A single‐stranded DNA aptamer against mannose‐capped lipoarabinomannan enhances anti‐tuberculosis activity of macrophages through downregulation of lipid‐sensing nuclear receptor peroxisome proliferator‐activated receptor γ expression

Mannose‐capped lipoarabinomannan (ManLAM) is an immunomodulatory epitope of Mycobacterium tuberculosis (Mtb). An aptamer (ZXL1) that specifically binds to ManLAM from the virulent Mtb H37Rv strain was previously generated and it was found that ZXL1 functions as an antagonist, inhibiting the ManLAM‐induced immunosuppression of DCs. In the present study, it was found that ZXL1 inhibits Mtb entry into murine macrophages and that ZXL1 enhances IL‐1β and IL‐12 mRNA expression and cytokine production in ManLAM‐treated macrophages but decreases IL‐10 production. Inducible nitric oxide synthase expression in macrophages was upregulated in the presence of ZXL1 after stimulation with ManLAM. ZXL1 was also found to inhibit expression of lipid‐sensing nuclear receptor peroxisome proliferator‐activated receptor γ (PPAR‐γ). These results suggest that ZXL1 promotes anti‐tuberculosis activity through downregulation of PPAR‐γ expression, which may contribute to M1 macrophage polarization and Mtb killing by macrophages.     

Molecular modeling of the binding modes of the iron‐sulfur protein to the Jac1 co‐chaperone from Saccharomyces cerevisiae by all‐atom and coarse‐grained approaches

The iron‐sulfur protein 1 (Isu1) and the J‐type co‐chaperone Jac1 from yeast are part of a huge ATP‐dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron‐sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1–Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I‐TASSER server and YASARA software and thereafter tested for stability in the all‐atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1–Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse‐grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ‐shaped Jac1 molecule by the β‐sheet section of Isu1. Residues L₁₀₅, L₁₀₉, and Y₁₆₃ of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1–12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N₉₅, T₉₈, P₁₀₂, H₁₁₂, V₁₅₉, L₁₆₇, and A₁₇₀ of Jac1, not yet tested experimentally, were also found to be important in binding. Proteins 2015; 83:1414–1426. © 2015 Wiley Periodicals, Inc.     

Bacillus coagulans tolerance to 1‐ethyl‐3‐methylimidazolium‐based ionic liquids in aqueous and solid‐state thermophilic culture

The use of ionic liquids (ILs) to disrupt the recalcitrant structure of lignocellulose and make polysaccharides accessible to hydrolytic enzymes is an emerging technology for biomass pretreatment in lignocellulosic biofuel production. Despite efforts to reclaim and recycle IL from pretreated biomass, residual IL can be inhibitory to microorganisms used for downstream fermentation. As a result, pathways for IL tolerance are needed to improve the activity of fermentative organisms in the presence of IL. In this study, microbial communities from compost were cultured under high‐solids and thermophilic conditions in the presence of 1‐ethyl‐3‐methylimidazolium‐based ILs to enrich for IL‐tolerant microorganisms. A strain of Bacillus coagulans isolated from an IL‐tolerant community was grown in liquid and solid‐state culture in the presence of the ILs 1‐ethyl‐3‐methylimidazolium acetate ([C2mim][OAc]) or 1‐ethyl‐3‐methylimidazolium chloride ([C2mim][Cl]) to gauge IL tolerance. Viability and respiration varied with the concentration of IL applied and the type of IL used. B. coagulans maintained growth and respiration in the presence of 4 wt% IL, a concentration similar to that present on IL‐pretreated biomass. In the presence of both [C2mim][OAc] and [C2mim][Cl] in liquid culture, B. coagulans grew at a rate approximately half that observed in the absence of IL. However, in solid‐state culture, the bacteria were significantly more tolerant to [C2mim][Cl] compared with [C2mim][OAc]. B. coagulans tolerance to IL under industrially relevant conditions makes it a promising bacterium for understanding mechanisms of IL tolerance and discovering IL tolerance pathways for use in other microorganisms, particularly those used in bioconversion of IL‐pretreated plant biomass. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:311–316, 2014     

A hybrid NMR/SAXS‐based approach for discriminating oligomeric protein interfaces using Rosetta

Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet‐V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. Proteins 2015; 83:309–317. © 2014 Wiley Periodicals, Inc.     

