BioMed Research International: Structural Biology The latest articles from Hindawi Publishing Corporation © 2016 , Hindawi Publishing Corporation . All rights reserved. Amino Acids in Nine Ligand-Prefer Ramachandran Regions Tue, 29 Sep 2015 10:02:41 +0000 Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function. Chen Cao, Lincong Wang, Xiaoyang Chen, Shuxue Zou, Guishen Wang, and Shutan Xu Copyright © 2015 Chen Cao et al. All rights reserved. Assessment of Morphological and Functional Changes in Organs of Rats after Intramuscular Introduction of Iron Nanoparticles and Their Agglomerates Thu, 19 Feb 2015 11:48:43 +0000 The research was performed on male Wistar rats based on assumptions that new microelement preparations containing metal nanoparticles and their agglomerates had potential. Morphological and functional changes in tissues in the injection site and dynamics of chemical element metabolism (25 indicators) in body were assessed after repeated intramuscular injections (total, 7) with preparation containing agglomerate of iron nanoparticles. As a result, iron depot was formed in myosymplasts of injection sites. The quantity of muscle fibers having positive Perls’ stain increased with increasing number of injections. However, the concentration of the most chemical elements and iron significantly decreased in the whole skeletal muscle system (injection sites are not included). Consequently, it increased up to the control level after the sixth and the seventh injections. Among the studied organs (liver, kidneys, and spleen), Caspase-3 expression was revealed only in spleen. The expression had a direct dependence on the number of injections. Processes of iron elimination from preparation containing nanoparticles and their agglomerates had different intensity. Elena Sizova, Sergey Miroshnikov, Elena Yausheva, and Valentina Polyakova Copyright © 2015 Elena Sizova et al. All rights reserved. Using Regional Homogeneity to Reveal Altered Spontaneous Activity in Patients with Mild Cognitive Impairment Mon, 09 Feb 2015 06:39:29 +0000 Most patients with mild cognitive impairment (MCI) are thought to be in an early stage of Alzheimer’s disease (AD). Resting-state functional magnetic resonance imaging reflects spontaneous brain activity and/or the endogenous/background neurophysiological process of the human brain. Regional homogeneity (ReHo) rapidly maps regional brain activity across the whole brain. In the present study, we used the ReHo index to explore whole brain spontaneous activity pattern in MCI. Our results showed that MCI subjects displayed an increased ReHo index in the paracentral lobe, precuneus, and postcentral and a decreased ReHo index in the medial temporal gyrus and hippocampus. Impairments in the medial temporal gyrus and hippocampus may serve as important markers distinguishing MCI from healthy aging. Moreover, the increased ReHo index observed in the postcentral and paracentral lobes might indicate compensation for the cognitive function losses in individuals with MCI. Yumei Wang, Xiaochuan Zhao, Shunjiang Xu, Lulu Yu, Lan Wang, Mei Song, Linlin Yang, and Xueyi Wang Copyright © 2015 Yumei Wang et al. All rights reserved. Importance of Silicon and Mechanisms of Biosilica Formation in Plants Wed, 21 Jan 2015 13:15:58 +0000 Silicon (Si) is one of the most prevalent macroelements, performing an essential function in healing plants in response to environmental stresses. The purpose of using Si is to induce resistance to distinct stresses, diseases, and pathogens. Additionally, Si can improve the condition of soils, which contain toxic levels of heavy metals along with other chemical elements. Silicon minimizes toxicity of Fe, Al, and Mn, increases the availability of P, and enhances drought along with salt tolerance in plants through the formation of silicified tissues in plants. However, the concentration of Si depends on the plants genotype and organisms. Hence, the physiological mechanisms and metabolic activities of plants may be affected by Si application. Peptides as well as amino acids can effectively create polysilicic species through interactions with different species of silicate inside solution. The carboxylic acid and the alcohol groups of serine and asparagine tend not to engage in any significant role in polysilicates formation, but the hydroxyl group side chain can be involved in the formation of hydrogen bond with Si(OH)4. The mechanisms and trend of Si absorption are different between plant species. Furthermore, the