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NASA NTRS1981

A balloon measurement of the isotopic composition of galactic cosmic ray boron, carbon and nitrogen

The isotopic compositions of galactic cosmic ray boron, carbon, and nitrogen were measured at energies near 300 MeV amu, using a balloon-borne instrument at an atmospheric depth of approximately 5 g/sq cm. The calibrations of the detectors comprising the instrument are described. The saturation properties of the cesium iodide scintillators used for measurement of particle energy are studied in the context of analyzing the data for mass. The achieved rms mass resolution varies from approximately 0.3 amu at boron to approximately 0.5 amu at nitrogen, consistent with a theoretical analysis of the contributing factors. Corrected for detector interactions and the effects of the residual atmosphere the results are B-10/B=0.33 (+0.17, -0.11), C-13/C=0.06 (+0.13, -0.11), and N-15/N=0.42 (+0.19, -0.17). A model of galactic propagation and solar modulation is described. Assuming a cosmic ray source composition of solar-like isotopic abundances, the model predicts abundances near Earth consistent with the measurements.

Zumberge, J. F.↗

NASA NTRS1981

Multi-parameter yield zone model for predicting spectrum crack growth

A phenomenological load interaction model referred to as the Multi-Parameter Yield Zone model is presented which accounts for crack growth retardation caused by previous overloads, acceleration due to current overloads, and underload effects. In the present model, load interaction effects are calculated utilizing a residual stress intensity concept. Crack growth retardation and acceleration are accounted for by decreasing or increasing, respectively, the effective stress ratio used in a modified Forman's (1967) crack growth equation. Results of spectrum crack growth predictions for 2219-T851 aluminum are presented.

Johnson, W. S.↗

NASA NTRS1990

TEMPUS: A facility for containerless electromagnetic processing onboard spacelab

The electromagnetic containerless processing facility TEMPUS was recently assigned for a flight on the IML-2 mission. In comparison to the TEMPUS facility already flown on a sounding rocket, several improvements had to be implemented. These are in particular related to: safety; resource management; and the possibility to process different samples with different requirements in one mission. The basic design of this facility as well as the expected processing capabilities are presented. Two operational aspects turned out to strongly influence the facility design: control of the sample motion (first experimental results indicate that crew or ground interaction will be necessary to minimize residual sample motions during processing); and exchange of RF-coils (during processing in vacuum, evaporated sample materials will condense at the cold surface and may force a coil exchange, when a critical thickness is exceeded).

Lenski, H.↗

NASA NTRS2016

Synthesis, Structure, Characterization, and Decomposition of Nickel Dithiocarbamates: Effect of Precursor Structure and Processing Conditions on Solid-State Products

Single-crystal X-ray structures of four nickel dithiocarbamate complexes, the homoleptic mixed-organic bis-dithiocarbamates Ni[S2CN(isopropyl)(benzyl)]2, Ni[S2CN(ethyl)(n-butyl)]2, and Ni[S2CN(phenyl)(benzyl)]2, as well as the heteroleptic mixed-ligand complex NiCl[P(phenyl)3][(S2CN(phenyl)(benzyl)], were determined. Synthetic, spectroscopic, structural, thermal, and sulfide materials studies are discussed in light of prior literature. The spectroscopic results are routine. A slightly distorted square-planar nickel coordination environment was observed for all four complexes. The organic residues adopt conformations to minimize steric interactions. Steric effects also may determine puckering, if any, about the nickel and nitrogen atoms, both of which are planar or nearly so. A trans-influence affects the Ni-S bond distances. Nitrogen atoms interact with the CS2 carbons with a bond order of about 1.5, and the other substituents on nitrogen display transoid conformations. There are no strong intermolecular interactions, consistent with prior observations of the volatility of nickel dithiocarbamate complexes. Thermogravimetric analysis of the homoleptic species under inert atmosphere is consistent with production of 1:1 nickel sulfide phases. Thermolysis of nickel dithiocarbamates under flowing nitrogen produced hexagonal or -NiS as the major phase; thermolysis under flowing forming gas produced millerite (-NiS) at 300 C, godlevskite (Ni9S8) at 325 and 350 C, and heazlewoodite (Ni3S2) at 400 and 450 C. Failure to exclude oxygen results in production of nickel oxide. Nickel sulfide phases produced seem to be primarily influenced by processing conditions, in agreement with prior literature. Nickel dithiocarbamate complexes demonstrate significant promise to serve as single-source precursors to nickel sulfides, a quite interesting family of materials with numerous potential applications.