Modulatory effects of interferon‐γ and interleukin‐4 on cellular immune responses against Hypoderma lineatum antigens

This study investigates the in vitro modulatory effects of interferon‐γ (IFN‐γ) and interleukin‐4 (IL‐4) on both proliferative bovine T cell responses and IL‐10 production induced by different antigens [crude larval extract and the purified fractions hypodermin A, B and C (HyA, HyB, HyC)] obtained from first instars of Hypoderma lineatum (Diptera: Oestridae), alone or in the presence of the mitogen concanavalin A. Incubation with the different parasitic antigens resulted in significant inhibition of T cell proliferation and IL‐10 production, which, in general, did not revert after the addition of IFN‐γ and IL‐4. In the absence of antigens, IL‐4 induced significant inhibition of mitogen‐induced T cell responses. Exogenous IFN‐γ exhibited an inhibitory effect on cell proliferation in the presence of the purified fractions HyB and HyC. These in vitro data suggest that far from neutralizing the effects of larval antigens, the addition of IFN‐γ potentiates their anti‐proliferative activity; by contrast, IL‐4 had no consistent effects on proliferative responses to Hypoderma. IL‐4 provoked an increment of IL‐10 levels in supernatants of HyB‐stimulated cells. In conclusion, exogenous IFN‐γ and IL‐4 were unable to counteract the suppressor effects of H. lineatum antigens.     

Regulatory effects of Spirulina complex polysaccharides on growth of murine RSV‐M glioma cells through Toll‐like receptor 4

This study is the first to report that Spirulina complex polysaccharides (CPS) suppress glioma growth by down‐regulating angiogenesis via a Toll‐like receptor 4 signal. Murine RSV‐M glioma cells were implanted s.c. into C3H/HeN mice and TLR4 mutant C3H/HeJ mice. Treatment with either Spirulina CPS or Escherichia coli (E. coli) lipopolysaccharides (LPS) strongly suppressed RSV‐M glioma cell growth in C3H/HeN, but not C3H/HeJ, mice. Glioma cells stimulated production of interleukin (IL)‐17 in both C3H/HeN and C3H/HeJ tumor‐bearing mice. Treatment with E. coli LPS induced much greater IL‐17 production in tumor‐bearing C3H/HeN mice than in tumor‐bearing C3H/HeJ mice. In C3H/HeN mice, treatment with Spirulina CPS suppressed growth of re‐transplanted glioma; however, treatment with E. coli LPS did not, suggesting that Spirulina CPS enhance the immune response. Administration of anti‐cluster of differentiation (CD)8, anti‐CD4, anti‐CD8 antibodies, and anti‐asialo GM1 antibodies enhanced tumor growth, suggesting that T cells and natural killer cells or macrophages are involved in suppression of tumor growth by Spirulina CPS. Although anti‐interferon‐γ antibodies had no effect on glioma cell growth, anti‐IL‐17 antibodies administered four days after tumor transplantation suppressed growth similarly to treatment with Spirulina CPS. Less angiogenesis was observed in gliomas from Spirulina CPS‐treated mice than in those from saline‐ or E. coli LPS‐treated mice. These findings suggest that, in C3H/HeN mice, Spirulina CPS antagonize glioma cell growth by down‐regulating angiogenesis, and that this down‐regulation is mediated in part by regulating IL‐17 production.     

Pressure‐induced structural transition of mature HIV‐1 protease from a combined NMR/MD simulation approach

We investigate the pressure‐induced structural changes in the mature human immunodeficiency virus type 1 protease dimer, using residual dipolar coupling (RDC) measurements in a weakly oriented solution. ¹D_NH RDCs were measured under high‐pressure conditions for an inhibitor‐free PR and an inhibitor‐bound complex, as well as for an inhibitor‐free multidrug resistant protease bearing 20 mutations (PR20). While PR20 and the inhibitor‐bound PR were little affected by pressure, inhibitor‐free PR showed significant differences in the RDCs measured at 600 bar compared with 1 bar. The structural basis of such changes was investigated by MD simulations using the experimental RDC restraints, revealing substantial conformational perturbations, specifically a partial opening of the flaps and the penetration of water molecules into the hydrophobic core of the subunits at high pressure. This study highlights the exquisite sensitivity of RDCs to pressure‐induced conformational changes and illustrates how RDCs combined with MD simulations can be used to determine the structural properties of metastable intermediate states on the folding energy landscape. Proteins 2015; 83:2117–2123. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.     

Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca2+‐ATPase

Sarco(endo)plasmic reticulum Ca²⁺‐ATPase transports two Ca²⁺ per ATP‐hydrolyzed across biological membranes against a large concentration gradient by undergoing large conformational changes. Structural studies with X‐ray crystallography revealed functional roles of coupled motions between the cytoplasmic domains and the transmembrane helices in individual reaction steps. Here, we employed “Motion Tree (MT),” a tree diagram that describes a conformational change between two structures, and applied it to representative Ca²⁺‐ATPase structures. MT provides information of coupled rigid‐body motions of the ATPase in individual reaction steps. Fourteen rigid structural units, “common rigid domains (CRDs)” are identified from seven MTs throughout the whole enzymatic reaction cycle. CRDs likely act as not only the structural units, but also the functional units. Some of the functional importance has been newly revealed by the analysis. Stability of each CRD is examined on the morphing trajectories that cover seven conformational transitions. We confirmed that the large conformational changes are realized by the motions only in the flexible regions that connect CRDs. The Ca²⁺‐ATPase efficiently utilizes its intrinsic flexibility and rigidity to response different switches like ligand binding/dissociation or ATP hydrolysis. The analysis detects functional motions without extensive biological knowledge of experts, suggesting its general applicability to domain movements in other membrane proteins to deepen the understanding of protein structure and function. Proteins 2015; 83:746–756. © 2015 Wiley Periodicals, Inc.     

Structure of the heme/hemoglobin outer membrane receptor ShuA from Shigella dysenteriae: Heme binding by an induced fit mechanism

Shigella dysentriae and other Gram‐negative human pathogens are able to use iron from heme bound to hemoglobin for growing. We solved at 2.6 Å resolution the 3D structure of the TonB‐dependent heme/hemoglobin outer membrane receptor ShuA from S. dysenteriae. ShuA binds to hemoglobin and transports heme across the outer membrane. The structure consists of a C‐terminal domain that folds into a 22‐stranded transmembrane β‐barrel, which is filled by the N‐terminal plug domain. One distal histidine ligand of heme is located at the apex of the plug, exposed to the solvent. His86 is situated 9.86 Å apart from His420, the second histidine involved in the heme binding. His420 is in the extracellular loop L7. The heme coordination by His86 and His420 involves conformational changes. The comparisons with the hemophore receptor HasR of Serratia marcescens bound to HasA‐Heme suggest an extracellular induced fit mechanism for the heme binding. The loop L7 contains hydrophobic residues which could interact with the hydrophobic porphyring ring of heme. The energy required for the transport by ShuA is derived from the proton motive force after interactions between the periplasmic N‐terminal TonB‐box of ShuA and the inner membrane protein, TonB. In ShuA, the TonB‐box is buried and cannot interact with TonB. The structural comparisons with HasR suggest its conformational change upon the heme binding for interacting with TonB. The signaling of the heme binding could involve a hydrogen bond network going from His86 to the TonB‐box. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Antiapoptotic Bcl‐2 homolog CED‐9 in Caenorhabditis elegans: Dynamics of BH3 and CED‐4 binding regions and comparison with mammalian antiapoptotic Bcl‐2 proteins

