaviors in most cases identical to cognate symdoxins. However, the semi- and symdoxin fossil stages behave differently when incorporated into an in vivo electron transfer complementation assay. Both can support bacterial growth dependent on protein expression. Growth rates of bacteria expressing the semidoxins are much more sensitive to oxygen than those of bacteria expressing symdoxins. Motivated by the in vivo functionality of designed semidoxins, we identified putative naturally occurring semidoxins in extant anaerobic microorganisms. This is consistent with the observed in vivo oxygen sensitivity of the semidoxin designs. One natural semidoxin is shown to be folded and redox active. However, it exists as a mixture of monomers and dimers, suggesting a potential connection between semidoxins and even simpler single iron–sulfur cluster-binding peptides.

59 BASIC BIOLOGICAL SCIENCES↗