Free energy landscape of activation in a signalling protein at atomic resolution.

The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signalling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and nuclear magnetic resonance, and discover unexpected features underlying efficient signalling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state.

ALADYN: a web server for aligning proteins by matching their large-scale motion.

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. The latter often accompany functional conformational changes in proteins and enzymes. The ALADYN dynamics-based alignment can therefore highlight functionally-oriented correspondences that could be more elusive to sequence- or structure-based comparisons. The ALADYN server takes the structure files of the two proteins as input. The optimal relative positioning of the molecules is found by maximizing the similarity of the pattern of structural fluctuations which are calculated via an elastic network model. The resulting alignment is presented via an interactive graphical Java applet and is accompanied by a number of quantitative indicators and downloadable data files. The ALADYN web server is freely accessible at the http://aladyn.escience-lab.org address.

PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains.

SUMMARY: The PiSQRD web resource can be used to subdivide protein structures in quasi-rigid dynamical domains. The latter are groups of amino acids behaving as approximately rigid units in the course of protein equilibrium fluctuations. The PiSQRD server takes as input a biomolecular structure and the desired fraction of protein internal fluctuations that must be accounted for by the relative rigid-body motion of the dynamical domains. Next, the lowest energy modes of fluctuation of the protein (optionally provided by the user) are calculated and used to identify the rigid subunits. The resulting optimal subdivision is returned through a web page containing both interactive graphics and detailed data output. AVAILABILITY: The PiSQRD web server, which requires Java, is available free of charge for academic users at http://pisqrd.escience-lab.org.

Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.

The possibility of accurately describing the internal dynamics of proteins, in terms of movements of a few approximately-rigid subparts, is an appealing biophysical problem with important implications for the analysis and interpretation of data from experiments or numerical simulations. The problem is tackled here by means of a novel variational approach that exploits information about equilibrium fluctuations of interresidues distances, provided, e.g., by atomistic molecular dynamics simulations or coarse-grained models. No contiguity in primary sequence or in space is enforced a priori for amino acids grouped in the same rigid unit. The identification of the rigid protein moduli, or dynamical domains, provides valuable insight into functionally oriented aspects of protein internal dynamics. To illustrate this point, we first discuss the decomposition of adenylate kinase and HIV-1 protease and then extend the investigation to several representatives of the hydrolase enzymatic class. The known catalytic site of these enzymes is found to be preferentially located close to the boundary separating the two primary dynamical subdomains.

Anharmonicity and self-similarity of the free energy landscape of protein G.

The near-native free-energy landscape of protein G is investigated through 0.4-micros-long atomistic molecular dynamics simulations in an explicit solvent. A theoretical and computational framework is used to assess the time dependence of salient thermodynamical features. While the quasiharmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free-energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.

The increase of oxygen requirement as index to identify the infants at high risk of pneumothorax during nasal continuous positive airway pressure.

AIM: The aim of this study was to evaluate the inspiration fraction of oxygen (FiO2) trend as an indicator of timing to suspend nasal continuous positive airway pressure (N-CPAP) and shift the babies to mechanical ventilation, in order to reduce the incidence of pneumothorax, comparing a similar population admitted in our division during the previous year. METHODS: Seventy-five newborns (mean gestational age 33.5 weeks, mean birth weight 2,072 g) admitted during 2003 in our Neonatal Intensive Care Unit, treated with Infant Flow System Nasal-CPAP, were included. Patients with more than 40% increase of the starting FiO2 in the first 24 h of treatment, were intubated and shift on mechanical ventilation. Seventy-seven infants, admitted during the previous year, with similar characteristics (mean gestational age 33.7 weeks, mean birth weight 2,047 g) were considered as control. RESULTS: Fifty-six neonates improved, 19 worsened and required mechanical ventilation. One of these developed pneumothorax (1.3%). Of the 77 infants admitted during the previous year, 26 worsened and were mechanically ventilated, and 8 developed pneumothorax (10.3%). The difference of incidence of pneumothorax was significant (P =0.0337). CONCLUSIONS: An increase of FiO2 more than 40% of the initial value during the first 24 h of N-CPAP may be considered a useful marker to identify infants at high risk of pneumothorax.

[Pneumothorax during nasal-CPAP: a predictable complication?]. / Pneumotorace in corso di CPAP nasale. E una complicanza prevedibile?

OBJECTIVE: Pneumothorax (PNX) is a relatively common complication of nasal-CPAP (N-CPAP). Aim of the study was to identify prognostic factors of its onset. METHODS: Seventy-seven newborns, admitted from January to December 2002 to the Neonatal Intensive Care Unit of Brescia, who were treated with N-CPAP with Infant Flow System as first intention, were included. Gestational age and birth weight were (mean +/- SD) 33.7 +/- 3.02 weeks and 2.047 +/- 684 grams, respectively. Infants were put on N-CPAP at 2.7 +/- 4.1 hours of life. The duration of treatment was 27.7 +/- 27.7 hours. RESULTS: Fifty-one neonates improved and N-CPAP was discontinued, 26 worsened and required intubation and mechanical ventilation. Eight of them developed PNX (10,3%). No significant differences were found among the three groups (improved, worsened without PNX and worsened with PNX) concerning mode of delivery, gestational age, birth weight and blood gases. The patients with PNX needed a FiO2 28% higher than the initial value after 12 hours of treatment, and 46% higher at 24 hours (p = 0,017). At diagnosis, FiO2 was 53,5% higher than the initial value (p = 0,005). CONCLUSION: A 40% increase of FiO2, during the first 24 hours of N-CPAP may represent an useful marker to identify the infants at high risk of developing a pneumothorax.