Biomedical subjects

Arvi Rauk

Publications and source records attributed to Arvi Rauk.

11 recordsLinked to original sources

PubMed2006

Ab initio modelling of the structure and redox behaviour of copper(I) bound to a His-His model peptide: relevance to the beta-amyloid peptide of Alzheimer's disease.

A contributing factor to the pathology of Alzheimer's disease is the generation of reactive oxygen species, most probably a consequence of the beta-amyloid (Abeta) peptide coordinating copper ions. Experimental and theoretical results indicate that His13 and His14 are the two most firmly established ligands in the coordination sphere of Cu(II) bound to Abeta. Abeta1-42 is known to reduce Cu(II) to Cu(I). The Abeta-Cu(II) complex has been shown to catalytically generate H(2)O(2) from reducing agents and O(2). Cu(II) in the presence of Abeta has been reported to have a formal reduction potential of +0.72-0.77 V (vs. the standard hydrogen electrode). Quantum chemical calculations using the B3LYP hybrid density functional method with the 6-31G(d) basis set were performed to model the reduction of previously studied Cu(II) complexes representing the His13-His14 portion of Abeta (Raffa et al. in J. Biol. Inorg. Chem. 10:887-902, 2005). The effects of solvation were accommodated using the CPCM method. The most stable complex between Cu(I) and the model compound, 3-(5-imidazolyl)propionylhistamine (1) involves tricoordinated Cu(I) in a distorted-T geometry, with the Npi of both imidazoles as well as the oxygen of the backbone carbonyl bound to copper. This model would be the most likely representation of a Cu(I) binding site for a His-His peptide in aqueous solution. A variety of possible redox processes are discussed.

Alzheimer Disease↗

PubMed2006

Effect of side chains on competing pathways for beta-scission reactions of peptide-backbone alkoxyl radicals.

High-level quantum chemistry calculations have been carried out to investigate beta-scission reactions of alkoxyl radicals located at the alpha-carbon of a peptide backbone. This type of alkoxyl radical may undergo three possible beta-scission reactions, namely C-C beta-scission of the backbone, C-N beta-scission of the backbone, and C-R beta-scission of the side chain. We find that the rates for the C-C beta-scission reactions are all very fast, with rate constants of the order 10(12) s(-1) that are essentially independent of the side chain. The C-N beta-scission reactions are all slow, with rate constants that range from 10(-0.7) to 10(-4.5) s(-1). The rates of the C-R beta-scission reactions depend on the side chain and range from moderately fast (10(7) s(-1)) to very fast (10(12) s(-1)). The rates of the C-R beta-scission reactions correlate well with the relative stabilities of the resultant side-chain product radicals (*R), as reflected in calculated radical stabilization energies (RSEs). The order of stabilities for the side-chain fragment radicals for the natural amino acids is found to be Ala < Glu < Gln approximately Leu approximately Met approximately Lys approximately Arg < Asp approximately Ile approximately Asn approximately Val < Ser approximately Thr approximately Cys < Phe approximately Tyr approximately His approximately Trp. We predict that for side-chain C-R beta-scission reactions to effectively compete with the backbone C-C beta-scission reactions, the side-chain fragment radicals would generally need an RSE greater than approximately 30 kJ mol(-1). Thus, the residues that may lead to competitive side-chain beta-scission reactions are Ser, Thr, Cys, Phe, Tyr, His, and Trp.

Alcohols↗

PubMed2005

Ab initio model studies of copper binding to peptides containing a His-His sequence: relevance to the beta-amyloid peptide of Alzheimer's disease.

