System Dy-Fe-O: thermodynamic properties of ternary oxides using Calvet calorimetry and solid-state electrochemical cell

The enthalpy increments and the standard molar Gibbs energies of formation-of DyFeO3(s) and Dy3Fe5O12(s) have been measured using a Calvet micro-calorimeter and a solid oxide galvanic cell, respectively. A co-operative phase transition, related to anti-ferromagnetic to paramagnetic transformation, is apparent. from the heat capacity data for DyFeO3 at similar to 648 K. A similar type of phase transition has been observed for Dy3Fe5O12 at similar to 560 K which is related to ferrimagnetic to paramagnetic transformation. Enthalpy increment data for DyFeO3(s) and Dy3Fe5O12(s), except in the vicinity of the second-order transition, can be represented by the following polynomial expressions:{H(0)m(T) - H(0)m(298.15 K)) (Jmol(-1)) (+/-1.1%) = -52754 + 142.9 x (T (K)) + 2.48 x 10(-3) x (T (K))(2) + 2.951 x 10(6) x (T (K))(-1); (298.15 less than or equal to T (K) less than or equal to 1000) for DyFeO3(s), and {H(0)m(T) - H(0)m(298.15 K)} (Jmol(-1)) (+/-1.2%) = -191048 + 545.0 x (T - (K)) + 2.0 x 10(-5) x (T (K))(2) + 8.513 x 10(6) x (T (K))(-1); (208.15 less than or equal to T (K) less than or equal to 1000)for Dy3Fe5O12(s). The reversible emfs of the solid-state electrochemical cells: (-)Pt/{DyFeO3(s) + Dy2O3(s) + Fe(s)}/YDT/CSZ//{Fe(s) + Fe0.95O(s)}/Pt(+) and (-)Pt/{Fe(s) + Fe0.95O(s)}//CSZ//{DyFeO3(s) + Dy3Fe5O12(s) + Fe3O4(s)}/Pt(+), were measured in the temperature range from 1021 to 1250 K and 1035 to 1250 K, respectively. The standard Gibbs energies of formation of solid DyFeO3 and Dy3Fe5O12 calculated by the least squares regression analysis of the data obtained in the present study, and data for Fe0.95O and Dy2O3 from the literature, are given by Delta(f)G(0)m(DyFeO3,s)(kJmol(-1))(+/-3.2)= -1339.9 + 0.2473 x (T(K)); (1021 less than or equal to T (K) less than or equal to 1548)and D(f)G(0)m(Dy3Fe5O12,s) (kJmol(-1)) (+/-3.5) = -4850.4 + 0.9846 x (T (K)); (1035 less than or equal to T (K) less than or equal to 1250) The uncertainty estimates for Delta(f)G(0)m include the standard deviation in the emf and uncertainty in the data taken from the literature. Based on the thermodynamic information, oxygen potential diagram and chemical potential diagrams for the system Dy-Fe-O were developed at 1250 K. (C) 2002 Editions scientifiques et medicales Elsevier SAS. All rights reserved.

Thermodynamic studies on NdFeO3(s)

