Influence of C-H...O interactions on the structural stability of β-lactamases

β-Lactamases produced by pathogenic bacteria cleave β-lactam antibiotics and render them ineffective. Understanding the principles that govern the structural stability of β-lactamases requires elucidation of the nature of the interactions that are involved in stabilization. In the present study, we systematically analyze the influence of CH...O interactions on determining the specificity and stability of β-lactamases in relation to environmental preferences. It is interesting to note that all the residues located in the active site of β-lactamases are involved in CH...O interactions. A significant percentage of CH...O interactions have a higher conservation score and short-range interactions are the predominant type of interactions in β-lactamases. These results will be useful in understanding the stability patterns of β-lactamases.     

The effect of a Pro²⁸Thr point mutation on the local structure and stability of human galactokinase enzyme-a theoretical study

Galactokinase is responsible for the phosphorylation of α-d-galactose, which is an important step in the metabolism of the latter. Malfunctioning of galactokinase due to a single point mutation causes cataracts and, in serious cases, blindness. This paper reports a study of the Pro²⁸Thr point mutation using a variety of theories including molecular dynamics (MD), MM-PBSA/GBSA calculations and AIM analysis. Altered H-bonding networks were detected based on geometric and electron density criteria that resulted in local unfolding of the β-sheet secondary structure. Another consequence was the decrease in stability (5–7 kcal mol⁻¹) around this region, as confirmed by ΔG_bind calculations for the extracted part of the whole system. Local unfolding was verified by several other MD simulations performed with different duration, initial velocities and force field. Based on the results, we propose a possible mechanism for the unfolding caused by the Pro²⁸Thr point mutation.     

Insights into protein - DNA interactions, stability and allosteric communications: a computational study of mutSα-DNA recognition complexes

DNA mismatch repair proteins (MMR) maintain genetic stability by recognizing and repairing mismatched bases and insertion/deletion loops mistakenly incorporated during DNA replication, and initiate cellular response to certain types of DNA damage. Loss of MMR in mammalian cells has been linked to resistance to certain DNA damaging chemotherapeutic agents, as well as to increase risk of cancer. Mismatch repair pathway is considered to involve the concerted action of at least 20 proteins. The most abundant MMR mismatch-binding factor in eukaryotes, MutSα, recognizes and initiates the repair of base-base mismatches and small insertion/deletion. We performed molecular dynamics simulations on mismatched and damaged MutSα-DNA complexes. A comprehensive DNA binding site analysis of relevant conformations shows that MutSα proteins recognize the mismatched and platinum cross-linked DNA substrates in significantly different modes. Distinctive conformational changes associated with MutSα binding to mismatched and damaged DNA have been identified and they provide insight into the involvement of MMR proteins in DNA-repair and DNA-damage pathways. Stability and allosteric interactions at the heterodimer interface associated with the mismatch and damage recognition step allow for prediction of key residues in MMR cancer-causing mutations. A rigorous hydrogen bonding analysis for ADP molecules at the ATPase binding sites is also presented. Due to extended number of known MMR cancer causing mutations among the residues proved to make specific contacts with ADP molecules, recommendations for further studies on similar mutagenic effects were made.     

Zwitterionic conformers of pyrrolysine and their interactions with metal ions—a theoretical study

A total of 16 pyrrolysine conformers in their zwitterionic forms are studied in gas and simulated aqueous phase using a polarizable continuum model (PCM). These conformers are selected on the basis of our study on the intrinsic conformational properties of non-ionic pyrrolysine molecule in gas phase [Das and Mandal (2013) J Mol Model 19:1695?1704]. In aqueous phase, the stable zwitterionic pyrrolysine conformers are characterized by full geometry optimization and vibrational frequency calculations using B3LYP/6-311++G(d,p) level of theory. Single point calculations are also carried out at MP2/6-311++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. The calculated relative energy range of the conformers at B3LYP/6-311++G(d,p) level is 5.19 kcal mol^?1 whereas the same obtained by single point calculations at MP2/6-311++G(d,p) level is 4.58 kcal mol^?1. A thorough analysis reveals that four types of intramolecular H-bonds are present in the conformers; all of which play key roles in determining the energetics and in imparting the observed conformations to the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of the H-bonds. This study also points out that conformers with diverse structural motifs may differ in their thermodynamical stability by a narrow range of relative energy. The effects of metal coordination on the relative stability order and structural features of the conformers are examined by complexing five zwitterionic conformers of pyrrolysine with Cu⁺² through their carboxylate groups. The interaction enthalpies and Gibbs energies, rotational constants, vibrational frequencies and dipole moments of the metal complexes calculated at B3LYP level are also reported. The zwitterionic conformers of pyrrolysine are not stable in gas phase; after geometry optimization they are converted to the non-ionic forms.     

