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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Protein structure, electron transfer and evolution of prokaryotic photosynthetic reaction centers

Photosynthetic reaction centers from a variety of organisms have been isolated and characterized. The groups of prokaryotic photosynthetic organisms include the purple bacteria, the filamentous green bacteria, the green sulfur bacteria and the heliobacteria as anoxygenic representatives as well as the cyanobacteria and prochlorophytes as oxygenic representatives. This review focuses on structural and functional comparisons of the various groups of photosynthetic reaction centers and considers possible evolutionary scenarios to explain the diversity of existing photosynthetic organisms.

NASA Discipline Exobiology↗
DOE OSTI2025

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

RcaE-Dependent Regulation of Carboxysome Structural Proteins Has a Central Role in Environmental Determination of Carboxysome Morphology and Abundance in Fremyella diplosiphon

Carboxysomes are proteinaceous subcellular compartments, or bacterial organelles, found in cyanobacteria that consist of a protein shell surrounding a core primarily composed of the enzyme ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) that is central to the carbon dioxide-concentrating mechanism (CCM) and carbon fixation. Whereas significant insights have been gained regarding the structure and synthesis of carboxysomes, limited attention has been given to how their size, abundance, and protein composition are regulated to ensure optimal carbon fixation in dynamic environments. Given the centrality of carboxysomes in photosynthesis, we provide an analysis of the role of a photoreceptor, RcaE, which functions in matching photosynthetic pigmentation to the external environment during complementary chromatic acclimation and thereby optimizing photosynthetic efficiency, in regulating carboxysome dynamics. Our data highlight a role for RcaE in perceiving external light cues and regulating carboxysome structure and function and, thus, in the cellular capacity for carbon fixation and organismal fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Effects of Protein Structure on Iron–Polypeptide Vibrational Dynamic Coupling in Cytochrome c

Cytochrome c (Cyt c) has a heme covalently bound to the polypeptide via a Cys-X-X-Cys-His (CXXCH) linker that is located in the interface region for protein–protein interactions. To determine whether the polypeptide matrix influences iron vibrational dynamics, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on 57 Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c-552, and variants M13V, M13V/K22M, and A7F, which have structural modifications that alter the composition or environment of the CXXCH pentapeptide loop. Simulations of the NRVS data indicate that the 150–325 cm –1 region is dominated by N His –Fe–S Met axial ligand and polypeptide motions, while the 325–400 cm –1 region shows dominant contributions from ν(Fe–N Pyr ) (Pyr = pyrrole) and other heme-based modes. Diagnostic spectral signatures that directly relate to structural features of the heme active site are identified using a quantum chemistry-centered normal coordinate analysis (QCC-NCA). In particular, spectral features that directly correlate with CXXCH loop stiffness, the strength of the Fe–His interaction, and the degree of heme distortion are identified. Cumulative results from our investigation suggest that compared to the wild type (wt), variants M13V and M13V/K22M have a more rigid CXXCH pentapeptide segment, a stronger Fe–N His interaction, and a more ruffled heme. Conversely, the A7F variant has a more planar heme and a weaker Fe–NHis bond. These results are correlated to the observed changes in reduction potential between wt protein and the variants studied here. Lastly, we discuss the implications of these results for Cyt c biogenesis and electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Lessons from bacteriophages part 1: Deriving utility from protein structure, function, and evolution

Historically, some of the most fundamental discoveries of modern molecular biology were revealed by examination of phage-infected cells. Some examples include the use of bacteriophage T2 to show that DNA, not protein, was the genetic material by Hershey and Chase in 1952. Crick and colleagues showed that codons are degenerate and encode for single amino acids by making use of T4 bacteriophage. Brenner and colleagues discovered that mRNA acts as the messenger in relaying the information from DNA to ribosomes with the aid of bacteriophage T2. Szybalski and colleagues demonstrated the semiconservative mechanism of DNA replication using λ phage. Restriction modification, a bacterial innate immune system that evolved as protection against invading mobile genetic elements such as plasmids and phages, was discovered in bacteriophage-infected cells. Restriction mapping was crucial for the completion of the human genome project. The mechanism of action of heat shock genes—which encode for molecular chaperones such as dnaK , dnaJ , and grpE , as well as the groE gene locus, which encodes for the molecular chaperones GroES and GroEL—were discovered in λ phage–infected Escherichia coli. The first capsid assembly inhibitor, the fluorescent dye 4,4’–bis(1-anilinonaphthalene-8-sulfonic acid) (bisANS), was discovered in experiments investigating assembly of phage P22. These are just some of the examples of contributions made by bacteriophage research in the past few decades. Here, we discuss additional discoveries derived from studies of phages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Detection of trans–cis flips and peptide-plane flips in protein structures

A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip. A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans–cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans–cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure–function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT-CHECK.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

AQuaRef: machine learning accelerated quantum refinement of protein structures

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.

Zubatyuk, Roman [Carnegie Mellon University, Pitts↗