Proteins belonging to Bcl‐2 family regulate intrinsic cell death pathway. Although mammalian antiapoptotic Bcl‐2 members interact with multiple proapoptotic proteins, the Caenorhabditis elegans Bcl‐2 homolog CED‐9 is known to have only two proapoptotic partners. The BH3‐motif of proapoptotic proteins bind to the hydrophobic groove of prosurvival proteins formed by the Bcl‐2 helical fold. CED‐9 is also known to interact with CED‐4, a homolog of the human cell death activator Apaf1. We have performed molecular dynamics simulations of CED‐9 in two forms and compared the results with those of mammalian counterparts Bcl‐X_L, Bcl‐w, and Bcl‐2. Our studies demonstrate that the region forming the hydrophobic cleft is more flexible compared with the CED‐4‐binding region, and this is generally true for all antiapoptotic Bcl‐2 proteins studied. CED‐9 is the most stable protein during simulations and its hydrophobic pocket is relatively rigid explaining the absence of functional redundancy in CED‐9. The BH3‐binding region of Bcl‐2 is less flexible among the mammalian proteins and this lends support to the studies that Bcl‐2 binds to less number of BH3 peptides with high affinity. The C‐terminal helix of CED‐9 lost its helical character because of a large number of charged residues. We speculate that this region probably plays a role in intracellular localization of CED‐9. The BH4‐motif accessibility in CED‐9 and Bcl‐w is controlled by the loop connecting the first two helices. Although CED‐9 adopts the same Bcl‐2 fold, our studies highlight important differences in the dynamic behavior of CED‐9 and mammalian antiapoptotic homologs. Proteins 2014; 82:1035–1047. © 2013 Wiley Periodicals, Inc.     

Optimized distance‐dependent atom‐pair‐based potential DOOP for protein structure prediction

The DOcking decoy‐based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance‐dependent atom‐pair interactions. To optimize the atom‐pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand–receptor systems (or just pairs). Thus, a total of 8609 ligand–receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand–receptor systems, 1000 evenly sampled docking decoys with 0–10 Å interface root‐mean‐square‐deviation (iRMSD) were generated with a method used before for protein–protein docking. A neural network‐based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel‐like energy landscape for the interaction between these hypothetical ligand–receptor systems. Thus, our method hierarchically models the overall funnel‐like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom‐pair‐based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation‐dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand–receptor systems and their decoys are freely available at http://agknapp.chemie.fu‐berlin.de/doop/ . Proteins 2015; 83:881–890. © 2015 Wiley Periodicals, Inc.     

Structure and function of Escherichia coli RimK,an ATP‐grasp fold,l‐glutamyl ligase enzyme

We report herein the crystal structure of Escherichia coli RimK at a resolution of 2.85 Å, an enzyme that catalyzes the post‐translational addition of up to 15 C‐terminal glutamate residues to ribosomal protein S6. The structure belongs to the ATP‐grasp superfamily and is organized as a tetramer, consistent with gel filtration analysis. Each subunit consists of three distinct structural domains and the active site is located in the cleft between these domains. The catalytic reaction appears to occur at the junction between the three domains as ATP binds between the B and C domains, and other substrates bind nearby.Proteins 2013; 81:1847–1854. © 2013 Wiley Periodicals, Inc.     

Conformational studies of parathyroid hormone (PTH)/PTH‐related protein (PTHrP) point‐mutated hybrids

The N‐terminal 1–34 segments of both parathyroid hormone (PTH) and parathyroid hormone‐related protein (PTHrP) bind and activate the same membrane receptor in spite of major differences between the two hormones in their amino acid sequence. Recently, it was shown that in (1–34)PTH/PTHrP segmental hybrid peptides, the N‐terminal 1–14 segment of PTHrP is incompatible with the C‐terminal 15–34 region of PTH leading to substantial reduction in potency. The sites of incompatibility were identified as positions 5 in PTH and 19 in PTHrP. In the present paper we describe the synthesis, biological evaluation, and conformational characterization of two point‐mutated PTH/PTHrP 1–34 hybrids in which the arginine residues at positions 19 and 21 of the native sequence of PTHrP have been replaced by valine (hybrid V²¹) and glutamic acid (hybrid E¹⁹), respectively, taken from the PTH sequence. Hybrid V²¹ exhibits both high receptor affinity and biological potency, while hybrid E¹⁹ binds weakly and is poorly active. The conformational properties of the two hybrids were studied in aqueous solution containing dodecylphosphocholine (DPC) micelles and in water/2,2,2‐trifluoroethanol (TFE) mixtures. Upon addition of TFE or DPC micelles to the aqueous solution, both hybrids undergo a coil‐helix transition. The maximum helix content in 1 : 1 water/TFE, obtained by CD data for both hybrids, is ∼ 80%. In the presence of DPC micelles, the maximum helix content is ∼ 40%. The conformational properties of the two hybrids in the micellar system were further investigated by combined 2D‐nmr, distance geometry (DG), and molecular dynamics (MD) calculations. The common structural motif, consisting of two helical segments located at N‐ and C‐termini, was observed in both hybrids. However, the biologically potent hybrid V²¹ exhibits two flexible sites, centered at residues 12 and 19 and connecting helical segments, while the flexibility sites in the weakly active hybrid E¹⁹ are located at position 11 and in the sequence 20–26. Our findings support the hypothesis that the presence and location of flexibility points between helical segments are essential for enabling the active analogs to fold into the bioactive conformation upon interaction with the receptor. © 1999 John Wiley & Sons, Inc. Biopoly 50: 525–535, 1999     