microscopy↗

DOE OSTI2010

The Structure of the L-myo-inositol-1-phosphate Synthase-NAD[superscript +]-2-deoxy-D-glucitol 6-(E)-Vinylhomophosphonate Complex Demands a Revision of the Enzyme Mechanism

1l-myo-inositol 1-phosphate (MIP) synthase catalyzes the conversion of D-glucose 6-phosphate to 1l-myo-inositol 1-phosphate, the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, enolization, intramolecular aldol cyclization, and reduction. Here we present the structure of MIP synthase in complex with NAD{sup +} and a high-affinity inhibitor, 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate. This structure reveals interactions between the enzyme active site residues and the inhibitor that are significantly different from that proposed for 2-deoxy-D-glucitol 6-phosphate in the previously published structure of MIP synthase-NAD{sup +}-2-deoxy-D-glucitol 6-phosphate. There are several other conformational changes in NAD{sup +} and the enzyme active site as well. Based on the new structural data, we propose a new and completely different mechanism for MIP synthase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Simulations of Ion Migration in the LCLS RF Gun and Injector

The motivation for this work was the observed surface contamination of the first LCLS RF gun copper cathode. We will present the results of simulations in regards to ion migration in the LCLS gun. Ions of residual gases will be created by interaction of molecular gas species with the UV drive laser beam and by the electron beam itself. The larger part of those ionized molecules remain in the vicinity of creation, are transported towards beam line walls or away from the cathode. However a small fraction gains enough kinetic energy, focused by RF and magnetic fields and propagates to the cathode, producing an undesirable increase of the cathode's surface work function. Although this fraction is small, during long term operation, this effect may become a significant factor limiting the source performance.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Fallout Cloud Regimes

The U.S. Department of Defense (DOD), Department of Energy (DOE), and other organizations maintain operational nuclear explosion and atmospheric dispersion models to provide critical guidance on the expected effects of an accidental or deliberate explosion of a nuclear weapon (in this paper simply referred to as “device”). To be effective, these models must represent, as accurately as possible, the complex interactions of the blast, fire, and residual radiological hazards with the environment and population. One hundred atmospheric nuclear tests that form the basis for many models were conducted at the Nevada Test Site (NTS) (now referred to as the Nevada Nuclear Security Site, NNSS) in a dry desert environment. Other environments should be studied, but have less data available and are beyond the scope of the work presented in this paper. The debris clouds produced by the NTS tests, frequently called “mushroom clouds,” are familiar, with common structural elements such as a buoyant cap connected to a skirt of raised dust at the desert surface by a thin, dirt-filled stem. The film scanning project at LLNL has investigated historical film records of nuclear weapons tests. Here, we summarize findings showing that the mushroom cloud behavior for historic U.S. tests conducted in Nevada, has similar characteristics based on the distance of the device from the ground surface or Height of Burst (HOB), scaled by the energy release, or yield, of the device. This scaled height is referred to as the scaled-height-of-burst (SHOB). The findings discussed below show that mushroom clouds look and behave similarly when detonated at the same SHOB. The amount of residual radiation that is produced by a nuclear detonation is proportional to the yield. But, the amount of that residual radiation that actually becomes local fallout is strongly dependent on the SHOB and the type of surface over which the detonation occurs. In order to develop a more comprehensive model that predicts the fraction of the residual radiation that becomes local fallout, it is convenient to define a series of regimes based on SHOB values in which all detonations that occur within a given regime can be modeled using the same algorithms. The purpose of this paper is to provide a framework for defining different regimes, and, in a qualitative way, a basic understanding of the fundamental characteristics of each of these regimes.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2012