Two of the defining hallmarks of Alzheimer's disease (AD) are deposits of the beta-amyloid peptide, Abeta, and the generation of reactive oxygen species, both of which may be due to the Abeta peptide coordinating metal ions. The Cu2+ concentrations in cores of senile plaques are significantly elevated in AD patients. Experimental results indicate that Abeta1-42 in particular has a very high affinity for Cu2+, and that His13 and His14 are the two most firmly established ligands in the coordination sphere of the copper ion. Quantum chemical calculations using the unrestricted B3LYP hybrid density functional method with the 6-31G(d) basis set were performed for geometries, zero point energies and thermochemistry. The effects of solvation were accommodated using the CPCM method. The enthalpies were calculated with the 6-311+G(2df,2p) basis set. Calculations show that when Cu(H2O)(4)2+ combines with the model compound 1 (3-(1H-imidazol-5-yl)-N-[2-(1H-imidazol-5-yl)ethyl] propanamide) in the aqueous phase, the most stable binding site involves the Npi atoms of His13 and His14 as well as the carbonyl of the intervening backbone amide group. These structures are fairly rigid and the implications for conformational changes to the Abeta backbone are discussed. In solution at pH=7, Cu2+ promotes the deprotonation and involvement in the binding of the backbone amide nitrogen in a beta-sheet like structure. This geometry does not induce strain in the peptide backbone, making it the most likely representation of that portion of the Cu2+-Abeta complex monomer in aqueous solution.

Alzheimer Disease↗

PubMed2005

Binding affinities for models of biologically available potential Cu(II) ligands relevant to Alzheimer's disease: an ab initio study.

A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.

Alzheimer Disease↗

PubMed2005

Computational studies of Cu(II)/Met and Cu(I)/Met binding motifs relevant for the chemistry of Alzheimer's disease.

A systematic study of the binding motifs of Cu(II) and Cu(I) to a methionine model peptide, namely, N-formylmethioninamide 1, has been carried out by quantum chemical computations. Geometries of the coordination modes obtained at the B3LYP/6-31G(d) level of theory are discussed in the context of copper coordination by the peptide backbone and the S atom of a methionine residue in peptides with special emphasis on Met35 of the amyloid-beta peptide (Abeta) of Alzheimer's disease. The relative binding free energies in the gas phase, DeltaG(g), are calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level of theory, and the solvation affects are included by means of the COSMO model to obtain the relative binding energies in solution, DeltaG(aq). A free energy of binding, DeltaG(aq) = -19.4 kJ mol(-1), relative to aqueous Cu(II) and the free peptide is found for the most stable Cu(II)/Met complex, 12. The most stable Cu(I)/Met complex, 23, is bound by -15.6 kJ mol(-1) relative to the separated species. The reduction potential relative to the standard hydrogen electrode is estimated to be E degrees (12/23) = 0.41 V. On the basis of these results, the participation of Met35 as a low affinity binding site of Cu(II) in Abeta, and its role in the redox chemistry underlying Alzheimer's disease is discussed.

Alzheimer Disease↗

PubMed2005

Electron attachment in ice-HCl clusters: an ab initio study.

Experimental work has shown that small amounts of HCl strongly enhance electron capture in ice films. The purpose of the present study was to investigate the effect of adsorbed HCl on the interaction of electrons with small clusters of water. Studies were made with clusters of 6 and 12 water molecules with various geometries both with and without one HCl attached. A number of distinct HCl coordination motifs were examined. All of the neutral structures with HCl exhibited zero thresholds for electron attachment and formed dipole bound anionic states (DBS). The relaxation processes for these "initial DBS" depended on the number of H(2)O (n) and on the number and type of H-bonds to the HCl (x). The initial DBS of systems with only O-H...Cl H-binding underwent dissociative electron attachment (DEA), forming H atoms. Relaxation for systems with ClH...OH(2) bonds was more complex. For the two layer n = 12 systems with x = 2 or 3 the HCl proton moved to the nearest oxygen to form H(3)O(+). Then rearrangement of the proton network occurred, and the Cl(-) became solvated by three HO-H...Cl(-) bonds. The presence of Cl(-) and H(3)O(+) increases the dipole moment and the electron binding energy (EBE) of the network. Further stabilization is achieved by decay into deeper DBS electron traps and/or by reaction of the excess electron with H(3)O(+) to form H(*) atoms. The HCl(H(2)O)(6) clusters with a single Cl-H...OH(2) bond behaved differently. They increased their stability by becoming more linear. This raised the dipole moment and the EBE therefore increased, reducing the total energy. None of these species showed any signs of increasing the number of H-bonds to Cl. The implication of these observations for the interpretation of the results of the experiments with 0.2 monolayer of HCl on 5 monolayer of H(2)O at 20 K, and on the possible role of cosmic ray-induced ionization in polar stratospheric clouds in ozone depletion is discussed.