Mock communities highlight the diversity of host‐associated eukaryotes

Host‐associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High‐throughput sequencing (HTS) tools have illuminated the vast diversity of host‐associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall‐Ngai et al. 2013 ). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al. 2011 ) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host‐associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host‐associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. 2014 ; Simon et al. 2015 ; de Vargas et al. 2015 ). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al. 2014 )]. In this issue of Molecular Ecology, Geisen et al. ( 2015 ) use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free‐living. By isolating the host‐associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high‐throughput sequencing (HTS) and reinforce the ubiquity of these host‐associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free‐living, but instead need to design studies that specifically enumerate the diversity and function of host‐associated eukaryotes. Doing so will allow the field to determine the role host‐associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host‐associated communities, disease ecology and more.     

Blocking integrin inactivation as an anti‐angiogenic therapy

During angiogenesis, endothelial cell migration is coordinated by integrin‐mediated contact with the extra‐cellular matrix (ECM), coupled with receptor tyrosine kinase signalling to regulate dynamic cytoskeletal and plasma membrane reorganization. A recent paper by Vitorino et al ( 2015 ) defined a new MAP4K4–moesin–talin–β1‐integrin pathway that could be therapeutically exploited to suppress pathologic angiogenesis.     

Identification of interleukin‐16 (IL‐16) and interleukin‐17D (IL‐17D) genes from Dabry's sturgeon (Acipenser dabryanus)

Dabry's sturgeon (Acipenser dabryanus) represents an ancient Actinopterygian lineage that are termed “living fossils”. Many diseases have been found in Dabry's sturgeon. In the present study, genes encoding interleukin (IL)‐16 and IL‐17D in Dabry's sturgeon were identified by RNA‐sequencing. Phylogenetic tree analysis suggested that they clustered together with the corresponding pro‐IL‐16 proteins and IL‐17D proteins from other fish. Sequence analysis revealed that IL‐17D protein was more conserved than pro‐IL‐16. Dabry's sturgeon pro‐IL‐16 contains four putative PDZ domains and do not include signal peptides, while IL‐17D only possesses signal peptides (1–25 aa). The expression patterns of IL‐16 and IL‐17D genes were investigated in Dabry's sturgeon to reveal their functions in disease. The expression level of IL‐16 showed no significant changes in embryos; however, the high expression level of IL‐17D at 0–14 hpf (hours post fertilization) implied the existence of maternal expression in the oocyte and an association with embryonic development. Tissue distribution analysis revealed that IL‐16 and IL‐17D proteins have potential functions in immune and non‐immune tissue compartments. IL‐16 and IL‐17D had different fold changes in primary spleen leukocytes after polyinosinic:polycytidylic acid (poly I:C) and lipopolysaccharide (LPS) administration, which suggested that IL‐16 has a stronger antiviral capability compared with its antibacterial response, and IL‐17D has a stronger antibacterial capability compared with its antiviral response. IL‐16 showed an earlier response to virus compared with IL‐17D, and IL‐17D showed earlier and shorter response to bacteria compared with IL‐16. Our findings suggested the roles of IL‐16 and IL‐17D in Dabry's sturgeon, and provided the theoretical basis for the prevention and control of diseases of Dabry's sturgeon.     

Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase

Biomolecular simulations at millisecond and longer time‐scales can provide vital insights into functional mechanisms. Because post‐simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi‐anharmonic analysis (QAA) (Ramanathan et al., PLoS One 2011;6:e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub‐states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth‐order statistics for characterizing atomic fluctuations. In this article, we extend QAA for analyzing long time‐scale simulations online. In particular, we present HOST4MD—a higher‐order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub‐states, and (3) identifies conformational transitions that enable the protein to access those sub‐states. We demonstrate HOST4MD on microsecond timescale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three subdomains (LID, CORE, and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate that HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time‐scale simulations. Proteins 2012. © 2012 Wiley Periodicals, Inc.     

Modeling conformational redox‐switch modulation of human succinic semialdehyde dehydrogenase

Succinic semialdehyde dehydrogenase (SSADH) converts succinic semialdehyde (SSA) to succinic acid in the mitochondrial matrix and is involved in the metabolism of the inhibitory neurotransmitter γ‐aminobutyric acid (GABA). The molecular structure of human SSADH revealed the intrinsic regulatory mechanism—redox‐switch modulation—by which large conformational changes are brought about in the catalytic loop through disulfide bonding. The crystal structures revealed two SSADH conformations, and computational modeling of transformation between them can provide substantial insights into detailed dynamic redox modulation. On the basis of these two clear crystal structures, we modeled the conformational motion between these structures in silico. For that purpose, we proposed and used a geometry‐based coarse‐grained mathematical model of long‐range protein motion and the related modeling algorithm. The algorithm is based on solving the special optimization problem, which is similar to the classical Monge–Kantorovich mass transportation problem. The modeled transformation was supported by another morphing method based on a completely different framework. The result of the modeling facilitates better interpretation and understanding of the SSADH biological role. Proteins 2015; 83:2217–2229. © 2015 Wiley Periodicals, Inc.     

Structural basis for cellulose binding by the type A carbohydrate‐binding module 64 of Spirochaeta thermophila

Spirochaeta thermophila secretes seven glycoside hydrolases for plant biomass degradation that carry a carbohydrate‐binding module 64 (CBM64) appended at the C‐terminus. CBM64 adsorbs to various β1‐4‐linked pyranose substrates and shows high affinity for cellulose. We present the first crystal structure of a CBM64 at 1.2 Å resolution, which reveals a jelly‐roll‐like fold corresponding to a surface‐binding type A CBM. Modeling of its interaction with cellulose indicates that CBM64 achieves association with the hydrophobic face of β‐linked pyranose chains via a unique coplanar arrangement of four exposed tryptophan side chains. Proteins 2016; 84:855–858. © 2016 Wiley Periodicals, Inc.     

Stability and kinetic behavior of immobilized laccase from Myceliophthora thermophila in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium ethylsulfate

The use of ionic liquids (ILs) as reaction media for enzymatic reactions has increased their potential because they can improve enzyme activity and stability. Kinetic and stability properties of immobilized commercial laccase from Myceliophthora thermophila in the water‐soluble IL 1‐ethyl‐3‐methylimidazolium ethylsulfate ([emim][EtSO₄]) have been studied and compared with free laccase. Laccase immobilization was carried out by covalent binding on glyoxyl–agarose beads. The immobilization yield was 100%, and the activity was totally recovered. The Michaelis‐Menten model fitted well to the kinetic data of enzymatic oxidation of a model substrate in the presence of the IL [emim][EtSO₄]. When concentration of the IL was augmented, the values of V_max for free and immobilized laccases showed an increase and slight decrease, respectively. The laccase–glyoxyl–agarose derivative improved the laccase stability in comparison with the free laccase regarding the enzymatic inactivation in [emim][EtSO₄]. The stability of both free and immobilized laccase was slightly affected by small amounts of IL (<50%). A high concentration of the IL (75%) produced a large inactivation of free laccase. However, immobilization prevented deactivation beyond 50%. Free and immobilized laccase showed a first‐order thermal inactivation profile between 55 and 70°C in the presence of the IL [emim][EtSO₄]. Finally, thermal stability was scarcely affected by the presence of the IL. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:790–796, 2014