Stacking interactions in PUF-RNA complexes

Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to 'target' versus 'off-target' interactions, and thus be an important consideration in the design of proteins with new specificities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Multiple, Ligand-Dependent Routes from the Active Site of Cytochrome P450 2C9

The active site of liver-specific, drug-metabolizing cytochrome P450 (CYP) monooxygenases is deeply buried in the protein and is connected to the protein surface through multiple tunnels, many of which were found open in different CYP crystal structures. It has been shown that different tunnels could serve as ligand passage routes in different CYPs. However, it is not understood whether one CYP uses multiple routes for substrate access and product release and whether these routes depend on ligand properties. From 300 ns of molecular dynamics simulations of CYP2C9, the second most abundant CYP in the human liver we found four main ligand exit routes, the occurrence of each depending on the ligand type and the conformation of the F-G loop, which is likely to be affected by the CYP-membrane interaction. A non-helical F-G loop favored exit towards the putative membrane-embedded region. Important protein features that direct ligand exit include aromatic residues that divide the active site and whose motions control access to two pathways. The ligands interacted with positively charged residues on the protein surface through hydrogen bonds that appear to select for acidic substrates. The observation of multiple, ligand-dependent routes in a CYP aids understanding of how CYP mutations affect drug metabolism and provides new possibilities for CYP inhibition.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2021

Lignin-enzyme interaction: A roadblock for efficient enzymatic hydrolysis of lignocellulosics

Efficiently producing second-generation biofuels from biomass is of strategic significance and meets sustainability targets, but it remains a long-term challenge due to the existence of biomass recalcitrance. Lignin contributes significantly to biomass recalcitrance by physically limiting the access of enzymes to carbohydrates, and this could be partially overcome by applying a pretreatment step to directly target lignin. However, lignin typically cannot be completely removed, and its structure is also significantly altered during the pretreatment. As a result, lignin residue in the pretreated materials still significantly hindered a complete conversion of carbohydrate to its monosugars by interacting with cellulase enzymes. The non-productive adsorption driven by hydrophobic, electrostatic, and/or hydrogen bonding interactions is widely considered as the major mechanism of action governing the unfavored lignin-enzyme interaction. One could argue this type of interaction between lignin residue and the activated enzymes is the major roadblock for efficient enzymatic hydrolysis of pretreated lignocellulosics. To alleviate the negative effects of lignin on enzyme performance, a deep understanding of lignin structural transformation upon different types of pretreatments as well as how and where does lignin bind to enzymes are prerequisites. In the last decade, the progress toward a fundamental understanding of lignin-enzyme interaction, structural characterization of lignin during pretreatment and/or conformation change of enzyme during hydrolysis is resulting in advances in the development of methodologies to mitigate the negative effect of lignin. Here in this review, the lignin structural transformation upon different types of pretreatments and the inhibition mechanism of lignin in the bioconversion of lignocellulose to bioethanol are summarized. Some technologies to minimize the adverse impact of lignin on the enzymatic hydrolysis, including chemical modification of lignin, adding blocking additives, and post-treatment to remove lignin were also introduced. The production of liquid biofuels from lignocellulosic biomass has shown great environmental benefits such as reducing greenhouse gas emissions and mitigate climate change. By addressing the root causes of lignin-enzyme interaction and how to retard this interaction, it is our hope that this comprehensive review will pave the way for significantly reducing the high cost associated with the enzymatic hydrolysis process, and ultimately achieving a cost-effective and sustainable biorefinery system.

