Monte Carlo simulation of protein folding in the presence of residue-specific binding sites

Ensemble growth Monte Carlo (EGMC) and dynamic Monte Carlo (DMC) simulations are used to study sequential folding and thermodynamic stability of hydrophobic-polar (HP) chains that fold to a compact structure. Molecularly imprinted cavities are modeled as hard walls having sites that are attractive to specific polar residues on the chain. Using EGMC simulation, we find that the folded conformation can be stabilized using a small number of carefully selected residue-specific sites while a random selection of surface-bound residues may only slightly contribute toward stabilizing the folded conformation, and in some cases may hinder the folding of the chain. DMC simulations of the surface-bound chain confirm increased stability of the folded conformation over a free chain. However, a different trend of the equilibrium population of folded chains as a function of residue-external site interactions is predicted with the two simulation methods.     

Nonparametric and parametric estimation for a linear germination-growth model

Seeds are planted on the interval [0, L] at various locations. Each seed has a location x and a potential germination time t epsilon [0, infinity), and it is assumed that the collection of such (x, t) pairs forms a Poisson process in [0, L] x [0, infinity) with intensity measure dxd lambda(t). From each seed that germinates, an inhibiting region grows bidirectionally at rate 2v. These regions inhibit germination of any seed in the region with a later potential germination time. Thus, seeds only germinate in the uninhibited part of [0, L]. We want to estimate lambda on the basis of one or more realizations of the process, the data being the locations and germination times of the germinated seeds. We derive the maximum likelihood estimator of v and a nonparametric estimator of lambda and describe methods of obtaining parametric estimates from it, illustrating these with reference to gamma densities. Simulation results are described and the methods applied to some neurobiological data. An Appendix outlines the S-PLUS code used.     

Influence of Irradiation on the Risk of Transmission of HIV in Bone Grafts Obtained from Appropriately Screened Donors and Followed by Radiation Sterilization

We studied the effects of radiation (electrons of 6.2 MeV) at different temperatures with respect to the inactivation of the human immunodeficiency virus to determine the radiosensitivity of the virus. Using a mathematical model describing the dependence on radiation dose of the proportion of sterile items in a population of bone allografts contaminated by HIV, and subjected to irradiation, we have commented on and explained the calculation of the sterility assurance level in bone transplantation according to different doses of irradiation at different temperatures. Simultaneous application of heat and radiation increases inactivation of HIV. Given the relative imprecision of viral sensitivity curves and the impossibility of knowing the number of viral particles in a patient at a given moment of the disease, irradiation does not authorize bone transplantation without screening. However, irradiation can be considered as a serious adjuvent to decrease the risk of contamination after screening.     

八倍体小滨麦与4D缺体杂交后代小染色体的传递与遗传效应

７２１８０ ４Ｄ缺体附加的１对小染色体（ｔｉ）为亚中部着丝点染色体,其大小为常染色体平均长度的１／３￣１／４。ＰＭＣ ＭＩ,染色体构型为１９．５９”（１８￣２０）＋０．４６’（０￣４）＋０．０９””（０￣１）＋０．９６ｔｉ”（０￣１）＋０．０８ｔｉ’（０￣２）,９６．１９％的细胞中,ｔｉ 色体联会成环状二价体,８２．３８％的ｔｉ”游离在赤道板两边,与常染色体不联会,且推后分离,与八倍体小滨麦杂交的     

Mechanisms of Long-Lasting Depression of Synaptic Transmission in the CA1 Region of the Rat Hippocampus

Low-frequency tetanic stimulation (2 sec^-1, 5 min) of Schaffer collaterals (SchC) in superfused slices of the dorsal hippocampus of 12- to 15-day-old rats was demonstrated to evoke homosynaptic long-lasting depression (LLD) of synaptic transmission. The same procedure applied to hippocampal slices of mature (8-week-old or older) rats failed to elicit LLD. Low-frequency tetanic stimulation of the alveus in hippocampal slices, applied under conditions of intensified NMDA glutamate receptor functioning, led to the development of heterosynaptic LLD of synaptic transmission in the SchC–dendrites of the CA1 pyramidal neurons system. Both LLD cases were either absent or weakened when hippocampal slices were treated with a competitive blocker of the NMDA glutamate receptors, D-2-amino-5-phosphonovalerate (50 M). Morphine hydrochloride (10 M), as well as inhibitors of calmodulin and calcineurin (trifluoroperasine and cyclosporin A in concentrations of 1 and 50 M, respectively), interfered with induction of LLD or decreased its intensity. A blocker of the L-type voltage-dependent Ca²⁺ channels, nifedipine (10 M), did not influence homosynaptic LLD, but decreased heterosynaptic depression. Both types of depression of synaptic transmission were facilitated upon application of substances possessing a nootropic activity, 1 mM pyracetam or 5 M carbacetam. A blocker of NO synthase, N-nitro-L-arginine (10 M) did not alter either type of LLD. When hippocampal slices were influenced with a blocker of the A1 adenosine receptors, 1,3-dipropyl-8-phenylxanthine (1 M, 15 min), both LLD forms were intensified, and the development of homosynaptic LLD of synaptic transmission became possible in hippocampal slices of mature rats. When hippocampal slices were treated with an inhibitor of protein kinase C, polymyxin B (50 M, 15 min), intensification of LLD and, in particular, the development of homosynaptic LLD of synaptic transmission were observed. When an inhibitor of phospholipase A2, mepacrine (25 M, 15 min), was applied to hippocampal slices, both forms of LLD of synaptic transmission were significantly suppressed.     