“Russian doll” complexes of [n]cycloparaphenylenes: a theoretical study

The formation of "Russian doll" complexes consisting of [n]cycloparaphenylenes was predicted using quantum chemistry tools. The electronic structures of multiple inclusion complexes containing up to four macrocycles were explored at the M06-2X/6-31G* level of theory. The binding energy between the macrocycles increases from the center to the periphery of the complex and can be >60?kcal?mol(-1) for macrocycles containing 14 and 19 repeating units. It has been demonstrated that additional electrostatic interactions originating from the asymmetric electron density distribution observed when comparing the concave and convex macrocycle sides are responsible for the high binding energies in these Russian doll complexes. Oxidation or reduction of the Russian doll complexes creates polarons that are delocalized across the complexes. In the case of polaron cations, most of the polarons are localized at the macrocycle with the smallest ionization potential; for polaron anions, the negative charge is localized across the outer rings of the complex. Because anion polarons are more delocalized than cation polarons, the relaxation energies of the polaron anions were found to be smaller than those of the polaron cations.     

Influence of cation–π interactions to the structural stability of prokaryotic and eukaryotic translation elongation factors

We have investigated the role of cation–π interactions on translation elongation factors. In our investigation, an average of four significant cation–π interactions were found, that is, an average of one cation–π interaction per 44 residues in the ten elongation factors were observed. The analysis on the influence of short (<±4), medium (>±4 to <±20) and long (>20) range contacts showed that cation–π interactions are mainly formed by medium and long-range contacts. Arg-Tyr pair was found largest in number but energetic contribution of Arg-Trp pair was found most. Preferred secondary structural conformation analysis of the residues involved in cation–π interaction indicates that the cationic Arg prefers to be in helix and Lys having equal probability for helix and strand, whereas the aromatic Phe and Trp were found mostly in helix while Tyr in strand regions. The cation–π interaction residues involved in these proteins were found highly conserved with 48.86% residues having conservation score of ≥6. Analysis of secondary structure preference of the energetically significant cation–π residues in different solvent accessible range indicates that most of the π residues are found buried or partially buried whereas cationic residues were found mostly at the protein surface. The results presented in this study will be useful for structural stability studies in translation elongation factors.     

Influence of lunar phases on suicide: the end of a myth? A population-based study

The hypothesis of lunar influence on suicide remains widespread, despite the fact that little scientific evidence to substantiate it. We conducted a population-based study to assess the influence of the lunar phases on suicides according to age, sex, and chosen method. The study included all suicides in Middle Franconia between 1998 and 2003. From a population-based sample of 3351 events, the files of 3054 suicides (1949 males and 1105 females) were complete for the study variables. Data were categorized by lunar phase, sex, age, and chosen method—“violent” vs. “non-violent” acts. No significant relationship was detected between the full, absent, and moon's interphases and suicide incidence. Nevertheless, there was a weak association between the absent moon and choice of a non-violent suicide method in men aged less than the median of 40.2 yrs. There was no evidence of a relationship between suicide and lunar phase. Some explanations for this phenomenon are discussed.     

Activity and stability of hyperthermophilic enzymes: a comparative study on two archaeal β-glycosidases

Sβgly and CelB are well-studied hyperthermophilic glycosyl hydrolases, isolated from the Archaea Sulfolobus solfataricus and Pyrococcus furiosus, respectively. Previous studies revealed that the two enzymes are phylogenetically related; they are very active and stable at high temperatures, and their overall three-dimensional structure is very well conserved. To acquire insight in the molecular determinants of thermostability and thermoactivity of these enzymes, we have performed a detailed comparison, under identical conditions, of enzymological and biochemical parameters of Sβgly and CelB, and we have probed the basis of their stability by perturbations induced by temperature, pH, ionic strength, and detergents. The major result of the present study is that, although the two enzymes are remarkably similar with respect to kinetic parameters, substrate specificity, and reaction mechanism, they are strikingly different in stability to the different physical or chemical perturbations induced. These results provide useful information for the design of further experiments aimed at understanding the structure–function relationships in these enzymes. Received: May 20, 1999 / Accepted: January 10, 2000     

