A xylose-stimulated xylanase–xylose binding protein chimera created by random nonhomologous recombination

Additional file 3. Hot spot residues at the protein–protein interface between the XBP and XynA domains by molecular dynamics simulations

Structure, thermostability and activity of xylanases: a molecular dynamics study

As xilanases (EC 3.2.1.8), enzimas produzidas por diversos organismos, são capazes de hidrolisar as ligações -1,4 da cadeia principal da xilana, o mais abundante polissacarídeo hemicelulósico da natureza. O grande potencial biotecnológico das xilanases consiste na sua aplicação nas etapas de branqueamento do papel, nas quais a xilana é hidrolisada sob condição de temperatura elevada para facilitar a remoção da lignina (substância responsável pela coloração), diminuindo a quantidade de compostos clorados utilizados nestas etapas. A termoestabilidade e a especificidade pela xilana são as propriedades responsáveis pelo grande interesse biotecnológico e comercial que as xilanases têm atraído. As xilanases mesofílica, XBC, de temperatura ótima 55ºC (produzida pela bactéria Bacillus circulans) e termofílica, XTL, de temperatura ótima 70ºC (produxida pelo fungo Thermomyces lanuginosus) foram estudadas comparativamente por simulação de dinâmica. Os sistemas foram modelados pelo campo de força GROMOS-96(43A1) e as simulações realizadas pelo programa GROMACS 3.2. O objetivo do trabalho é relacionar as diferenças estruturais, energéticas e dinâmicas com as diferentes termostabilidades exibidas por estas enzimas. Os estudos por simulação sugerem claramente a existência de dois grandes tipos de regiões nas enzimas xilanases XBC e XTL: uma conservada e de grande estabilidade, que é o domínio palma, e a outra que pode sofrer grande movimentação, no caso o domínio polegar. Uma movimentação do tipo abre-fecha de dobradiça foi identificada. O monitoramento das ligações de hidrogênio inter/intramoleculares e pontes salinas ao longo do tempo e em função da temperatura permitem explicar clara e detalhadamente as diferentes termoestabilidades exibidas por duas proteínas da mesma família que compartilham de uma estrutura tridimensional altamente semelhante. Foi possível identificar 14 resíduos carregados que estão presentes na XTL e ausentes na XBC, tais resíduos devem ser considerados sítios potenciais de mutação na XBC. De uma maneira geral, tanto na XBC quanto na XTL, a presença do substrato não altera as características de cada domínio/região mas confere estabilidade para o domínio polegar. Nenhuma diferença clara na afinidade pelo substrato foi detectada pelas interações intermoleculares proteína-substrato.The enzymes xylanases (EC 3.2.1.8) are produced by several microorganisms and used to hydrolyze the -1,4 bonds of the xylan main chain, the most abundant hemicellulose in nature. The great biotechnological potential of the xylanases is due to its application in the pulp-bleaching processes when the xylan is hydrolyzed under high temperature condition to optimize the lignin removal. This procedure presents the advantage to reduce the amount of chlorine chemicals used in the pulp-bleaching process. The required properties of a biotechnologically useful xylanase include thermostability and high affinity for xylan. The mesophilic, XBC, (from Bacillus circulans) and thermophilic, XTL, (from Thermomyces lanuginosus) xylanases were studied by molecular dynamics simulations. The primary structures of these enzymes are almost completely different while the tertiary structures are identical. The objective of the study is to get some insight on the factors that are responsible for the xylanase thermostability. The systems were modeled by the GROMOS96-(43A1) force field and the molecular dynamic simulations were performed by the GROMACS 3.2 package in the temperature range from 25 to 80ºC. The results obtained with both xylanases were compared. The existence of two kinds of regions was identified in XBC and XTL: the first one conserved and highly stable is formed by the so-called palm and fingers domains. The second region exhibits large movements: this is the thumb domain. A kind of open-close motion was identified that maybe can facilitate the access of the xylane to the active center. The inter/intramolecular hydrogen bonds and salt bridges allow to explain at great length the thermostability differences between the two enzymes. It was possible to identify 14 charged residues present in the XTL with no similar in the XBC: such residues must be considered outstanding mutation sites in XBC. In the presence of the substrate, the characteristics of each domain/region are not modified but the stability of the thumb domain is increased. No difference in the affinity for the substrate was detected between the xylanases and it can be suggested that the activation energies are similar. Two water molecules were found in the active site supporting the hydrolysis mechanisms proposed in the literature