Anions↗

PubMed2005

Alzheimer's disease and the 'ABSENT' hypothesis: mechanism for amyloid beta endothelial and neuronal toxicity.

Alzheimer's disease [AD] is the most common cause of dementia among people age 65 and older. One of the biggest stumbling blocks in developing effective drug therapy for Alzheimer's disease has been the lack of a comprehensive hypothesis that explains the mechanism behind all of the histopathological changes seen in patients suffering from Alzheimer's disease. An overview of the currently popular 'amyloid' and 'vascular' hypotheses for AD demonstrates that neither hypothesis by itself can explain all the known histopathological and biochemical lesions seen in Alzheimer's disease. The paper presents a hypothesis that tries to explain the mechanism behind almost all the histopathological changes, and varying clinical manifestations seen in both diagnosed AD and Vascular Dementia [VaD]. The new hypothesis is based on the known dual toxicity of beta amyloid to both vascular and neuronal tissues, their synergy and the resultant net effect on the onset and progression of AD. The new hypothesis therefore will be known as the Amyloid Beta Synergistic Endothelial and Neuronal Toxicity [ABSENT] hypothesis. The ABSENT hypothesis will try to show the common chemical mechanism behind almost all of the pathological changes seen in AD. According to the ABSENT hypothesis, beta amyloid itself generates all the free radicals that cause both vascular dysfunction and the neuronal damage seen in AD. The chemical mechanism proposed is based on evidence from physical chemistry experiments, calculations as well as in vitro/in vivo experiments. The ABSENT hypothesis does not favor one mode of beta amyloid-induced brain damage over the other, rather it considers the net effects of the neuronal stress/damage caused by both the cerebrovascular dysfunction and direct neurotoxicity caused by beta amyloid. The hypothesis states that each patient has a different balance of predisposing factors that modulate the extent of neurotoxicity and cerebrovascular dysfunction caused by beta amyloid and thereby explains the wide range and mixed nature of damage and dysfunction seen in the studies done on patients diagnosed with AD, VaD or 'mixed dementias'. According to the hypothesis, beta amyloid peptides are necessary if not sufficient to cause AD, VaD and mixed senile dementias. The hypothesis, therefore, proposes the term Beta Amyloid Dementias [BAD] to describe the conditions currently covered by the diagnoses of 'AD', 'VaD' and 'Mixed [senile] Dementias'. Finally, the ABSENT hypothesis tries to put forth a direct chemical mechanism behind the apparent synergy and increased association between old age, pre- and coexisting vascular disease, diabetes and AD.

Aged↗

PubMed2002

Computational studies of Cu(II)[peptide] binding motifs: Cu[HGGG] and Cu[HG] as models for Cu(II) binding to the prion protein octarepeat region.

The binding of Cu(II) to the prion protein is investigated by computations at the B3LYP level of theory on models of the octarepeat domain of the prion protein. The models incorporate the functionality of the glycine (G) and histidine (H) residues which occur in the octarepeat domain, PHGGGWGQ. The copper complexes are designated Cu[HG] and Cu[HGGG]. Coordination to the metal via the imidazole ring of the histidine, the amide carbonyl groups, and the backbone nitrogen atom of the amide groups were examined, as well as several protonation/deprotonation states of each structure. EPR and CD titration experiments suggest that the octarepeat segments of the unstructured N-terminal domain of prion protein can bind Cu(II) in a 1:1 Cu-to-octarepeat ratio. The results identify the extent to which the Cu(II) facilitates peptide backbone deprotonation, and the propensity of binding in the forward (toward the C-terminus) direction from the anchoring histidine residue. A plausible mechanism is suggested for changing from amide O-atom to deprotonated amide N-atom coordination, and for assembly of the observed species in solutions of Cu[PrP] and truncated models of it. A structure is proposed which has the N2O2 coordination pattern for the minor component observed experimentally by EPR spectroscopy for the Cu[HGGG] model. The most stable neutral Cu[HGGG] structure found, with coordination environment N3O1, corresponds to that observed for Cu[HGGGW] and Cu[HGGG] both in the solid state and as the major component in solution at neutral pH.

Amino Acid Motifs↗

PubMed2002

The radical model of Alzheimer's disease: specific recognition of Gly29 and Gly33 by Met35 in a beta-sheet model of Abeta: an ONIOM study.

