Understanding structural/functional properties of immunoconjugates for cancer therapy by computational approaches.

Monoclonal antibodies coupled to highly toxic molecules (immunoconjugates) are currently being developed for cancer therapy. We have used an in silico procedure for evaluating some physicochemical properties of two tumor-targeting anti-HER2 immunoconjugates: (a) the single-chain antibody scFv(FRP5) linked to a bacterial toxin, that has been recently progressed to phase I clinical trial in human cancer; (b) the putative molecule formed by the intrinsically stable scFv(800E6), which has been proposed as toxin carrier to cancer cells in human therapy, joined to the same toxin of (a). Structural models of the immunoconjugates have been built by homology modeling and assessed by molecular dynamics simulations. The trajectories have been analyzed to extract some biochemical properties and to assess the potential effects of the toxin on the structure and dynamics of the anti-HER2 antibodies. The results of the computational approach indicate that the antibodies maintain their correct folding even in presence of the toxin, whereas a certain stiffness in correspondence of some structural regions is observed. Furthermore, the toxin does not seem to affect the antibody solubility, whereas it enhances the structural stability. The proposed computational approach represent a promising tool for analyzing some physicochemical properties of immunoconjugates and for predicting the effects of the linked toxin on structure, dynamics, and functionality of the antibodies.

Quenching of majority-channel quasiparticle excitations in cobalt.

The low-energy electronic excitations in cobalt are studied by a theoretical method that includes many-body effects and a realistic description of the band structure. Angle-resolved photoemission spectra measured on a thick film of hexagonal close-packed Co on Cu(111) agree well with calculated spectral functions. Because of many-body effects no sharp quasiparticle peaks exist for binding energies larger than 2 eV and in this energy region the spectrum is essentially incoherent. The many-body corrections are much stronger in the majority-spin channel and drastically affect the spin polarization of the spectra.

Low-frequency vibrational modes in proteins: a neutron scattering investigation.

The low-frequency dynamics of plastocyanin, an electron transfer copper protein, has been investigated by incoherent neutron scattering at different temperatures. The contribution to the dynamic structure factor arising from H/D exchangeable and non-exchangeable protein protons has been evaluated by analyzing two differently exchanged protein samples. The dynamic structure factor of a hydrated plastocyanin sample with all the exchangeable hydrogens (about 150) replaced by deuterium exhibits an excess of vibrational modes, at about 3.5 meV, reminiscent of the boson peak found in other proteins and glassy systems. When only fast exchangeable hydrogens (about 50) are substituted by deuterium, the protein, besides the above-mentioned peak, shows an additional peak at about 1 meV. These vibrational peaks are discussed in connection with the topological disorder of the systems and the fluctuations of the intramolecular hydrogen bonds.

Molecular dynamics simulation and essential dynamics study of mutated plastocyanin: structural, dynamical and functional effects of a disulfide bridge insertion at the protein surface.

A molecular dynamics simulation (1.1 ns) at 300 K, of fully hydrated Ile21Cys, Glu25Cys plastocyanin mutant has been performed to investigate the structural, dynamical and functional effects of a disulfide bridge insertion at the surface of the protein. A detailed analysis of the root mean square fluctuations, H-bonding pattern and dynamical cross-correlation map has been performed. An essential dynamics method has also been applied as complementary analysis to identify concerted motions (essential modes), that could be relevant to the electron transfer function. The results have been compared with those previously obtained for wild-type plastocyanin and have revealed that the mutant shows a different pattern of H-bonds, with several interactions lost and a higher flexibility, especially around the electron transfer copper site. The analysis of dynamical cross-correlation map and of essential modes, has shown that the mutant performs different functional concerted motions, which might be related to the binding recognition with its electron transfer partners in comparison with the wild-type protein.

Concerted motions in copper plastocyanin and azurin: an essential dynamics study.

Essential dynamics analysis of molecular dynamics simulation trajectories (1.1 ns) of two copper containing electron transfer proteins, plastocyanin and azurin, has been performed. The protein essential modes have been analysed in order to identify large concerted motions which could be relevant for the electron transfer function exerted by these proteins. The analysis, conducted for temporal windows of different lengths along the protein trajectories, shows a rapid convergence and indicates that for both the proteins the predominant internal motions occur in a subspace of only a few degrees of freedom. Moreover, it is found that for both the proteins the likely binding sites (i.e. the hydrophobic and negative patches) with the reaction partners move in a concerted fashion with a few structural regions far from the active site. Such results are discussed in connection with the possible involvement of large concerted motions in the recognition and binding interaction with physiological electron transfer partners.