Structure, thermostability and activity of xylanases: a molecular dynamics study

As xilanases (EC 3.2.1.8), enzimas produzidas por diversos organismos, são capazes de hidrolisar as ligações -1,4 da cadeia principal da xilana, o mais abundante polissacarídeo hemicelulósico da natureza. O grande potencial biotecnológico das xilanases consiste na sua aplicação nas etapas de branqueamento do papel, nas quais a xilana é hidrolisada sob condição de temperatura elevada para facilitar a remoção da lignina (substância responsável pela coloração), diminuindo a quantidade de compostos clorados utilizados nestas etapas. A termoestabilidade e a especificidade pela xilana são as propriedades responsáveis pelo grande interesse biotecnológico e comercial que as xilanases têm atraído. As xilanases mesofílica, XBC, de temperatura ótima 55ºC (produzida pela bactéria Bacillus circulans) e termofílica, XTL, de temperatura ótima 70ºC (produxida pelo fungo Thermomyces lanuginosus) foram estudadas comparativamente por simulação de dinâmica. Os sistemas foram modelados pelo campo de força GROMOS-96(43A1) e as simulações realizadas pelo programa GROMACS 3.2. O objetivo do trabalho é relacionar as diferenças estruturais, energéticas e dinâmicas com as diferentes termostabilidades exibidas por estas enzimas. Os estudos por simulação sugerem claramente a existência de dois grandes tipos de regiões nas enzimas xilanases XBC e XTL: uma conservada e de grande estabilidade, que é o domínio palma, e a outra que pode sofrer grande movimentação, no caso o domínio polegar. Uma movimentação do tipo abre-fecha de dobradiça foi identificada. O monitoramento das ligações de hidrogênio inter/intramoleculares e pontes salinas ao longo do tempo e em função da temperatura permitem explicar clara e detalhadamente as diferentes termoestabilidades exibidas por duas proteínas da mesma família que compartilham de uma estrutura tridimensional altamente semelhante. Foi possível identificar 14 resíduos carregados que estão presentes na XTL e ausentes na XBC, tais resíduos devem ser considerados sítios potenciais de mutação na XBC. De uma maneira geral, tanto na XBC quanto na XTL, a presença do substrato não altera as características de cada domínio/região mas confere estabilidade para o domínio polegar. Nenhuma diferença clara na afinidade pelo substrato foi detectada pelas interações intermoleculares proteína-substrato.The enzymes xylanases (EC 3.2.1.8) are produced by several microorganisms and used to hydrolyze the -1,4 bonds of the xylan main chain, the most abundant hemicellulose in nature. The great biotechnological potential of the xylanases is due to its application in the pulp-bleaching processes when the xylan is hydrolyzed under high temperature condition to optimize the lignin removal. This procedure presents the advantage to reduce the amount of chlorine chemicals used in the pulp-bleaching process. The required properties of a biotechnologically useful xylanase include thermostability and high affinity for xylan. The mesophilic, XBC, (from Bacillus circulans) and thermophilic, XTL, (from Thermomyces lanuginosus) xylanases were studied by molecular dynamics simulations. The primary structures of these enzymes are almost completely different while the tertiary structures are identical. The objective of the study is to get some insight on the factors that are responsible for the xylanase thermostability. The systems were modeled by the GROMOS96-(43A1) force field and the molecular dynamic simulations were performed by the GROMACS 3.2 package in the temperature range from 25 to 80ºC. The results obtained with both xylanases were compared. The existence of two kinds of regions was identified in XBC and XTL: the first one conserved and highly stable is formed by the so-called palm and fingers domains. The second region exhibits large movements: this is the thumb domain. A kind of open-close motion was identified that maybe can facilitate the access of the xylane to the active center. The inter/intramolecular hydrogen bonds and salt bridges allow to explain at great length the thermostability differences between the two enzymes. It was possible to identify 14 charged residues present in the XTL with no similar in the XBC: such residues must be considered outstanding mutation sites in XBC. In the presence of the substrate, the characteristics of each domain/region are not modified but the stability of the thumb domain is increased. No difference in the affinity for the substrate was detected between the xylanases and it can be suggested that the activation energies are similar. Two water molecules were found in the active site supporting the hydrolysis mechanisms proposed in the literature

An insight into the thermostability of a pair of xylanases: the role of hydrogen bonds

Xylanases are enzymes that are very tolerant to temperature. Their potential use in several biotechnological applications, such as animal food manufacture and pulp bleaching, is due to their intrinsic thermostability. The present report deals with two xylanases, the mesophilic xylanase from Bacillus circulans, BCX, and the thermophilic xylanase from Thermomyces lanuginosus,TLX. These enzymes belong to family 11, and they are the most structurally similar mesophilic-thermophilic pair. Molecular dynamics simulations were employed to investigate the factors responsible for the different thermostabilities exhibited by these structurally similar enzymes. Their active site is their most rigid region, and it is equally rigid at all temperatures. Inter and intramolecular interactions, hydrogen bonds in particular, are the key to the main differences between BCX and TLX. The intramolecular hydrogen bonds and salt bridges are important for maintenance of the backbone rigidity even at high temperature, and the highly solvated surface is a clear optimization in TLX compared with BCX. The main differences between these two enzymes can be found on the fingers domain, which indicates that this domain must be the target for the site-directed mutagenesis responsible for improving the temperature tolerance of this family of enzymes.CNPq Conselho Nacional de Desenvolvimento Cientifico e TecnologicoFAPESP Fundacao de Amparo a Pesquisa do Estado de Sao Paul