09 BIOMASS FUELS↗

DOE OSTI2018

Newly Synthesized Heteronuclear Ruthenium(II)/Ferrocene Complexes Suppress the Growth of Mammary Carcinoma in 4T1-Treated BALB/c Mice by Promoting Activation of Antitumor Immunity

The two new heterometallic Ru(II)-tpy/ferrocene complexes [Ru(tpy)Cl2(mtefc)] (1) and [Ru(tpy)Cl2(mtpfc)] (2) (where tpy = 2,2′:6′,2′′-terpyridine, mtefc = (2-(methylthio)ethyl)ferrocene, and mtpfc = (3-(methylthio)propyl)ferrocene) have been synthesized and then characterized through elemental analysis, followed by various spectroscopic (IR, UV-vis, 1D and 2D NMR) and mass spectrometric techniques (MALDI TOF and ESI Q-TOF MS). UV-vis and fluorescence spectroscopy and viscometry were employed to study the interactions of the complexes 1 and 2 with calf thymus DNA. Both 1 and 2 expelled ethidium bromide (EB) from the EB/DNA complex (Ksv = (1.5-1.8) × 104 M-1), which suggested that the complexes intercalated into the double helix of DNA. Both complexes strongly quenched the fluorescence of tryptophan residues in serum albumin through both static and dynamic quenching. Molecular docking confirmed the intercalative mode of complex interaction with DNA. The docking results implied that 1 and 2 interacted with hydrophobic residues of albumin, particularly with those lying in the proximity of Tyr 160. We here demonstrate the high cytotoxic potential of complexes 1 and 2 against the breast cancer cells that originated either from humans (MDA-MB-231) or from mice (4T1), with apoptosis being the main mechanism of complex-induced cell death. It is worth noting that both complexes promoted activation of innate and acquired antitumor immunity, which contributed to the reduced growth and progression of mammary carcinoma in vivo. Copyright © 2018 American Chemical Society.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

The structure of the Caenorhabditis elegans manganese superoxide dismutase MnSOD-3-azide complex

C. elegans MnSOD-3 has been implicated in the longevity pathway and its mechanism of catalysis is relevant to the aging process and carcinogenesis. The structures of MnSOD-3 provide unique crystallographic evidence of a dynamic region of the tetrameric interface (residues 41–54). We have determined the structure of the MnSOD-3-azide complex to 1.77-Å resolution. The analysis of this complex shows that the substrate analog, azide, binds end-on to the manganese center as a sixth ligand and that it ligates directly to a third and new solvent molecule also positioned within interacting distance to the His30 and Tyr34 residues of the substrate access funnel. This is the first structure of a eukaryotic MnSOD-azide complex that demonstrates the extended, uninterrupted hydrogen-bonded network that forms a proton relay incorporating three outer sphere solvent molecules, the substrate analog, the gateway residues, Gln142, and the solvent ligand. This configuration supports the formation and release of the hydrogen peroxide product in agreement with the 5-6-5 catalytic mechanism for MnSOD. The high product dissociation constant k₄ of MnSOD-3 reflects low product inhibition making this enzyme efficient even at high levels of superoxide.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2013

Stable isotope-assisted NMR characterization of interaction between lipid A and sarcotoxin IA, a cecropin-type antibacterial peptide

Highlights: ► Recombinant sarcotoxin IA was successfully produced with {sup 13}C- and {sup 15}N-labeling. ► Sarcotoxin IA adopts an N-terminal α-helix upon binding to lipid A-embedding micelles. ► Two lysine residues are involved in lipid A-mediated antibacterial activities. -- Abstract: Sarcotoxin IA is a 39-residue cecropin-type peptide from Sarcophaga peregrina. This peptide exhibits antibacterial activity against Gram-negative bacteria through its interaction with lipid A, a core component of lipopolysaccharides. To acquire detailed structural information on this specific interaction, we performed NMR analysis using bacterially expressed sarcotoxin IA analogs with {sup 13}C- and {sup 15}N-labeling along with lipid A-embedding micelles composed of dodecylphosphocholine. By inspecting the stable isotope-assisted NMR data, we revealed that the N-terminal segment (Leu3–Arg18) of sarcotoxin IA formed an amphiphilic α-helix upon its interaction with the aqueous micelles. Furthermore, chemical shift perturbation data indicated that the amino acid residues displayed on this α-helix were involved in the specific interaction with lipid A. On the basis of these data, we successfully identified Lys4 and Lys5 as key residues in the interaction with lipid A and the consequent antibacterial activity. Therefore, these results provide unique information for designing chemotherapeutics based on antibacterial peptide structures.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2013