Synthesis and properties of (2-pyridyl)alkylamine- and (2-pyridyl)alkylamine–amide-coordinated copper(II) complexes: Structures and non-covalent interactions

Reaction of the ligand N-methyl-N-((6-pivaloylamido-2-pyridyl)methyl)-N-(2-pyridylethyl)amine (mpppa) with equimolar amounts of [Cu(H₂O)₆][ClO₄]₂ or CuCl₂ · 2H₂O in MeCN afforded mononuclear copper(II) complexes [Cu(mpppa)][ClO₄]₂ (1) and [Cu(mpppa)Cl₂] (2). Crystal structure analysis reveals CuN₃O (two pyridyl, an aliphatic amine, and an amide oxygen) coordination in 1 and CuN₃Cl₂ (two pyridyl, an aliphatic amine, and two chlorides) coordination in 2. Crystal packing diagram of 1 reveals that one of the perchlorate counteranions provides weak coordination to copper(II) centers and in turn the copper(II) centers assume pseudo-six-coordination, generating 1D chain. Notably, one of the copper(II)-coordinated chloride ions in 2 participates in an intramolecular N–H?Cl interaction. Intermolecular C–H?Cl interactions in the solid state generate helical structure. Spectroscopic (IR, UV–Vis, and EPR) and redox properties of the two complexes have been investigated and compared.     

Characterization of halogen···halogen interactions in crystalline dihalomethane compounds (CH2Cl2, CH2Br2 and CH2I2): a theoretical study

To improve understanding of the unimolecular decomposition mechanism of 1,2,4-butanetriol trinitrate (BTTN) in the gas phase, density functional theory calculations were performed to determine various decomposition pathways at the B3LYP/6-311G** level. Two main mechanisms for the unimolecular decomposition of BTTN were found. In the first, homolysis of one of the O–NO₂ bonds occurs to form ?NO₂ and CH₂ONO₂CHONO₂CH₂CH₂O?, which subsequently decomposes to form CH₃CHO + ?CHO + 3NO₂ + HCHO. In the second, successive HONO elimination reactions yield three HONO and OHCCH₂CHONO₂CH₂ONO₂ fragments, which subsequently decompose to form CH₃CHO + 2CO + 3HONO. We also found that the first pathway has a slightly lower activation energy than the second. The results show that the pathway involving O–NO₂ cleavage is slightly more energetically favorable than that involving HONO elimination.     

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

Glycogen synthase kinase 3β (GSK-3β) is a serine-threonine kinase belonging to the CMGC family that plays a key role in many biological processes, such as glucose metabolism, cell cycle regulation, and proliferation. Like most protein kinases, GSK-3β is regulated via multiple pathways and sites. We performed all-atom molecular dynamics simulations on the unphosphorylated and phosphorylated unbound GSK-3β and the phosphorylated GSK-3β bound to a peptide substrate, its product, and a derived inhibitor. We found that GSK-3β autophosphorylation at residue Tyr(216) results in widening of the catalytic groove, thereby facilitating substrate access. In addition, we studied the interactions of the phosphorylated GSK-3β with a substrate and peptide inhibitor located at the active site and observed higher affinity of the inhibitor to the kinase. Furthermore, we detected a potential remote binding site which was previously identified in other kinases. In agreement with experiments we observed that binding of specific peptides at this remote site leads to stabilization of the activation loop located in the active site. We speculate that this stabilization could enhance the catalytic activity of the kinase. We point to this remote site as being structurally conserved and suggest that the allosteric phenomenon observed here may occur in the protein kinase superfamily.     