Characterization of temperature dependent and substrate-binding cleft movements in Bacillus circulans family 11 xylanase: A molecular dynamics investigation

Background: Xylanases (EC 3.2.1.8) hydrolyze xylan, one of the most abundant plant polysaccharides found in nature, and have many potential applications in biotechnology. Methods: Molecular dynamics simulations were used to investigate the effects of temperature between 298 to 338 K and xylobiose binding on residues located in the substrate-binding cleft of the family 11 xylanase from Bacillus circulans (BcX). Results: In the absence of xylobiose the BcX exhibits temperature dependent movement of the thumb region which adopts an open conformation exposing the active site at the optimum catalytic temperature (328 K). In the presence of substrate, the thumb region restricts access to the active site at all temperatures, and this conformation is maintained by substrate/protein hydrogen bonds involving active site residues, including hydrogen bonds between Tyr69 and the 2` hydroxyl group of the substrate. Substrate access to the active site is regulated by temperature dependent motions that are restricted to the thumb region, and the BcX/substrate complex is stabilized by extensive intermolecular hydrogen bonding with residues in the active site. General significance: These results call for a revision of both the ""hinge-bending"" model for the activity of group 11 xylanases, and the role of Tyr69 in the catalytic mechanism. (C) 2009 Elsevier B.V. All rights reserved.CNPq Conselho Nacional cle Desenvolvimento Cientifico e TecnologicoFAPESP Funda Ao de Amparo a Pesquisa do Estado de Sao Paul

Mapping of suramin binding sites on the group IIA human secreted phospholipase A(2)

Suramin is a polysulphonated napthylurea used as an antiprotozoal/anthelminitic drug, which also inhibits a broad range of enzymes. Suramin binding to recombinant human secreted group IIA phospholipase A(2) (hsPLA(2)GIIA) was investigated by molecular dynamics simulations (MD) and isothermal titration calorimetry (ITC). MD indicated two possible bound suramin conformations mediated by hydrophobic and electrostatic interactions with amino-acids in three regions of the protein. namely the active-site and residues located in the N- and C-termini, respectively. All three binding sites are located on the phospholipid membrane recognition surface, suggesting that suramin may inhibit the enzyme, and indeed a 90% reduction in hydrolytic activity was observed in the presence of 100 nM suramin. These results correlated with ITC data, which demonstrated 2.7 suramin binding sites on the hsPLA(2)GIIA, and indicates that suramin represents a novel class of phosphohpase A(2) inhibitor. (C) 2009 Elsevier Inc. All rights reserved.CNPq[304982/2006-7]CNPq[152669/2007-8]FAPESP[05/50379-0]Universidade de São Paulo - Pró-Reitoria de Pesquisa PRP-US

Characterization of suramin binding sites on the human group IIA secreted phospholipase A(2) by site-directed mutagenesis and molecular dynamics simulation

Suramin is a polysulphonated naphthylurea with inhibitory activity against the human secreted group IIA phospholipase A(2) (hsPLA2GIIA), and we have investigated suramin binding to recombinant hsPLA2GIIA using site-directed mutagenesis and molecular dynamics (MD) simulations. The changes in suramin binding affinity of 13 cationic residue mutants of the hsPLA2GIIA was strongly correlated with alterations in the inhibition of membrane damaging activity of the protein. Suramin binding to hsPLA2GIIA was also studied by MD simulations, which demonstrated that altered intermolecular potential energy of the suramin/mutant complexes was a reliable indicator of affinity change. Although residues in the C-terminal region play a major role in the stabilization of the hsPLA2GIIA/suramin complex, attractive and repulsive hydrophobic and electrostatic interactions with residues throughout the protein together with the adoption of a bent suramin conformation, all contribute to the stability of the complex. Analysis of the h5PLA2GIIA/suramin interactions allows the prediction of the properties of suramin analogues with improved binding and higher affinities which may be candidates for novel phospholipase A(2) inhibitors. (C) 2012 Elsevier Inc. All rights reserved.FAPESP [2009/13902-7, 2002/12746-2]FAPESPCNPqCNPq [152669/2007-8, 504807/2009-9, 304982/2006-7]PRPUSPPRP-US