The comparative enzymology of triosephosphate dehydrogenase
Preparation, sedimentation, electrophoretic properties, amino acid composition, immunology, and crystallization of triose phosphate dehydrogenase
CRYSTALLIZATION↗
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Results for “AMINO ACID”
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The genetic code. II.
Amino acid genetic code in which long sequences in DNA spell out instructions transcribed into RNA AND subsequently into proteins
AMINO ACID↗
Elemental and isotopic analysis of inorganic salts by laser desorption ionization mass spectrometry
Laser desorption ionization mass spectrometry is applied for the analysis of elements as well as their isotopic composition in different inorganic salts. At very low laser energies the inorganic ions are desorbed and ionized from the thin layer of the sample surface. The naturally occurring isotopes of alkali and silver ions are resolved using time of flight mass spectrometer. Further increase in laser energy shows the appearance of Al, Cr, and Fe ions in the mass spectra. This indicates the penetration laser beam beyond the sample surface leading to the ablation of sample target at higher energies. The simultaneous appearance of atomic ions from the sample target at relatively higher laser energies hampers the unambiguous identification of amino acid residues from the biomolecular ions in MALDI-MS.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases
Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. Here, one set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.
59 BASIC BIOLOGICAL SCIENCES↗
Fast internal dynamics in alcohol dehydrogenase
Large-scale domain motions in alcohol dehydrogenase (ADH) have been observed previously by neutron spin-echo spectroscopy (NSE). We have extended the investigation on the dynamics of ADH in solution by using high-resolution neutron time-of-flight (TOF) and neutron backscattering (BS) spectroscopy in the incoherent scattering range. The observed hydrogen dynamics were interpreted in terms of three mobility classes, which allowed a simultaneous description of the measured TOF and BS spectra. In addition to the slow global protein diffusion and domain motions observed by NSE, a fast internal process could be identified. Around one third of the protons in ADH participate in the fast localized diffusive motion. The diffusion coefficient of the fast internal motions is around two third of the value of the surrounding D{sub 2}O solvent. It is tempting to associate the fast internal process with solvent exposed amino acid residues with dangling side chains.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sterol regulatory element binding protein-1: Molecular cloning, tissue distribution and gene expression level in response to nutritional regulation in mud crab, Scylla paramamosain
Highlights: • The complete SREBP-1 cDNA sequence was cloned from the hepatopancreas of mud crab based on the RACE technology. • Tissue distribution analysis revealed that SREBP-1 transcripts were widely distributed in various organs, with higher mRNA levels in the eyestalk and cranial ganglia. • The expression level of SREBP-1 mRNA were up-regulated in proportion to the replacement of dietary fish oil with soybean oil. In the present study, SREBP-1 cDNA was cloned from the hepatopancreas of mud crab (Scylla paramamosain) and characterized by performing rapid-amplification of cDNA ends. The 3361bp long full-length cDNA encodes a polypeptide with 1039 amino acids. Tissue distribution analysis revealed that SREBP-1 transcripts were widely distributed in various organs, with higher mRNA levels in the eyestalk and cranial ganglia. Further, expression level of SREBP-1 mRNA were up-regulated in proportion to the replacement of dietary fish oil (FO) with soybean oil (SO). These results may contribute to better understanding of the long-chain polyunsaturated fatty acids (LC-PUFA) biosynthetic pathway and regulation mechanism in mud crab.
60 APPLIED LIFE SCIENCES↗
Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
60 APPLIED LIFE SCIENCES↗
Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019
Nontypeable Haemophilus influenzae is an opportunistic human pathogen causing otitis media in children and chronic bronchitis and pneumonia in patients with chronic obstructive pulmonary disease. The outer membrane of nontypeable H. influenzae is dominated by lipooligosaccharides (LOS), many of which incorporate sialic acid as a terminal nonreducing sugar. Sialic acid has been demonstrated to be an important factor in the survival of the bacteria within the host environment. H. influenzae is incapable of synthesizing sialic acid and is dependent on scavenging free sialic acid from the host environment. To achieve this, H. influenzae utilizes a tripartite ATP-independent periplasmic transporter. In this study, we characterize the binding site of the extracytoplasmic solute receptor (SiaP) from nontypeable H. influenzae strain 2019. A crystal structure of N-acetyl-5-neuraminic acid (Neu5Ac)-bound SiaP was determined to 1.4 {angstrom} resolution. Thermodynamic characterization of Neu5Ac binding shows this interaction is enthalpically driven with a substantial unfavorable contribution from entropy. This is expected because the binding of SiaP to Neu5Ac is mediated by numerous hydrogen bonds and has several buried water molecules. Point mutations targeting specific amino acids were introduced in the putative binding site. Complementation with the mutated siaP constructs resulted either in full, partial, or no complementation, depending on the role of specific residues. Mass spectrometry analysis of the O-deacylated LOS of the R127K point mutation confirmed the observation of reduced incorporation of Neu5Ac into the LOS. The decreased ability of H. influenzae to import sialic acid had negative effects on resistance to complement-mediated killing and viability of biofilms in vitro, confirming the importance of sialic acid transport to the bacterium.