The Radical Model of Alzheimer's Disease (AD) is presented in some detail. The model provides a unified picture for the role of the amyloid beta peptide (Abeta), Met35, copper ions, oxygen, beta sheet secondary structure, and the generation of hydrogen peroxide, in mediating oxidative stress in AD. It predicts a role for glycyl radicals as long-lived species which can transport the damage into cell membranes and initiate lipid peroxidation. Previous work has established the thermodynamic and kinetic viability of most of the steps. In the present work, QM/MM and Amber calculations reveal that self assembly of antiparallel beta-sheet which brings Met35 into the required close proximity to a glycine residue is more likely if the residue is Gly29 or Gly33, than any of the other four glycine residues of Abeta.

Alzheimer Disease↗

PubMed1998

Chiroptical Properties of the Ketene and Diazo Chromophores. 1. Conformation and Optical Activity of 1-Alken-1-ones and 1-Diazoalkanes vs Aldehydes.

Ab initio methods have been employed to study the conformational behavior and chiroptical properties of acyclic, structurally related aldehydes, ketenes, and diazoalkanes of the type MeCHRCH=XY. The study involved aldehydes 1, 4, and 7 (XY = O, R = H, Me, Et, correspondingly), ketenes (1-alken-1-ones) 2, 5, and 8 (XY = CO, R = H, Me, Et), and 1-diazoalkanes 3, 6, and 9 (XY = NN, R = H, Me, Et). Geometries were optimized at the B3LYP/6-31G level, stationary points were characterized by vibrational frequency analysis, and final energies of 7-9 were obtained at the B3LYP/6-311+G//B3LYP/6-31G level. The chiroptical properties were calculated by the CIS/6-31+G method. It was found that rotational barriers of the functional group (CHXY) about the CC bond are lowered in the following order: aldehydes (1.5-2.1 kcal mol(-1)) > ketenes (1.3-1.6) > diazoalkanes (0.5-0.7). A conformer with the C=X bond eclipsed by an alpha-hydrogen is the global minimum of the ketenes and diazoalkanes, unlike the aldehydes where eclipsing by an alpha-alkyl group is preferred over a hydrogen. In all three classes of compounds, the optical rotational strength of the n-pi transition is greatest for conformers with the dihedral angle, CCCX, in the range 80-100 degrees. Within this range, the signs of the n-pi rotational strengths for the ketenes and diazoalkanes are opposite to ones for the aldehydes. As a whole, the torsional dependencies of the n-pi rotational strength of the ketene and diazo chromophores can be explained within the framework of a model of "through-bond" perturbation. CD spectra of (S)-alpha-methyl-substituted butanal (7), 1-penten-1-one (8), and 1-diazobutane (9) were obtained experimentally. The calculated chiroptical properties of equilibrium mixtures of conformers of compounds 7-9 are in agreement with experimental data.

Journal Article↗

PubMed1996

Why Do Catalytic Quantities of Lewis Acid Generally Yield More Product than 1.1 Equiv in the Intramolecular Diels-Alder Reaction with a Furan Diene? 2.(1) AM1 Calculations and Mathematical Simulation of the Equilibria.

The results presented here provide additional support for our hypothesis based on the relative basicity of the reaction controlling functional group to rationalize experimental observations on intramolecular Diels-Alder reactions with a furan diene (IMDAF) regarding the quantity (0.1 or 1.1 equiv) of Lewis acid required to facilitate the reaction most effectively. Heats of formation, DeltaH(f), and heats of reaction, DeltaH(R), have been obtained using AM1 calculations for 26 IMDAF reactions. These DeltaH(R) are generally exothermic (indicating that these IMDAF reactions are favorable) and can be qualitatively correlated with experimental yields of adduct, thereby providing a means of predicting the feasibility of the IMDAF promoted by 0.1 equiv of Lewis acid. The equilibria involved in the Lewis acid-promoted IMDAF reaction have been qualitatively interpreted using reaction coordinate diagrams and quantitatively investigated by generating a mathematical simulation of the reaction scheme. This demonstrates that the experimental behavior of the IMDAF reaction is well represented by the relative basicity hypothesis and that the LA concentration-dependent behavior should also be observed for other Lewis acid-promoted organic reactions.

Journal Article↗