Structural and optical properties of silicon nanocrystals grown by plasma-enhanced chemical vapor deposition.

Silicon nanocrystals (Si-nc) embedded in SiO2 matrix have been prepared by high temperature thermal annealing (1000-1250 degrees C) of substoichiometric SiOx films deposited by plasma-enhanced chemical vapor deposition (PECVD). Different techniques have been used to examine the optical and structural properties of Si-nc. Transmission electron microscopy analysis shows the formation of nanocrystals whose sizes are dependent on annealing conditions and deposition parameters. The spectral positions of room temperature photoluminescence are systematically blue shifted with reduction in the size of Si-nc obtained by decreasing the annealing temperature or the Si content during the PECVD deposition. A similar trend has been found in optical absorption measurements. X-ray absorption fine structure measurements indicate the presence of an intermediate region between the Si-nc and the SiO2 matrix that participates in the light emission process. Theoretical observations reported here support these findings. All these efforts allow us to study the link between dimensionality, optical properties, and the local environment of Si-nc and the surrounding SiO2 matrix.

Two-photon autofluorescence microscopy and spectroscopy of Antarctic fungus: new approach for studying effects of UV-B irradiation.

We combined two-photon fluorescence microscopy and spectroscopy to provide functional images of UV-B (280-315 nm) induced stress on an Antarctic fungus. Two-photon excitation microscopy was used to characterize the distribution of autofluorescence inside the spore and the hyphae of the fungus. The imaging analysis clearly shows that the autofluorescence response of spores is higher than that of hyphae. The imaging analysis at different depths shows that, strikingly enough, the spore autofluorescence originates from the cell wall and membrane fluorophores. The spectroscopic results show moreover that the fluorescence spectra of spores are redshifted upon UV-B irradiation. Tentative identification of the chromophores involved in the autofluorescence response and their biological relevance are also discussed on the basis of a previous steady-state fluorescence spectroscopic study performed on both whole spore suspension and organic-soluble extracts.

In situ Raman microspectroscopic identification and localization of carotenoids: approach to monitoring of UV-B irradiation stress on Antarctic fungus.

The in situ Raman microspectroscopic properties of an Antarctic fungus are investigated to assess the nature and the spatial localization of the main chromophores and to study their spectral changes under enhanced UV-B irradiation. The Raman spectroscopic features of spores in situ are consistent with those of carotenoid-like pigments. In particular, the Raman shifts seem to be related either to the frequency modes of long conjugated double-bond carotenoids or to protein bound beta-carotene. The spectroscopic analysis at different spore depths clearly shows the strongest Raman signal arises from cell wall and membrane structures. The intensity of such a signal shows a drastic reduction upon UV-B irradiation without any significant frequency change. The use of Raman microspectroscopy for nondestructively monitoring the UV-B effects on Arthrobotrys ferox spores is also discussed.

Incoherent neutron scattering of copper azurin: a comparison with molecular dynamics simulation results.

The low-frequency dynamics of copper azurin has been studied at different temperatures for a dry and deuterium hydrated sample by incoherent neutron scattering and the experimental results have been compared with molecular dynamics (MD) simulations carried out in the same temperature range. Experimental Debye-Waller factors are consistent with a dynamical transition at approximately 200 K which appears partially suppressed in the dry sample. Inelastic and quasielastic scattering indicate that hydration water modulates both vibrational and diffusive motions. The low-temperature experimental dynamical structure factor of the hydrated protein shows an excess of inelastic scattering peaking at about 3 meV and whose position is slightly shifted downwards in the dry sample. Such an excess is reminiscent of the "boson peak" observed in glass-like materials. This vibrational peak is quite well reproduced by MD simulations, although at a lower energy. The experimental quasielastic scattering of the two samples at 300 K shows a two-step relaxation behaviour with similar characteristic times, while the corresponding intensities differ only by a scale factor. Also, MD simulations confirm the two-step diffusive trend, but the slow process seems to be characterized by a decay faster than the experimental one. Comparison with incoherent neutron scattering studies carried out on proteins having different structure indicates that globular proteins display common elastic, quasielastic and inelastic features, with an almost similar hydration dependence, irrespective of their secondary and tertiary structure.

Long-term molecular dynamics simulation of copper azurin: structure, dynamics and functionality.