08 HYDROGEN↗
Cyanide binding to human plasma heme-hemopexin: A comparative study
Highlights: Black-Right-Pointing-Pointer Cyanide binding to ferric HHPX-heme-Fe. Black-Right-Pointing-Pointer Cyanide binding to ferrous HHPX-heme-Fe. Black-Right-Pointing-Pointer Dithionite-mediated reduction of ferric HHPX-heme-Fe-cyanide. Black-Right-Pointing-Pointer Cyanide binding to HHPX-heme-Fe is limited by ligand deprotonation. Black-Right-Pointing-Pointer Cyanide dissociation from HHPX-heme-Fe-cyanide is limited by ligand protonation. -- Abstract: Hemopexin (HPX) displays a pivotal role in heme scavenging and delivery to the liver. In turn, heme-Fe-hemopexin (HPX-heme-Fe) displays heme-based spectroscopic and reactivity properties. Here, kinetics and thermodynamics of cyanide binding to ferric and ferrous hexa-coordinate human plasma HPX-heme-Fe (HHPX-heme-Fe(III) and HHPX-heme-Fe(II), respectively), and for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex, at pH 7.4 and 20.0 Degree-Sign C, are reported. Values of thermodynamic and kinetic parameters for cyanide binding to HHPX-heme-Fe(III) and HHPX-heme-Fe(II) are K = (4.1 {+-} 0.4) Multiplication-Sign 10{sup -6} M, k{sub on} = (6.9 {+-} 0.5) Multiplication-Sign 10{sup 1} M{sup -1} s{sup -1}, and k{sub off} = 2.8 Multiplication-Sign 10{sup -4} s{sup -1}; and H = (6 {+-} 1) Multiplication-Sign 10{sup -1} M, h{sub on} = 1.2 Multiplication-Sign 10{sup -1} M{sup -1} s{sup -1}, and h{sub off} = (7.1 {+-} 0.8) Multiplication-Sign 10{sup -2} s{sup -1}, respectively. The value of the rate constant for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex is l = 8.9 {+-} 0.8 M{sup -1/2} s{sup -1}. HHPX-heme-Fe reactivity is modulated by proton acceptor/donor amino acid residue(s) (e.g., His236) assisting the deprotonation and protonation of the incoming and outgoing ligand, respectively.
60 APPLIED LIFE SCIENCES↗
Carbon dioxide control for manned spacecraft
Regenerative amino acid salt sorber and other means to control carbon dioxide and reclaim oxygen during manned missions up to 180 days
CARBON DIOXIDE REMOVAL↗
A Survey of Thermodynamic Properties of the Compounds of the Elements CHNOPS NINTH Preliminary Report, 1 Jul. - 30 Sep. 1966
Thermodynamic properties of amino acids plus furan and urea, and inorganic and organic compounds
ORGANIC COMPOUND↗
The role of N-terminal segment and membrane association in MyD88-mediated signaling
Highlights: • 21 AA MYD88 deletion mutant fails to support MyD88-mediated signaling. • WT MyD88 and 21 AA NTD peptide bind to the phosphatidic acid (PA). • Anchoring of MyD88 to cell membrane and addition of PA augments cell signaling. MyD88 is a central signaling mediator of innate immunity, composed of the N-terminal death (DD) and C-terminal Toll/interleukin-1 receptor (TIR) domain linked by an intermediary (INT) domain. We showed that the N-terminal domain (NTD), composed of apparently unstructured 21 amino-acid residues, is involved in localization and clustering of MyD88 and is required for the efficient signaling, since the deletion mutant is unable to reconstitute MyD88-dependent signaling. Furthermore, we found that the NTD peptide interacts with phosphatidic acid, which potentiates MyD88-mediated signaling through TLRs. Propranolol and expression of lysophosphatidyl acid acyltransferase 1, which increase the level of phosphatidic acid augment cell activation via MyD88. Moreover, anchoring of MyD88 to the cell membrane augments signaling supporting the importance of membrane localization in MyD88-mediated signaling.