transportation of Si requires an energy mechanism; thus, low temperatures and metabolic repressors inhibit Si transportation. Mahbod Sahebi, Mohamed M. Hanafi, Abdullah Siti Nor Akmar, Mohd Y. Rafii, Parisa Azizi, F. F. Tengoua, Jamaludin Nurul Mayzaitul Azwa, and M. Shabanimofrad Copyright © 2015 Mahbod Sahebi et al. All rights reserved. Dental Wear: A Scanning Electron Microscope Study Sun, 07 Dec 2014 10:50:45 +0000 Dental wear can be differentiated into different types on the basis of morphological and etiological factors. The present research was carried out on twelve extracted human teeth with dental wear (three teeth showing each type of wear: erosion, attrition, abrasion, and abfraction) studied by scanning electron microscopy (SEM). The study aimed, through analysis of the macro- and micromorphological features of the lesions (considering the enamel, dentin, enamel prisms, dentinal tubules, and pulp), to clarify the different clinical and diagnostic presentations of dental wear and their possible significance. Our results, which confirm current knowledge, provide a complete overview of the distinctive morphology of each lesion type. It is important to identify the type of dental wear lesion in order to recognize the contributing etiological factors and, consequently, identify other more complex, nondental disorders (such as gastroesophageal reflux, eating disorders). It is clear that each type of lesion has a specific morphology and mechanism, and further clinical studies are needed to clarify the etiological processes, particularly those underlying the onset of abfraction. Luca Levrini, Giulia Di Benedetto, and Mario Raspanti Copyright © 2014 Luca Levrini et al. All rights reserved. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling Tue, 08 Jul 2014 09:13:47 +0000 The interaction of patulin with human serum albumin (HSA) was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis), circular dichroism (CD), atomic force microscopy (AFM), and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K) were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The , , and values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments. Li Yuqin, You Guirong, Yang Zhen, Liu Caihong, Jia Baoxiu, Chen Jiao, and Guo Yurong Copyright © 2014 Li Yuqin et al. All rights reserved. Crystal Structure of Mouse Thymidylate Synthase in Tertiary Complex with dUMP and Raltitrexed Reveals N-Terminus Architecture and Two Different Active Site Conformations Tue, 03 Jun 2014 10:34:01 +0000 The crystal structure of mouse thymidylate synthase (mTS) in complex with substrate dUMP and antifolate inhibitor Raltitrexed is reported. The structure reveals, for the first time in the group of mammalian TS structures, a well-ordered segment of 13 N-terminal amino acids, whose ordered conformation is stabilized due to specific crystal packing. The structure consists of two homodimers, differing in conformation, one being more closed (dimer AB) and thus supporting tighter binding of ligands, and the other being more open (dimer CD) and thus allowing weaker binding of ligands. This difference indicates an asymmetrical effect of the binding of Raltitrexed to two independent mTS molecules. Conformational changes leading to a ligand-induced closing of the active site cleft are observed by comparing the crystal structures of mTS in three different states along the catalytic pathway: ligand-free, dUMP-bound, and dUMP- and Raltitrexed-bound. Possible interaction routes between hydrophobic residues of the mTS protein N-terminal segment and the active site are also discussed. Anna Dowierciał, Piotr Wilk, Wojciech Rypniewski, Wojciech Rode, and Adam Jarmuła Copyright © 2014 Anna Dowierciał et al. All rights reserved. Chondroitin Sulfate Proteoglycans: Structure-Function Relationship with Implication in Neural Development and Brain Disorders Wed, 14 May 2014 00:00:00 +0000 Chondroitin sulfate proteoglycans (CSPGs) are extracellular matrix components that contain two structural parts with distinct functions: a protein core and glycosaminoglycan (GAG) side chains. CSPGs are known to be involved in important cell processes like cell adhesion and growth, receptor binding, or cell migration. It is recognized that the presence of CSPGs is critical in neuronal growth mechanisms including axon guidance following injury of nervous system components such as spinal cord and brain. CSPGs are upregulated in the central nervous system after injury and participate in the inhibition of axon