A long-term molecular dynamics simulation (1.1 ns), at 300 K, of fully hydrated azurin has been performed to put into relationship the protein dynamics to functional properties with particular attention to those structural elements involved in the electron transfer process. A detailed analysis of the root mean square deviations and fluctuations and of the intraprotein H-bonding pattern has allowed us to demonstrate that a rigid arrangement of the beta-stranded protein skeleton is maintained during the simulation run, while a large mobility is registered in the solvent-exposed connecting regions (turns) and in the alpha-helix. Moreover, the structural elements, likely involved in the electron transfer path, show a stable H-bonding arrangement and low fluctuations. Analysis of the dynamical cross-correlation map has revealed the existence of correlated motions among residues connected by hydrogen bonds and of correlated and anti-correlated motions between regions which are supposed to be involved in the functional process, namely the hydrophobic patch and the regions close to the copper reaction center. The results are briefly discussed also in connection to the current through-bond tunneling model for the electron transfer process. Finally, a comparison with the structural and the dynamical behaviour of plastocyanin, whose structure and functional role are very similar to those of azurin, has been performed.

A molecular dynamics simulation study of the solvent isotope effect on copper plastocyanin.

The effect of heavy water on the structure and dynamics of copper plastocyanin as well as on some aspects of the solvent dynamics at the protein-solvent interfacial region have been investigated by molecular dynamics simulation. The simulated system has been analyzed in terms of the atomic root mean square deviation and fluctuations, intraprotein H-bond pattern, dynamical cross-correlation map and the results have been compared with those previously obtained for plastocyanin in H2O (Ciocchetti et al. Biophys. Chem. 69 (1997), 185-198). The simulated plastocyanin structure in the two solvents, averaging 1 ns, is very similar along the beta-structure regions, while the most significant differences are registered, analogous to the turns and the regions likely involved in the electron transfer pathway. Moreover, plastocyanin in D2O shows an increase in the number of both the intraprotein H-bonds and the residues involved in correlated motions. An analysis of the protein-solvent coupling evidenced that D2O makes the H-bond formation more difficult with the solvent molecules for positively charged and polar residues, while an opposite trend is observed for negatively charged residues. On the other hand, the frequency of exchange of the solvent molecules involved in the protein-solvent H-bond formation is significantly depressed in D2O. The results are discussed also in connection with protein functionality and briefly with some experimental results connected with the thermostability of proteins in D2O.

Minimal carcinoma in prostate needle biopsy specimens: diagnostic features and radical prostatectomy follow-up.

Prostate cancer screening and early detection efforts have resulted in the identification of smaller volume carcinomas of the prostate. We evaluated the diagnostic features of minimal (< 1 mm) carcinoma in sextant needle biopsy specimens of the prostate and in follow-up analyzed the features of the corresponding carcinomas in the whole gland. We reviewed specimens from 50 consecutive patients who had minimal carcinoma in needle biopsy tissue and who had undergone radical prostatectomy. Histologic grade, tumor size, pathologic stage, and margin status of the 50 carcinomas in the whole gland in which the carcinoma size was minimal in the sextant needle biopsy specimen were compared with those of 50 carcinomas in the whole gland in which carcinoma size was greater than 1 mm in the needle biopsy specimen. The most common morphologic features of these minimal carcinomas were nucleomegaly (96%), infiltrative growth pattern (88%), intraluminal secretions (78%), prominent nucleoli (64%), associated high-grade prostatic intraepithelial neoplasia (40%), amphophilic cytoplasm (36%), hyperchromatic nuclei (30%), and intraluminal crystalloids (22%). Perineural invasion (2%), collagenous micronodules (2%) and mitotic figures (2%) were uncommon. The mean tumor volume in the whole gland of carcinomas corresponding to minimal carcinoma in a needle biopsy specimen was significantly smaller (P=.029) at 1.1 mL than it was in carcinomas with tumor greater than 1 mm in the needle biopsy specimen at 1.6 mL, but other pathologic features of carcinoma in the whole gland were not significantly different. In conclusion, a constellation of morphologic attributes is important for establishment of a diagnosis of minimal carcinoma of the prostate in needle biopsy specimen. Most (82%) of the corresponding prostate cancers in the whole gland were pathologically significant.

Percentage of free serum prostate-specific antigen as a predictor of pathologic features of prostate cancer in a screening population.