60 APPLIED LIFE SCIENCES↗
Synthesis and structural characterization of a new chiral porous hybrid organic–inorganic material based on γ-zirconium phosphates and L-(+)-phosphoserine
In the present work, a chiral layered derivative of γ-zirconium phosphate (γ-ZrP) containing L-(+)-phosphoserine (γ-ZrP-PS*) covalently attached to inorganic layers has been prepared by means of topotactic exchange reaction. This organic–inorganic derivative is characterized by X-ray diffractometry, Solid {sup 13}C–NMR and FT-IR spectrophotometries and thermal analyses. A maximum level of topotactic replacement of 20% is achieved. Under both the acidic environment of the interlayer region of γ-ZrP and the acidic synthesis conditions, the hydrolysis of the ester bond of PS* is expected to take place to some extent. For this reason, it was impossible to exceed the recent percentage, which in turn reflects the relative moderate stability of the above mentioned bond under these conditions. In order to be more certain with regard to an expected further hydrolysis for this bond after separation, a sample of γ-ZrP-PS* was stored in a desiccator over a saturated solution of BaCl{sub 2} (90% relative humidity) for three months, and then the sample re-analyzed once again. Surprisingly, the results show that the sample still keeps almost the same level of exchange (i.e., 20%). Second, it is revealed that the sample almost gives the same spectroscopic and thermal behavior. This could be attributed to the less acidic character of the partially exchanged inorganic layers of the sample in comparison with that of the precursor γ-ZrP. Therefore, the PS* molecules persist and stay there into the interlayer gallery without further hydrolysis. - Graphical abstract: • Red: oxygen • White: zirconium • Cyan: carbon • Yellow: phosphorus • Blue: nitrogen. Highlights: • L-(+)-Phosphoserine (PS*) is exchanged with γ-ZrP by means of topotactic exchange. • The maximum exchange level is 20%. • γ-ZrP is functionalized with chiral amino acid group. • γ-ZrP-PS* has large chiral space for huge guest molecules to be intercalated.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nuclear import of influenza B virus nucleoprotein: Involvement of an N-terminal nuclear localization signal and a cleavage-protection motif
The nucleoprotein of influenza B virus (BNP) shares several characteristics with its influenza A virus counterpart (ANP), including localization in the host's nucleus. However, while the nuclear localization signal(s) (NLS) of ANP are well characterized, little is known about those of BNP. In this study, we showed that the fusion protein bearing the BNP N-terminus fused with GFP (N70–GFP) is exclusively nuclear, and identified a highly conserved KRXR motif spanning residues 44–47 as a putative NLS. In addition, we demonstrated that residues 3–15 of BNP, though not an NLS, are also crucial for nuclear import. Results from mutational analyses of N70–GFP and the full-length BNP suggest that this region may be required for protection of the N-terminus from proteolytic cleavage. Altogether, we propose that the N-terminal region of BNP contains the NLS and cleavage-protection motif, which together drive its nuclear localization. - Highlights: • The N-terminal region of BNP is required for nuclear accumulation. • The conserved motif at position 44–47 is a putative nuclear localization signal. • The first 15 amino acids of BNP may function as a cleavage-protection motif. • BNP may get access to the nucleus via a mechanism distinct from ANP.