regeneration mainly through their GAG side chains. Recently, it was shown that some CSPGs members like aggrecan, versican, and neurocan were strongly involved in brain disorders like bipolar disorder (BD), schizophrenia, and ADHD. In this paper, we present the chemical structure-biological functions relationship of CSPGs, both in health state and in genetic disorders, addressing methods represented by genome-wide and crystallographic data as well as molecular modeling and quantitative structure-activity relationship. Speranta Avram, Sergey Shaposhnikov, Catalin Buiu, and Maria Mernea Copyright © 2014 Speranta Avram et al. All rights reserved. Crystallographic Analysis of Ground and Space Thermostable T1 Lipase Crystal Obtained via Counter Diffusion Method Approach Thu, 02 Jan 2014 16:01:17 +0000 Three-dimensional structure of thermostable lipase is much sought after nowadays as it is important for industrial application mainly found in the food, detergent, and pharmaceutical sectors. Crystallization utilizing the counter diffusion method in space was performed with the aim to obtain high resolution diffracting crystals with better internal order to improve the accuracy of the structure. Thermostable T1 lipase enzyme has been crystallized in laboratory on earth and also under microgravity condition aboard Progress spacecraft to the ISS in collaboration with JAXA (Japanese Aerospace Exploration Agency). This study is conducted with the aims of improving crystal packing and structure resolution. The diffraction data set for ground grown crystal was collected to 1.3?Å resolution and belonged to monoclinic C2 space group with unit cell parameters ?Å, ?Å, and ?Å, whereas the diffraction data set for space grown crystal was collected to 1.1?Å resolution and belonged to monoclinic C2 space group with unit cell parameters ?Å, ?Å, and ?Å. The major difference between the two crystal growth systems is the lack of convection and sedimentation in microgravity environment resulted in the growth of much higher quality crystals of T1 lipase. Sayangku Nor Ariati Mohamad Aris, Adam Leow Thean Chor, Mohd Shukuri Mohamad Ali, Mahiran Basri, Abu Bakar Salleh, and Raja Noor Zaliha Raja Abd. Rahman Copyright © 2014 Sayangku Nor Ariati Mohamad Aris et al. All rights reserved. Molecular Modeling of Lectin-Like Protein from Acacia farnesiana Reveals a Possible Anti-Inflammatory Mechanism in Carrageenan-Induced Inflammation Mon, 30 Dec 2013 15:53:55 +0000 Acacia farnesiana lectin-like protein (AFAL) is a chitin-binding protein and has been classified as phytohaemagglutinin from Phaseolus vulgaris (PHA). Legume lectins are examples for structural studies, and this family of proteins shows a remarkable conservation in primary, secondary, and tertiary structures. Lectins have ability to reduce the effects of inflammation caused by phlogistic agents, such as carrageenan (CGN). This paper explains the anti-inflammatory activity of AFAL through structural comparison with anti-inflammatory legume lectins. The AFAL model was obtained by molecular modeling and molecular docking with glycan and carrageenan were performed to explain the AFAL structural behavior and biological activity. Pisum sativum lectin was the best template for molecular modeling. The AFAL structure model is folded as a β sandwich. The model differs from template in loop regions, number of β strands and carbohydrate-binding site. Carrageenan and glycan bind to different sites on AFAL. The ability of AFAL binding to carrageenan can be explained by absence of the sixth β-strand (posterior β sheets) and two β strands in frontal region. AFAL can inhibit pathway inflammatory process by carrageenan injection by connecting to it and preventing its entry into the cell and triggers the reaction. Vanessa Erika Ferreira Abrantes, Bruno Anderson Matias da Rocha, Raphael Batista da Nóbrega, José Caetano Silva-Filho, Claudener Souza Teixeira, Benildo Sousa Cavada, Carlos Alberto de Almeida Gadelha, Sergio Henrique Ferreira, Jozi Godoy Figueiredo, Tatiane Santi-Gadelha, and Plinio Delatorre Copyright © 2013 Vanessa Erika Ferreira Abrantes et al. All rights reserved. Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts Thu, 26 Dec 2013 10:48:06 +0000 Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N--C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N--C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles in collagen-like models may have interesting implications for triple helix stability. Luciana Esposito, Nicole Balasco, Alfonso De Simone, Rita Berisio, and Luigi Vitagliano Copyright © 2013 Luciana Esposito et al. All rights reserved. Increasing Affinity of Interferon- Receptor 1 to Interferon- by Computer-Aided Design Wed, 02 Oct 2013 11:46:41 +0000 We describe a computer-based protocol to design protein mutations increasing binding affinity between ligand and its receptor. The method was applied to mutate interferon- receptor 1 (IFN--Rx) to increase its affinity to natural ligand IFN-, protein important for innate immunity. We analyzed all four available crystal structures of the IFN--Rx/IFN- complex to identify 40 receptor residues forming the interface with IFN-. For these 40 residues, we performed computational mutation analysis by substituting each of the interface receptor residues by the remaining standard amino acids. The corresponding changes of the free energy were calculated by a protocol consisting of FoldX and molecular dynamics calculations. Based on the computed changes of the free energy and on sequence conservation criteria obtained by the analysis of 32 receptor sequences from 19 different species, we selected 14 receptor variants predicted to increase the receptor affinity to IFN-. These variants were expressed as recombinant proteins in Escherichia coli, and their affinities to IFN- were determined experimentally by surface plasmon resonance (SPR). The SPR measurements showed that the simple computational protocol succeeded in finding two receptor variants with affinity to IFN- increased about fivefold compared to the wild-type receptor. Pavel Mikulecký, Jiří Černý, Lada Biedermannová, Hana Petroková, Milan Kuchař, Jiří Vondrášek, Petr Malý, Peter Šebo, and Bohdan Schneider Copyright © 2013 Pavel Mikulecký et al. All rights reserved. Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates Thu, 01 Aug 2013 11:55:11 +0000 ABC efflux transporters are polyspecific members of the ABC superfamily that, acting as drug and metabolite carriers, provide a biochemical barrier against drug penetration and contribute to detoxification. Their overexpression is linked to multidrug resistance issues in a diversity of diseases. Breast cancer resistance protein (BCRP) is the most expressed ABC efflux transporter throughout the intestine and the blood-brain barrier, limiting oral absorption and brain bioavailability of its substrates. Early recognition of BCRP substrates is thus essential to optimize oral drug absorption, design of novel therapeutics for central nervous system conditions, and overcome BCRP-mediated cross-resistance issues. We present the development of an ensemble of ligand-based machine learning algorithms for the early recognition of BCRP substrates, from a database of 262 substrates and nonsubstrates compiled from the literature. Such dataset was rationally partitioned into training and test sets by application of a 2-step clustering procedure. The models were developed through application of linear discriminant analysis to random subsamples of Dragon molecular descriptors. Simple data fusion and statistical comparison of partial areas under the curve of ROC curves were applied to obtain the best 2-model combination, which presented 82% and 74.5% of overall accuracy in the training and test set, respectively. Melisa Edith Gantner, Mauricio Emiliano Di Ianni, María Esperanza Ruiz, Alan Talevi, and Luis E. Bruno-Blanch Copyright © 2013 Melisa Edith Gantner et al. All rights reserved. Crystal Structure of the FAD-Containing Ferredoxin-NADP+ Reductase from the Plant Pathogen Xanthomonas axonopodis pv. citri Thu, 01 Aug 2013 10:41:43 +0000 We have solved the structure of ferredoxin-NADP(H) reductase, FPR, from the plant pathogen Xanthomonas axonopodis pv. citri, responsible for citrus canker, at a resolution of 1.5 Å. This structure reveals differences in the mobility of specific loops when compared to other FPRs, probably unrelated to the hydride transfer process, which contributes to explaining the structural and functional divergence between the subclass I FPRs. Interactions of the C-terminus of the enzyme with the phosphoadenosine of the cofactor FAD limit its mobility, thus affecting the entrance of nicotinamide into the active site. This structure opens the possibility of rationally designing drugs against the X. axonopodis pv. citri phytopathogen. María Laura Tondo, Ramon Hurtado-Guerrero, Eduardo A. Ceccarelli, Milagros Medina, Elena G. Orellano, and Marta Martínez-Júlvez Copyright © 2013 María Laura Tondo et al. All rights reserved.