Impact of fluorination on proteolytic stability of peptides: a case study with α-chymotrypsin and pepsin

Protease stability is a key consideration in the development of peptide-based drugs. A major approach to increase the bioavailability of pharmacologically active peptides is the incorporation of non-natural amino acids. Due to the unique properties of fluorine, fluorinated organic molecules have proven useful in the development of therapeutically active small molecules as well as in materials and crop science. This study presents data on the ability of fluorinated amino acids to influence proteolytic stability when present in peptide sequences that are based on ideal protease substrates. Different model peptides containing fluorinated amino acids or ethylglycine in the P2, P1′or P2′ positions were designed according to the specificities of the serine protease, α-chymotrypsin (EC 3.4.21.1) or the aspartic protease, pepsin (EC 3.4.23.1). The proteolytic stability of the peptides toward these enzymes was determined by an analytical RP-HPLC assay with fluorescence detection and compared to a control sequence. Molecular modeling was used to support the interpretation of the structure–activity relationship based on the analysis of potential ligand-enzyme interactions. Surprisingly, an increase in proteolytic stability was observed only in a few cases. Thus, this systematic study shows that the proteolytic stability of fluorinated peptides is not predictable, but rather is a very complex phenomenon that depends on the particular enzyme, the position of the substitution relative to the cleavage site and the fluorine content of the side chain.     

Resonance Raman studies of the peroxotitanate(IV) complexes K2(Ti(O2)(SO4)2)·5H2O and K2(Ti(O2)(C2O4)2)·3H2O

The resonance Raman spectra of K₂(Ti(O₂)(SO₄)₂)·5H₂O and K₂(Ti(O₂)(C₂O₄)₂)·3H₂O are recorded. The results are consistent with the triangular structure of the peroxotitanium unit, Ti(O₂), with C_2ν symmetry. The ν(OO), ν_s(TiO) and ν_as(TiO) are observed around 890, 610 and 535 cm⁻¹, respectively. The resonance effects are shown to be associated with the 425 nm absorption band. This band is assigned to the O₂²⁻ → Ti(IV) charge-transfer transition. The calculated force constant values for the O₂²⁻ and TiO bonds are 320 and 275 N m⁻¹, respectively.     

Influence of the nuclear and extranuclear substitution on the singlet molecular oxygen [O 2(1Δg)]-mediated photooxidation of tyrosine derivatives: A kinetic study

Summary The effect of the substitution pattern on the kinetics of the Type II (O₂(¹_g)-mediated) dye-sensitized photooxidation of a series of nine tyrosine derivatives was investigated. Overall (k_t) and reactive (k_r) rate constants for the interaction of the excited oxygen species with the amino acid derivatives were determined. A parallel study on solvent and pH effects was carried out.The presence of different substituents in nuclear positions or in the amino acid side chain greatly affect the photooxidation rates.An upper limit for photooxidation quantum yield, calculated from the kinetic data, varies from 0.03 to 0.25, being the higher for halogenated tyrosines and the lower for esterified tyrosines and for the nitro-derivative.The variation of solvent polarity and pH of the reaction medium confirm that the presence of the ionized phenolate group in tyrosine, clearly dominates the quenching process. As already postulated for generic phenolic derivatives, it proceeds through a polar intermediate complex which posses some component of charge-transfer character.Esterification of the carboxilic acid of tyrosine selectively decreases the contribution of the reactive step to the overall process of O₂(¹_g) quenching. An amide group in the same position does not produce noticiable changes in this sense. The presence of a highly deactivating nitro group in nuclear positions greatly diminishes the magnitude of both overall and reactive interactions.For all three, o-, m- and p-tyrosine the values of photooxidation quantum yields show an excellent parallelism with the rates of consumption of the — NH₂ group of the amino acid chain, upon sensitized irradiation. It could react, in the cases of 0- and m-tyrosine in a secondary, non photochemical, step.Abbreviations O ₂(³ _g ^– ) ground state triplet oxygen - O ₂(¹_g) singlet molecular oxygen - Tyr L tyrosine - TyrD tyrosine derivatives - Eos eosine - RB rose bengal - FFA furfuryl alcohol - DMA 9, 10-dimethyl anthracene     

Influence of counter anions on the structures and magnetic properties of trinuclear Cu(II) complexes containing a μ3-OH core and Schiff base ligands