60 APPLIED LIFE SCIENCES↗
A pollen-specific novel calmodulin-binding protein with tetratricopeptide repeats
Calcium is essential for pollen germination and pollen tube growth. A large body of information has established a link between elevation of cytosolic Ca(2+) at the pollen tube tip and its growth. Since the action of Ca(2+) is primarily mediated by Ca(2+)-binding proteins such as calmodulin (CaM), identification of CaM-binding proteins in pollen should provide insights into the mechanisms by which Ca(2+) regulates pollen germination and tube growth. In this study, a CaM-binding protein from maize pollen (maize pollen calmodulin-binding protein, MPCBP) was isolated in a protein-protein interaction-based screening using (35)S-labeled CaM as a probe. MPCBP has a molecular mass of about 72 kDa and contains three tetratricopeptide repeats (TPR) suggesting that it is a member of the TPR family of proteins. MPCBP protein shares a high sequence identity with two hypothetical TPR-containing proteins from Arabidopsis. Using gel overlay assays and CaM-Sepharose binding, we show that the bacterially expressed MPCBP binds to bovine CaM and three CaM isoforms from Arabidopsis in a Ca(2+)-dependent manner. To map the CaM-binding domain several truncated versions of the MPCBP were expressed in bacteria and tested for their ability to bind CaM. Based on these studies, the CaM-binding domain was mapped to an 18-amino acid stretch between the first and second TPR regions. Gel and fluorescence shift assays performed with CaM and a CaM-binding synthetic peptide further confirmed MPCBP binding to CaM. Western, Northern, and reverse transcriptase-polymerase chain reaction analysis have shown that MPCBP expression is specific to pollen. MPCBP was detected in both soluble and microsomal proteins. Immunoblots showed the presence of MPCBP in mature and germinating pollen. Pollen-specific expression of MPCBP, its CaM-binding properties, and the presence of TPR motifs suggest a role for this protein in Ca(2+)-regulated events during pollen germination and growth.
NASA Discipline Plant Biology↗
Biochemical and functional analysis of CTR1, a protein kinase that negatively regulates ethylene signaling in Arabidopsis
CTR1 encodes a negative regulator of the ethylene response pathway in Arabidopsis thaliana. The C-terminal domain of CTR1 is similar to the Raf family of protein kinases, but its first two-thirds encodes a novel protein domain. We used a variety of approaches to investigate the function of these two CTR1 domains. Recombinant CTR1 protein was purified from a baculoviral expression system, and shown to possess intrinsic Ser/Thr protein kinase activity with enzymatic properties similar to Raf-1. Deletion of the N-terminal domain did not elevate the kinase activity of CTR1, indicating that, at least in vitro, this domain does not autoinhibit kinase function. Molecular analysis of loss-of-function ctr1 alleles indicated that several mutations disrupt the kinase catalytic domain, and in vitro studies confirmed that at least one of these eliminates kinase activity, which indicates that kinase activity is required for CTR1 function. One missense mutation, ctr1-8, was found to result from an amino acid substitution within a new conserved motif within the N-terminal domain. Ctr1-8 has no detectable effect on the kinase activity of CTR1 in vitro, but rather disrupts the interaction with the ethylene receptor ETR1. This mutation also disrupts the dominant negative effect that results from overexpression of the CTR1 amino-terminal domain in transgenic Arabidopsis. These results suggest that CTR1 interacts with ETR1 in vivo, and that this association is required to turn off the ethylene-signaling pathway.
Non-NASA Center↗
Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method
A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effect of the Liquid-Vacuum Transition on the Relative Abundances of Amino and Fatty Acids Sought as Biosignatures on Icy Ocean Worlds
Interpreting measurements by robotic missions searching for signs of life in material erupted by cryovolcanic ocean worlds (e.g., Enceladus, Europa, Ceres) requires linking the composition of this material to that of its subsurface liquid source. Irrespective of the properties of –and processes along– the path of ejection, material erupted on airless worlds undergoes a transition from liquid to vacuum. Here, we investigate experimentally the effect of a direct transition from liquid to vacuum environments on the relative abundances of amino and carboxylic (fatty) acids, a metric used to distinguish between biological and abiotic sources for these compounds. Amino acids were dissolved in parent solutions prepared with 1 wt.% NaCl and pH 9–10 to match properties inferred from Enceladus plume grains. Compositional analysis of the dry solids resulting from the injection of this solution into vacuum indicates a < 50% change in amino acid abundances relative to glycine. Injection of two fatty acids, phenylacetic acid (soluble and undersaturated in the parent solution) and palmitic acid (insoluble and supersaturated) resulted in a change of less than a factor of 7 in their relative abundances. At this bulk scale (all grains aggregated together), proportions of amino and fatty acids were sufficiently conserved to allow distinction between end-member example biological and abiotic sources. We did not find strong correlations between the relative enrichment or depletion of amino or fatty acids with molecular properties such as molecular mass, hydrophobicity, functionality, or charge, other than high under-or supersaturation. Most of the organic residue was deposited along the experimental injection path, which suggests that cryovolcanic conduit walls on icy ocean worlds may be enriched in organic material relative to material having undergone the liquid-vacuum transition.
Amino acids↗