Molecular insight into conformational transmission of human P-glycoprotein

P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

The Response of the Quasi-Biennial Oscillation to Increased CO and its Modulation by Composition Feedbacks

The Quasi-Biennial Oscillation (QBO) impacts the large-scale circulation by altering lower stratospheric meridional temperature gradients which alter the propagation of upward propagating planetary waves. Proposed teleconnections of the QBO include impacts on the stratospheric polar vortices, extratropical surface winter climate, and the Madden-Julian Oscillation. However, long-term projections of the QBO remain highly uncertain. While recent multi-model investigations (Richter et al. 2019, Butchart et al. 2020) show that the amplitude of the QBO weakens robustly among models, changes in QBO period and stability remain highly uncertain. Here we examine the QBO response to increased greenhouse gases using the NASA Goddard Institute for Space Studies Middle Atmosphere Model E2.2 (Rind et al., 2020; Orbe et al. 2020). Compared to lower vertical resolution versions of ModelE, E2.2 also has a higher model top (0.002 hPa) and employs additional interactive non-orographic gravity wave drag sources from convection and shear, which produce a sufficiently realistic QBO, thus rendering it suitable for use in climate change studies. Overall, we find that both the QBO period and amplitude decrease in response to increased CO , the former related to increased lower stratospheric momentum fluxes (associated with convection) and the latter associated partly with a stronger residual mean circulation. Experiments integrated using fully interactive chemistry also reveal that ozone feedbacks significantly impact the magnitude of the QBO amplitude response. Finally, integrations using fixed (pre-industrial) sea surface temperatures (SST) show that the QBO amplitude responds differently to rapid adjustments versus SST feedbacks, as compared to the QBO period.

Quasi-Biennial Oscillation↗

DOE OSTI2018

3D-QSAR study of steroidal and azaheterocyclic human aromatase inhibitors using quantitative profile of protein–ligand interactions

Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, including sexual diferentiation and maturation, aromatase is a potential target for endocrine disrupting chemicals as well as breast cancer therapy. In this work, 3D-QSAR combined with quantitative profle of protein–ligand interactions was employed in the identifcation and characterization of critical steric and electronic features of aromatase-inhibitor complexes and the estimation of their quantitative contribution to inhibition potency. Bioactivity data on pIC 50 values of 175 steroidal and 124 azaheterocyclic human aromatase inhibitors (AIs) were used for the 3D-QSAR analysis. For the quantitative description of the efects of the hydrophobic contact and nitrogen–heme–iron coordination on aromatase inhibition, the hydrophobicity density feld model and the smallest dual descriptor Δf(r) S were introduced, respectively. The model revealed that hydrophobic contact and nitrogen–heme–iron coordination primarily determines inhibition potency of steroidal and azaheterocyclic AIs, respectively. Moreover, hydrogen bonds with key amino acid residues, in particular Asp309 and Met375, and interaction with the heme–iron are required for potent inhibition. Phe221 and Thr310 appear to be quite fexible and adopt diferent conformations according to a substituent at 4- or 6-position of steroids. Flexible docking results indicate that proper representation of the residues’ fexibility is critical for reasonable description of binding of the structurally diverse inhibitors. Our results provide a quantitative and mechanistic understanding of inhibitory activity of steroidal and azaheterocyclic AIs of relevance to adverse outcome pathway development and rational drug design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ

The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH

Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca 2+ -triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca 2+ -bound holo s2b (1.4 Å resolution, R = 15.0%, R free = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, R free = 20.7%), as well as of Ca 2+ -free apo s2a (1.8 Å resolution, R = 20.7%, R free = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, R free = 21.2%; 1.6 Å resolution, R = 16.2%, R free = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca 2+ pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B -factor analyses suggest that in the presence of Ca 2+ the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca 2+ binding. Conserved residues not only interact with Ca 2+ , but also position the Ca 2+ -interacting water molecule. Ca 2+ aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca 2+ binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

Bauer, Ryan↗