781 research outputs found
A new perspective on the analysis of helix-helix packing preferences in globular proteins
For many years it had been believed that steric compatibility of helix
interfaces could be the source of the observed preference for particular angles
between neighbouring helices as emerging from statistical analysis of protein
databanks. Several elegant models describing how side chains on helices can
interdigitate without steric clashes were able to account quite reasonably for
the observed distributions. However, it was later recognized (Bowie, 1997 and
Walther, 1998) that the ``bare'' measured angle distribution should be
corrected to avoid statistical bias. Disappointingly, the rescaled
distributions dramatically lost their similarity with theoretical predictions
casting many doubts on the validity of the geometrical assumptions and models.
In this report we elucidate a few points concerning the proper choice of the
random reference distribution. In particular we show the existence of crucial
corrections due to the correct implementation of the approach used to
discriminate whether two helices are in contact or not and to measure their
relative orientations. By using this new rescaling, the ``true'' packing angle
preferences are well described, even more than with the original ``bare''
distribution, by regular packing models.Comment: 23 pages, 5 figure
Simple solvation potential for coarse-grained models of proteins
We formulate a simple solvation potential based on a coarsed-grain
representation of amino acids with two spheres modeling the atom and
an effective side-chain centroid. The potential relies on a new method for
estimating the buried area of residues, based on counting the effective number
of burying neighbours in a suitable way. This latter quantity shows a good
correlation with the buried area of residues computed from all atom
crystallographic structures. We check the discriminatory power of the solvation
potential alone to identify the native fold of a protein from a set of decoys
and show the potential to be considerably selective.Comment: 18 pages, 8 tables, 3 figure
A model for the analysis of security policies in service function chains
Two emerging architectural paradigms, i.e., Software Defined Networking (SDN)
and Network Function Virtualization (NFV), enable the deployment and management
of Service Function Chains (SFCs). A SFC is an ordered sequence of abstract
Service Functions (SFs), e.g., firewalls, VPN-gateways,traffic monitors, that
packets have to traverse in the route from source to destination. While this
appealing solution offers significant advantages in terms of flexibility, it
also introduces new challenges such as the correct configuration and ordering
of SFs in the chain to satisfy overall security requirements. This paper
presents a formal model conceived to enable the verification of correct policy
enforcements in SFCs. Software tools based on the model can then be designed to
cope with unwanted network behaviors (e.g., security flaws) deriving from
incorrect interactions of SFs in the same SFC
Elucidation of the disulfide folding pathway of hirudin by a topology-based approach
A theoretical model for the folding of proteins containing disulfide bonds is
introduced. The model exploits the knowledge of the native state to favour the
progressive establishment of native interactions. At variance with traditional
approaches based on native topology, not all native bonds are treated in the
same way; in particular, a suitable energy term is introduced to account for
the special strength of disulfide bonds (irrespective of whether they are
native or not) as well as their ability to undergo intra-molecular reshuffling.
The model thus possesses the minimal ingredients necessary to investigated the
much debated issue of whether the re-folding process occurs through partially
structured intermediates with native or non-native disulfide bonds. This
strategy is applied to a context of particular interest, the re-folding process
of Hirudin, a thrombin-specific protease inhibitor, for which conflicting
folding pathways have been proposed. We show that the only two parameters in
the model (temperature and disulfide strength) can be tuned to reproduce well a
set of experimental transitions between species with different number of formed
disulfide. This model is then used to provide a characterisation of the folding
process and a detailed description of the species involved in the rate-limiting
step of Hirudin refolding.Comment: 14 pages, 9 figure
Brownian yet non-Gaussian diffusion: from superstatistics to subordination of diffusing diffusivities
A growing number of biological, soft, and active matter systems are observed
to exhibit normal diffusive dynamics with a linear growth of the mean squared
displacement, yet with a non-Gaussian distribution of increments. Based on the
Chubinsky-Slater idea of a diffusing diffusivity we here establish and analyze
a minimal model framework of diffusion processes with fluctuating diffusivity.
In particular, we demonstrate the equivalence of the diffusing diffusivity
process with a superstatistical approach with a distribution of diffusivities,
at times shorter than the diffusivity correlation time. At longer times a
crossover to a Gaussian distribution with an effective diffusivity emerges.
Specifically, we establish a subordination picture of Brownian but non-Gaussian
diffusion processes, that can be used for a wide class of diffusivity
fluctuation statistics. Our results are shown to be in excellent agreement with
simulations and numerical evaluations.Comment: 19 pages, 6 figures, RevTeX. Physical Review X, at pres
Pengaruh Gaya Kepemimpinan Transformasional dan Self Efficacy terhadap Komitmen Organisasi (pada Hotel Grand Zuri Pekanbaru)
This study aims to analyze the transformational leadership style and effectiveness selff and its influence on organizational commitment at Grand Zuri Hotel Pekanbaru. Transformational leadership as a variable (X1), Selff Eficacy as a variable (X2), and Organizational Commitment as a variable (Y). Method in this research is descriptive and quantitative by using program of SPSS 21, where sample used is 89 employees conducted by census. Technical data through questionnaire The results of analysis using validity test, reliability test, determination test, simple linear regression test, multiple linear regression test, t test and F test can be concluded significant transformational leadership towards organizational commitment at Grand Zuri Hotel Pekanbaru, It can be concluded significant Self efficacy to organizational commitment at Grand Zuri Hotel Pekanbaru as well as transformational leadership and significant effectiveness towards organizational commitment at Grand Zuri Hotel Pekanbaru
Pengaruh Pemberian Motivasi dan Lingkungan Kerja terhadap Komitmen Organisasi Karyawan (Studi pada Bank Bri Cabang Pekanbaru)
This study aims to determine the effect of motivation and work environment on employee organizational commitment (study at Bank BRI Pekanbaru Branch). Motivation (X1), Work environment (X2) and organizational commitment (Y).The method in this research is quantitative with SPSS program, where the samples used are employees of Bank BRI Pekanbaru that is as much as 94 respondents. In accordance with opinion (Roscoe, 2009) that the appropriate size in the study is 30 to 500. That number can already represent the population. Technique of collecting data through questionnaire.The result of this research conclude that motivation and work environment variable have significant influence to organizational commitment of employees of Bank BRI Pekanbaru Branch
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