The enthalpy increments and the standard molar Gibbs energy of formation of NdFeO3(s) have been measured using a hightemperature Calvet microcalorimeter and a solid oxide galvanic cell, respectively. A lambda-type transition, related to magnetic order-disorder transformation (antiferromagnetic to paramagnetic), is apparent from the heat capacity data at similar to 687 K. Enthalpy increments, except in the vicinity of transition, can be represented by a polynomial expression: {Hdegrees(m)(T)-Hdegrees(m) (298.15 K)} /J(.)mol(-1) (+/- 0.7%)=-53625.6+146.0(T/K) +1.150 X 10(-4)(T/K)(2) +3.007 x 10(6)(T/K)(-1); (298.15 less than or equal to T/K less than or equal to 1000). The heat capacity, the first differential of {Hdegrees(m)(T)-Hdegrees(m)(298.15 K)}with respect to temperature, is given by Cdegrees(pm)/J(.)K(-1.)mol(-1)=146.0+ 2.30x10(-4) (T/K) - 3.007 X 10(6)(T/K)(-2). The reversible emf's of the cell, (-) Pt/{NdFeO3(s) +Nd2O3(s)+Fe(s)}//YDT/CSZ// Fe(s)+'FeO'(s)}/Pt(+), were measured in the temperature range from 1004 to 1208 K. It can be represented within experimental error by a linear equation: E/V=(0.1418 +/- 0.0003)-(3.890 +/- 0.023) x 10(-5)(T/K). The Gibbs energy of formation of solid NdFeO, calculated by the least-squares regression analysis of the data obtained in the present study, and data for Fe0.95O and Nd2O3 from the literature, is given by Delta(f)Gdegrees(m)(NdFeO3 s)/kJ (.) mol(-1)( +/- 2.0)=1345.9+0.2542(T/K); (1000 less than or equal to T/K less than or equal to 1650). The error in Delta(f)Gdegrees(m)(NdFeO3, s, T) includes the standard deviation in emf and the uncertainty in the data taken from the literature. Values of Delta(f)Hdegrees(m)(NdFeO3, s, 298.15 K) and Sdegrees(m) (NdFeO3 s, 298.15 K) calculated by the second law method are - 1362.5 (+/-6) kJ (.) mol(-1) and 123.9 (+/-2.5) J (.) K-1 (.) mol(-1), respectively. Based on the thermodynamic information, an oxygen potential diagram for the system Nd-Fe-O was developed at 1350 K. (C) 2002 Elsevier Science (USA).

Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

Deiodination of Thyroid Hormones by Iodothyronine Deiodinase Mimics: Does an Increase in the Reactivity Alter the Regioselectivity?

Organoselenium compounds as functional mimics of iodothyronine deiodinase are described. The naphthyl-based compounds having two selenol groups are remarkably efficient in the inner-ring deiodination of thyroxine. The introduction of a basic amino group in close proximity to one of the selenol moieties enhances the deiodination. This study suggests that an increase in the nucleophilic reactivity of the conserved Cys residue at the active site of deiodinases is very important for effective deiodination.

The destabilization of human GCAP1 by a proline to leucine mutation might cause cone-rod dystrophy

Guanylate cyclase activating protein-1 (GCAP1) is required for activation of retinal guanylate cyclase-1 (RetGC1), which is essential for recovery of photoreceptor cells to the dark state. In this paper, experimentally derived observations are reported that help in explaining why a proline→leucine mutation at position 50 of human GCAP1 results in cone–rod dystrophy in a family carrying this mutation. The primary amino acid sequence of wild-type GCAP1 was mutated using site-directed mutagenesis to give a leucine at position 50. In addition, serine replaced a glutamic acid residue at position 6 to promote N‐terminal myristoylation, yielding the construct GCAP1 E6S/P50L. The enzyme was over-expressed in Escherichia coli cells, isolated and purified before being used in assays with RetGC1, characterized by circular dichroism (CD) spectroscopy, and investigated for protease resistance and thermal stability. Assays of cyclic guanosine monophosphate (cGMP) synthesis from guanosine triphosphate by RetGC1 in the presence of E6S/P50L showed that E6S/P50L could activate RetGC1 and displayed similar calcium sensitivity to wild-type GCAP1. In addition, E6S/P50L and wild-type GCAP1 possess similar CD spectra. However, there was a marked increase in the susceptibility to protease degradation and also a reduction in the thermal stability of E6S/P50L as observed by both the cGMP assay and CD spectroscopy. It is therefore suggested that although GCAP1 E6S/P50L has a similar activity and calcium dependency profile to the wild-type GCAP1, its lower stability could reduce its cellular concentration, which would in turn alter [Ca2+] and result in death of cells.

Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair

Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg 128 into the DNA double helix and its interaction with the O6MG: C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.

Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large [Delta]Cp's

Maltose binding protein (MBP) is a large, monomeric two domain protein containing 370 amino acids. In the absence of denaturant at neutral pH, the protein is in the native state, while at pH 3.0 it forms a molten globule. The molten globule lacks a tertiary circular dichroism signal but has secondary structure similar to that of the native state. The molten globule binds 8-anilino-1-naphthalene sulfonate (ANS). The unfolding thermodynamics of MBP at both pHs were measured by carrying out a series of isothermal urea melts at temperatures ranging from 274–329 K. At 298 K, values of [Delta]G°, [Delta]Cp, and Cm were 3.1 ± 0.2 kcal mol−1, 5.9 ± 0.8 kcal mol−1 K−1 (15.9 cal (mol-residue)−1 K−1), and 0.8 M, respectively, at pH 3.0 and 14.5 ± 0.4 kcal mol−1, 8.3 ± 0.7 kcal mol−1 K−1 (22.4 kcal (mol-residue)−1 K−1), and 3.3 M, respectively, at pH 7.1. Guanidine hydrochloride denaturation at pH 7.1 gave values of [Delta]G° and [Delta]Cp similar to those obtained with urea. The m values for denaturation are strongly temperature dependent, in contrast to what has been previously observed for small globular proteins. The value of [Delta]Cp per mol-residue for the molten globule is comparable to corresponding values of [Delta]Cp for the unfolding of typical globular proteins and suggests that it is a highly ordered structure, unlike molten globules of many small proteins. The value of [Delta]Cp per mol-residue for the unfolding of the native state is among the highest currently known for any protein.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Thermodynamic properties of SmFeO3(S) and SM3R5O12(S)

The enthalpy increments and the standard molar Gibbs energy (G) of formation of SmFeO3(S) and SM3Fe5O12(s) have been measured using a Calvet micro-calorimeter and a solid oxide galvanic cell, respectively. A X-type transition, related to magnetic order-disorder transformation (antiferromagnetic to paramagnetic), is apparent from the heat capacity data at similar to673 K for SmFeO3(s) and at similar to560 K for Sm3Fe5O12(S). Enthalpy increment data for SmFeO3(s) and SM3Fe5O12(s), except in the vicinity of X-transition, can be represented by the following polynomial expressions: {H-m(0)(T) - H-m(0)(298.15 K){/J mol-(1)(+/-1.2%) = -54 532.8 + 147.4 . (T/K) + 1.2 . 10(-4) . (T/K)(2) +3.154 . 10(6) . (T/K)(-1); (298.15 less than or equal to T/K less than or equal to 1000) for SmFeO3(s), and {H-m(0)(T) - H-m(0)(298.15 K)}/J mol(-1) (+/-1.4%) = -192 763 + 554.7 . (T/K) + 2.0 . 10(-6) . (T/K)(2) + 8.161 . 10(6) - (T/K)(-1); (298.15 less than or equal to T/K less than or equal to 1000) for Sm3Fe5O12(s). The reversible emf of the solid-state electrochemical cells, (-)Pt/{SmFeO3(s) + Sm2O3(S) + Fe(s)) // YDT / CSZ // {Fe(s) + Fe0.95O(s)} / Pt(+) and (-)Pt/{Fe(s) + Fe0.95O(S)} // CSZ // {SmFeO3(s) + Sm3Fe5O12(s) + Fe3O4(s) / Pt(+), were measured in the temperature ranges of 1005-1259 K and 1030-1252 K, respectively. The standard molar G of formation of solid SmFeO3 and Sm3Fe5O12 calculated by the least squares regression analysis of the data obtained in the current study, and data for Fe0.95O and Sm2O3 from the literature, are given by: Delta(f)G(m)(0)(SmFeO3, s)/kj . mol(-1)(+/-2.0) = -1355.2 + 0.2643 . ; (1005 less than or equal to T/K less than or equal to 1570) and Delta(f)G(m)(0)(Sm3Fe5O12, s)/kj . mol(-1) (+/- 3.1) = -4891.0 + 1.0312 . (T/K); (1030 less than or equal to T/K less than or equal to 1252) The uncertainty estimates for Delta(f)G(m)(0) include the standard deviation in the emf and uncertainty in the data taken from the literature. Based on these thermodynamic data, the oxygen potential diagram for the system Sm-Fe-O was constructed at 1250 K.