OBJECTIVES: Measurement of the percentage of free prostate-specific antigen (%FPSA) in serum can improve the specificity of prostate cancer screening. We evaluated the ability of %FPSA to predict pathologic features of screen-detected clinically localized prostate cancer. METHODS: We evaluated the correlation between %FPSA in serum before cancer diagnosis and the pathologic features of the cancers detected in 108 men with clinically localized prostate cancer who were treated with radical prostatectomy and for whom complete embedding of the radical prostatectomy specimen was performed. Ninety-seven men (90%) had a previous negative screening evaluation before prostate cancer was detected. RESULTS: There was a negative correlation of %FPSA with penetration of cancer through the prostatic capsule, cancerous surgical margins, Gleason score, percentage of cancer in the gland, and tumor volume (r = -0.2 to -0.4). After controlling for other preoperative predictors, %FPSA predicted capsular penetration (adjusted odds ratio [OR] 1.6, 95% confidence interval [CI] 1.1 to 2.4, for each 5% decrease in %FPSA) and cancer volume 0.5 cc or greater (adjusted OR 1.6, 95% CI 1.1 to 2.3). Preoperative %FPSA also predicted possibly harmless cancer (OR 1.5, 95% CI 1.1 to 2.2, for each 5% increase in %FPSA). CONCLUSIONS: In a select group of men for whom cancer was detected early via screening, a lower %FPSA in serum suggests a potentially more threatening cancer. This information may aid patients and clinicians in making more informed decisions about the management of prostate cancer, such as selecting patients for watchful waiting. However, more research is needed to determine the performance characteristics of %FPSA in clinical practice.

Stability of serum total and free prostate specific antigen under varying storage intervals and temperatures.

PURPOSE: Measurement of total serum prostate specific antigen (PSA) is widely used as an aid to early detection of prostate cancer. Measurement of the ratio of free-to-total PSA (percentage of free PSA) may help increase specificity of PSA testing. We prospectively studied the effects of varying the storage temperature and interval on total and free PSA levels. MATERIALS AND METHODS: We measured the baseline total and free serum PSA levels in 36 volunteers (mean age 66 years) and then retested aliquots of these serum samples after varying storage intervals (24 hours, 2 weeks and 9 months) at 3 different temperatures (4C, -20C and -70C). Volunteers represented a spectrum of prostatic conditions (PSA levels 2.0 to 4.0 ng./ml., PSA levels greater than 4.0 ng./ml. without cancer and PSA levels greater than 2.0 ng./ml. with prostate cancer). We used repeated measures analysis of variance to test for changes in total and free PSA levels as a function of time and temperature. We also evaluated the impact of storage at different temperatures and times on the percentage of free PSA. RESULTS: Across groups total and free serum PSA decreased from the baseline level differentially as a function of longer storage interval and higher temperature (p <0.05). No significant difference was found for change in total PSA at 24 hours, 2 weeks or 9 months for storage temperatures of -20C compared with -70C. A significant change from baseline level was found for free PSA when stored in -20C compared with -70C for 2 weeks but the magnitude of the change was modest. CONCLUSIONS: For storage intervals up to 9 months total PSA is more stable than free PSA under temperature conditions ranging from 4C to -70C. This differential stability has important implications for the clinical evaluation of percentage of free PSA to distinguish between benign and malignant diseases of the prostate.

Prostate-specific antigen as a screening test for prostate cancer. The United States experience.

Serum PSA-based early detection for prostate cancer has been studied fairly extensively for the past several years. It appears that we can state fairly categorically what the relative performances of total serum PSA, DRE, and TRUS are in detecting early-stage prostate cancer; that initial screening is effective in detecting histologically significant and pathologically organ-confined prostate cancer; that annual, serial, repetitive screening, at least over a 4- to 5-year horizon, does not overdetect prostate cancer, and that the results of early detection will improve as our ability to use certain PSA transformations such as PSA density, PSA slope, age-specific PSA adjustment, and knowledge of free versus total serum PSA is better characterized. These advances in our ability to diagnose early-stage prostate cancer likely will be coupled with an increased ability to predict the behavior, curability, and significance of individual tumors. It is hoped that information soon will be available to allow physicians to categorize an individual tumor as insignificant, significant and surgically curable, or significant and incurable by standard approaches. This ability, coupled with the demonstrated ability to detect prostate cancer, will make an even more compelling argument for widespread PSA-based screening. At present, annual DRE and total serum PSA measurements are recommended for men older than 50 and among younger men at high risk for prostate cancer. All suspicious DRE findings should be evaluated with prostatic biopsy. Among younger men, PSA levels over 2.5 ng/mL should be considered worrisome and further evaluated. For men older than 65, serum PSA levels above 4 ng/mL should be considered abnormal and warrant biopsy. Men with persistent serum PSA elevation and a negative biopsy should undergo repeat biopsy at least once, and perhaps more often if PSA slope exceeds 0.75 per year, if density is greater than 0.10, or if f-PSA is less than 20%.

