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Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals

In this work, we present a methodology to combine residue interaction data obtained from coevolutionary information and cross-linking/mass spectrometry distance constraints in order to identify functional states of proteins.

Parametric Models to Compute Tryptophan Fluorescence Wavelengths from Classical Protein Simulations

Fluorescence spectroscopy is an important method to study protein conformational dynamics and solvation structures. Tryptophan (Trp) residues are the most important and practical intrinsic probes for protein fluorescence due to the variability of their fluorescence wavelengths: Trp residues emit in wavelengths ranging from 308 to 360 nm depending on the local molecular environment. Fluorescence involves electronic transitions, thus its computational modeling is a challenging task.

On hardening silver nanocubes by high-velocity impacts: a fully atomistic molecular dynamics investigation

Gradient nanograins (GNG) creation in metals has been a promising approach to obtain ultra-strong materials. Recently, R. Thevamaran et al. (Science 354:312 in 2016) proposed a single-step method based on high-velocity impacts of silver nanocubes (SNC) to produce almost perfect GNG. However, after certain time, these grains spontaneously coalesce, which compromises the induced hardening and other mechanical properties.

Novo portal reunirá bancos de dados genômicos da América Latina

A ideia é que esse portal contenha links para os diferentes bancos de dados de variantes genéticas estabelecidos na região. Caso os dados ainda estejam sendo gerados e não estejam disponíveis publicamente, podemos colocar ao menos os links para os projetos para que todos saibam o que está acontecendo em termos de pesquisa genômica na América Latina”, disse Iscia Lopes-Cendes, professora da Faculdade de Ciências Médicas da Universidade Estadual de Campinas (FCM-Unicamp) e membro do Comitê Diretivo da BIPMed.

Molecular mechanism of activation of Burkholderia cepacia Lipase at aqueous-organic interfaces

Lipases are water-soluble enzymes which catalyze the hydrolysis of lipids. Since lipids are mostly hydrophobic, lipase activity occur preferentially at interfaces of aqueous and organic phases. In this work, we study the molecular mechanisms by which the Burkholderia cepacia lipase (BCL) is activated at interfaces of water with octane and with methyl caprylate (CAME). We show that BCL assumes very rapidly a preferential orientation at the interfaces, in which the active site is exposed to the organic phase.

Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions

Preferential solvation is a fundamental parameter for the interpretation of solubility and solute structural stability. The molecular basis for solute-solvent interactions can be obtained through distribution functions, and the thermodynamic connection to experimental data depends on the computation of distribution integrals, specifically Kirkwood-Buff integrals for the determination of preferential interactions. Standard radial distribution functions, however, are not convenient for the study of the solvation of complex, non-spherical solutes, as proteins.

Best Paper Award at SBAC-PAD 2017

The article "Data Coherence Analysis and Optimization for Heterogeneous Computing" by Rafael Sousa, Fernando Pereira, Marcio Pereira and Guido Araujo received the Best Paper Award at the 2017 edition of the International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD).

A network model predicts the intensity of residue-protein thermal coupling

Motivation: The flow of vibrational energy in proteins has been shown not to obey expectations for isotropic media. The existence of preferential pathways for energy transport, with probable connections to allostery mechanisms, has been repeatedly demonstrated.

Aspergillus niger beta-glucosidase has a cellulase-like tadpole molecular shape: insights into GH3 beta-glucosidases structure and function

Aspergillus niger is known to secrete large amounts of β-glucosidases, which have a variety of biotechnological and industrial applications. Here, we purified an A. niger β-glucosidase (AnBgl1) and conducted its biochemical and biophysical analyses. Surprisingly, the small-angle X-ray experiments reveal that AnBgl1 has a tadpole-like structure, with the N-terminal catalytic domain and C-terminal fibronectin III-like domain (FnIII) connected by the long linker peptide in an extended conformation.

Molecular basis of substrate recognition and specificity revealed in family 12 glycoside hydrolases

Fungal GH12 enzymes are classified as xyloglucanases when they specifically target xyloglucans, or promiscuous endoglucanases when they exhibit catalytic activity against xyloglucan and β-glucan chains. Several structural and functional studies involving GH12 enzymes tried to explain the main patterns of xyloglucan activity, but what really determines xyloglucanase specificity remains elusive. Here, three fungal GH12 enzymes from Aspergillus clavatus (AclaXegA), A. zonatus (AspzoGH12), and A.

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