Four trinuclear Cu(II) complexes, [(CuL¹)₃(μ₃-OH)](NO₃)₂ (1), [(CuL²)₃(μ₃-OH)](I)₂·H₂O (2), [(CuL³)₃(μ₃-OH)](I)₂ (3) and [(CuL¹)₃(μ₃-OH)][Cu^II₃] (4), where HL¹ (8-amino-4-methyl-5-azaoct-3-en-2-one), HL² [7-amino-4-methyl-5-azaoct-3-en-2-one] and HL³ [7-amino-4-methyl-5-azahept-3-en-2-one] are the three tridentate Schiff bases, have been synthesized and structurally characterized by X-ray crystallography. All four complexes contain a partial cubane core, [(CuL)₃(μ₃-OH)]²⁺ in which the three [CuL] subunits are interconnected through two types of oxygen bridges afforded by the oxygen atoms of the ligands and the central OH⁻ group. The copper(II) ions are in a distorted square-pyramidal environment. The equatorial plane consists of the bridging oxygen of the central OH⁻ group together with three atoms (N, N, O) from the Schiff base. The oxygen atom of the Schiff base also coordinates to the axial position of Cu(II) of another subunit to form the cyclic trimer. Magnetic susceptibilities have been determined for these complexes over the temperature range of 2-300 K. The isotropic Hamiltonian, H = −J₁₂S₁S₂ − J₁₃S₁S₃ − J₂₃S₂S₃ has been used to interpret the magnetic data. The best fit parameters obtained are: J = −54.98 cm⁻¹, g = 2.24 for 1; J = −56.66 cm⁻¹, g = 2.19 for 2;J = −44.39 cm⁻¹, g = 2.16 for 3; J = −89.92 cm⁻¹, g = 2.25 for 4. The EPR data at low temperature indicate that the phenomenon of spin frustration occurs for complexes 1-3.     

Pathogen–pathogen interactions: a comparative study of Escherichia coli interactions with the clinical and environmental isolates of Acanthamoeba

In this study, we compared the interactions of invasive and non-invasive strains of E. coli with clinical and environmental isolates of Acanthamoeba. The environmental isolate of Acanthamoeba exhibited significantly higher association with E. coli compared with the clinical isolates of Acanthamoeba. The ratio of E. coli per amoebae was more than 8-fold higher in the environmental isolate compared with the clinical isolates of Acanthamoeba. Interestingly, non-pathogenic environmental Acanthamoeba showed uptake and/or survival of the non-invasive E. coli. In contrast, clinical isolates of Acanthamoeba did not support uptake and/or survival of non-invasive E. coli. Using several mutants derived from K1, we demonstrated that outer membrane protein A (OmpA) and lipopolysaccharide (LPS) are crucial bacterial determinants responsible for E. coli K1 interactions and in the intracellular survival of E. coli in Acanthamoeba. The use of Acanthamoeba as a model to study E. coli K1 pathogenesis and to understand bacterial immune evasion strategies is discussed further.     

Ground state intermolecular proton transfer in the supersystems thymine–(H2O)n and thymine–(CH3OH)n, n = 1,2: a theoretical study

Twelve binary and eight ternary supersystems between thymine and methanol, and water were investigated in the ground state at the B3LYP and MP2 levels of theory using B3LYP/6-311 + + G(d,p) basis functions. The thermodynamics of complex formations and the mechanisms of intermolecular proton transfers were clarified in order to find out the most stable H-boned system. It was established that the energy barriers of the water/methanol-assisted proton transfers are several times lower than those of the intramolecular proton transfers in the DNA/RNA bases. The X-ray powder spectra of thymine, and this precrystallized from water and methanol showed that water molecules are incorporated in the crystal lattice of thymine forming H-bridges between thymine molecules. Figure Intermolecular H-bonding of thymine     

Influence of seeing a female on the male–male interactions of a jumping spider, Hypoblemum albovittatum

An important prediction from game theory is that resource value influences the level to which competitors will escalate conflict. An earlier study considered whether this prediction applies to the male–male interactions of Hypoblemum albovittatum, a jumping spider (Salticidae) from New Zealand. The males of this species escalated conflicts in the presence of a moving mount made from a conspecific female. However, because the control was only a similar-sized motionless cork, an alternative hypothesis (that the cue for escalation is seeing movement of any female-size object, rather than seeing specifically a female) was not ruled out. Here we show that a moving cork, without a mount present, is indeed sufficient to cause males to escalate, but a moving mount (made from a conspecific female) causes males to escalate further. The level of escalation in the presence of a moving mount made from prey (housefly) or from a rival (conspecific male) did not differ significantly from the level of escalation when only a moving cork was present. These findings suggest that, although seeing a moving object similar in size to a conspecific female is sufficient for priming males to escalate, males can also discern by sight that specifically a female is present and, when they have this precise information, they make strategic decisions to escalate conflict further.