Ligand-modulated Parallel Mechanical Unfolding Pathways of Maltose-binding Proteins

Protein folding and unfolding are complex phenomena, and it is accepted that multidomain proteins generally follow multiple pathways. Maltose-binding protein (MBP) is a large (a two-domain, 370-amino acid residue) bacterial periplasmic protein involved in maltose uptake. Despite the large size, it has been shown to exhibit an apparent two-state equilibrium unfolding in bulk experiments. Single-molecule studies can uncover rare events that are masked by averaging in bulk studies. Here, we use single-molecule force spectroscopy to study the mechanical unfolding pathways of MBP and its precursor protein (preMBP) in the presence and absence of ligands. Our results show that MBP exhibits kinetic partitioning on mechanical stretching and unfolds via two parallel pathways: one of them involves a mechanically stable intermediate (path I) whereas the other is devoid of it (path II). The apoMBP unfolds via path I in 62% of the mechanical unfolding events, and the remaining 38% follow path II. In the case of maltose-bound MBP, the protein unfolds via the intermediate in 79% of the cases, the remaining 21% via path II. Similarly, on binding to maltotriose, a ligand whose binding strength with the polyprotein is similar to that of maltose, the occurrence of the intermediate is comparable (82% via path I) with that of maltose. The precursor protein preMBP also shows a similar behavior upon mechanical unfolding. The percentages of molecules unfolding via path I are 53% in the apo form and 68% and 72% upon binding to maltose and maltotriose, respectively, for preMBP. These observations demonstrate that ligand binding can modulate the mechanical unfolding pathways of proteins by a kinetic partitioning mechanism. This could be a general mechanism in the unfolding of other large two-domain ligand-binding proteins of the bacterial periplasmic space.

Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB)

Lysine biosynthesis proceeds by the nucleotide-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) by dihydrodipicolinate reductase (DHDPR). The S. aureus DHDPR structure reveals different conformational states of this enzyme even in the absence of a substrate or nucleotide-cofactor. Despite lacking a conserved basic residue essential for NADPH interaction, S. aureus DHDPR differs from other homologues as NADPH is a more preferred co-factor than NADH. The structure provides a rationale-Lys35 compensates for the co-factor site mutation. These observations are significant for bi-ligand inhibitor design that relies on ligand-induced conformational changes as well as co-factor specificity for this important drug target. Structured summary of protein interactions: DHDPR binds to DHDPR by molecular sieving (View interaction). DHDPR binds to DHDPR by dynamic light scattering (View interaction). DHDPR binds to DHDPR by X-ray crystallography (View interaction). (C) 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical `b-ion' series, exhibiting initial backbone cleavage explicitly at the beta-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the `b' or/and the `y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the beta-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the `y-type'. Complementary NMR data showed that, while all metal ions were located around the beta-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent beta-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme. (C) 2011 Elsevier B.V. All rights reserved.

Accessing the disallowed conformations of peptides employing amide-to-imidate modification

Selective modification of the C-terminal amide in peptides to dihydrooxazine (a novel stable imidate isostere) by intramolecular nucleophilic cyclo-O-alkylation of the corresponding N-(3-bromopropyl)amides results in constraining of the C-terminal residue in natively disallowed conformations both in crystals and in solution.

Endonuclease Active Site Plasticity Allows DNA Cleavage with Diverse Alkaline Earth and Transition Metal Ions

A majority of enzymes show a high degree of specificity toward a particular metal ion in their catalytic reaction. However, Type II restriction endonuclease (REase) R.KpnI, which is the first member of the HNH superfamily of REases, exhibits extraordinary diversity in metal ion dependent DNA cleavage. Several alkaline earth and transition group metal ions induce high fidelity and promiscuous cleavage or inhibition depending upon their concentration. The metal ions having different ionic radii and co-ordination geometries readily replace each other from the enzyme's active site, revealing its plasticity. Ability of R KpnI to cleave DNA with both alkaline earth and transition group metal ions having varied ionic radii could imply utilization of different catalytic site(s). However, mutation of the invariant His residue of the HNH motif caused abolition of the enzyme activity with all of the cofactors, indicating that the enzyme follows a single metal ion catalytic mechanism for DNA cleavage. Indispensability of His in nucleophile activation together with broad cofactor tolerance of the enzyme indicates electrostatic stabilization function of metal ions during catalysis. Nevertheless, a second metal ion is recruited at higher concentrations to either induce promiscuity or inhibit the DNA cleavage. Regulation of the endonuclease activity and fidelity by a second metal ion binding is a unique feature of R.KpnI among REases and HNH nucleases. The active site plasticity of R.KpnI opens up avenues for redesigning cofactor specificities and generation of mutants specific to a particular metal ion.