Renal masses: urologic management.

This article reviews the differential diagnoses for solid renal masses and staging for renal cell carcinoma, and also discusses several areas of controversy in regard to the management of solid renal masses, such as the role of nephron-sparing surgery, extended lymphadenectomy, and ipsilateral adrenalectomy. The management of renal cell carcinoma associated with tumor thrombus within the vena cava is discussed, as are issues regarding both surgical and medical management (including chemotherapy and immunotherapy) of metastatic disease. Lastly, the emerging role of laparoscopic nephrectomy is examined.

[Association of pulmonary and portal hypertension]. / Associazione tra ipertensione arteriosa polmonare ed ipertensione portale.

The association between portal venous hypertension and pulmonary arterial hypertension has received scarce attention in the italian medical literature. Nevertheless the association is relatively frequent, it needs a multidisciplinary approach and it is a stimulus for the search of causes of so-called primary pulmonary hypertension. The purpose of the article is to review the frequency of the association, the main pathogenetic hypothesis formulated to explain the appearance of pulmonary hypertension, the clinical and the laboratory findings, the evolution of the association and to present briefly a personal series of cases. The pulmonary arterial hypertension has been found in approximately 2% of patients with portal hypertension due to either hepatic cirrhosis or extraepatic lesions. Microembolism from the portocavat system or a number of vasoactive substances which enter the pulmonary circulation without being inactivated by the liver have been held responsible for the appearance of pulmonary hypertension in predisposed patients. Clinical and laboratory findings do not differ from those a patients with primary pulmonary hypertension. Also the prognosis is similar. In conclusion on accurate examination of the pulmonary circulation by noninvasive methods, in particular by echocardiography, appears to be mandatory in patients with chronic hepatic lesions. When pulmonary arterial hypertension is detected the study of the biochemical factors which at present are known to determine pulmonary hypertension may be warranted. The study may enhance our knowledge of the pathogenesis of the so-called primary pulmonary hypertension.

[Late ventricular potentials in patients with dilated cardiomyopathy. Correlations with spontaneous ventricular tachycardia and clinical course]. / Potenziali tardivi ventricolari nei pazienti con cardiomiopatia dilatativa. Correlazione con le tachicardie ventricolari spontanee e decorso clinico.

In a series of 55 patients with dilated cardiomyopathy, the presence of noninvasive recordings of late ventricular potentials (LVP) was correlated to ventricular tachycardia (VT), as detected by a 24-hour Holter monitoring obtained one week within LVP recording. LVPs were found in 12/55 patients (21.8%) and in 2 of a series of 66 normal subjects of the same age and sex. In all patients with LVP either non sustained (11 cases) or sustained (1 case) VT was present at Holter monitoring. In the other 43 patients without LVP only 13 (30%) had non sustained VT (p < 0.01). During the follow-up period (mean 17 months) six patients died suddenly; three of them had LVP and VT (sustained in one); two had non sustained VT, but no LVP; one had neither. This study suggests that the presence of LVP predicts VT recording in ambulatory ECGs. On the contrary, VT may be recorded in patients without LVP. Further studies are necessary to ascertain the value of LVP as a marker of sudden death in patients with dilated cardiomyopathy.

Interferon-gamma (r-IFN-gamma) induced activation of alveolar macrophages (AM) from anergic patients with chronic obstructive pulmonary disease (COPD).

Forty-six anergic patients (37 males and 9 females, age range 55-79 yr) were selected from ninety-one patients suffering from COPD due to frequent exacerbations and impaired delayed cutaneous reactivity (43.9%). The phenotype of circulating lymphocytes, their proliferative response to a panel of polyclonal T-cell activators and the candidacidal activity (CA) of circulating PMNs (polymorphonuclear cells) were measured. In 13 patients presenting a defective CA of circulating PMNs, the in vitro response of alveolar macrophage CA to r-IFN-gamma was also determined. We found: 1) a significant reduction in the CL response to PHA in COPD patients vs controls; 2) a low PMN-CA in 23 (57%) COPD patients; 3) a non-significant difference in phenotype analysis in patients and controls; 4) lower CA of AMs in COPD patients than in controls; 5) restoration in vitro of CA by r-IFN-gamma in the group of anergic COPD patients presenting depressed CA. We conclude that a defective cell-mediated immunity could be the basis of the enhanced susceptibility to infectious exacerbations in many COPD patients and that, in vitro, it could be reversed by r-IFN-gamma treatment.