Amyloid fibril formation from full-length and fragments of amylin

Amyloiddeposits of fibrillar human amylin (hA) in the pancreas may be a causative factor in type-2 diabetes. A detailed comparison of in vitro fibril formation by full-length hA(1-37) versus fragments of this peptide-hA(8-37) and hA(20-29)-is presented. Circular dichroism spectroscopy revealed that fibril formation was accompanied by a conformational change: random coil to beta-sheet/alpha-helical structure. Fibril morphologies were visualized by electron microscopy and displayed a remarkable diversity. hA(20-29) formed flat ribbons consisting of numerous 3. 6-nm-wide protofibrils. In contrast, hA(1-37) and hA(8-37) formed polymorphic higher order fibrils by lateral association and/or coiling together of 5.0-nm-wide protofibril subunits. For full-length hA(1-37), the predominant fibril type contained three protofibrils and for hA(8-37), the predominant type contained two protofibrils. Polymerization was also monitored with the thioflavin-T binding assay, which revealed different kinetics of assembly for hA(1-37) and hA(8-37) fibrils. hA(20-29) fibrils did not bind thioflavin-T. Together the results demonstrate that the N-terminal region of the hA peptide influences the relative frequencies of the various higher order fibril types and thereby the overall kinetics of fibril formation. Furthermore, while residues 20-29 contribute to the fibrils' beta-sheet core, the flanking C- and N-terminal regions of the hA peptide determine the interactions involved in the formation of higher order coiled polymorphic superstructures.     

Partitioning of Tetrachlorophenol into Lipid Bilayers and Sarcoplasmic Reticulum: Effect of Length of Acyl Chains,Carbonyl Group of Lipids and Biomembrane Structure

We report results of a partitioning study of 2,3,4,6-tetrachlorophenol (TeCP). In the study we explored (1) the effect of the length of acyl chains of lipids (C16:1 – C24:1) and alkanes (C6–C16), (2) the role of the carbonyl group of lipids, and (3) the effect of molecular structure of the sarcoplasmic reticulum membrane on TeCP partitioning. Mole fraction partition coefficients have been measured using equilibrium dialysis for un-ionized (HA), and ionized (A) species, Kp_x^HA, Kp_x^A. Their values are concentration-dependent. Partition coefficients were analyzed in terms of a model that accounts for saturation of membrane associated with the finite area of partition site, and electrostatic interactions of (A-) species with charged membrane. Limiting values of partition coefficients, corresponding to infinite dilution of solute, Kp_x0^HA, Kp_x0^A were obtained. Kp_x0^HA and Kp_x0^A measure the strength of solute-membrane interactions. Studies were done with single-layered vesicles of lipids with variable chain length: 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (C16:1), 1,2-dioleoyl-sn-glycero-3-phosphocholine (C18:1), 1,2-dierucoyl-sn-glycero-3-phosphocholine (C22:1), and 1 ,2-dinervonoyl-sn-glycero-3-phosphocholine (C24:1), and egg-PC. Kp_x0 for transfer of TeCP from water into lipid membranes was found to be independent of the length of acyl chains, whereas Kp_x0 for transfer from water into alkanes increased with the length of alkane. The effect of the carbonyl CO group of lipids on partitioning was measured using 1,2-di-o-octadecenyl-sn-glycero-3-phosphocholine (CO absent) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (CO present) liposomes. Carbonyl groups, known to change dipolar potential, had no effect on partitioning. Partition coefficients of un-ionized and ionized forms of TeCP were invariant to the presence of proteins and other membrane components of sarcoplasmic reticulum (SR) membrane.     

The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function

A combination of experimental structural data, homology modelling and elastic network normal mode analysis is used to explore how coupled motions between the two myosin heads and the dimerization domain (S2) in smooth muscle myosin II determine the domain movements required to achieve the inhibited state of this ATP-dependent molecular motor. These physical models rationalize the empirical requirement for at least two heptads of non-coiled alpha-helix at the junction between the myosin heads and S2, and the dependence of regulation on S2 length. The results correlate well with biochemical data regarding altered conformational-dependent solubility and stability. Structural models of the conformational transition between putative active states and the inhibited state show that torsional flexibility of the S2 alpha-helices is a key mechanical requirement for myosin II regulation. These torsional motions of the myosin heads about their coiled coil alpha-helices affect the S2 domain structure, which reciprocally affects the motions of the myosin heads. This inter-relationship may explain a large body of data on function of molecular motors that form dimers through a coiled-coil domain.     

Detection of multiple viruses in queens of the honey bee Apis mellifera L

Individual honey bee Apis mellifera L. queens were examined for the presence of six honey bee viruses including acute bee paralysis virus, chronic bee paralysis virus, black queen cell virus, deformed wing virus, Kashmir bee virus, and sacbrood virus. All viruses, except ABPV, were detected in the samples. Among queens examined for virus infections, 93% had multiple virus infections. The detection of viruses in queens raises the possibility of a vertical transmission pathway wherein infected queens can pass virus through their eggs to their offspring.