Macromolecule-Assisted <i>de novo</i> Protein Folding

Choi, Seong Il,Son, Ahyun,Lim, Keo-Heun,Jeong, Hotcherl,Seong, Baik L. Molecular Diversity Preservation International (MD 2012 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.13 No.8

<P>In the processes of protein synthesis and folding, newly synthesized polypeptides are tightly connected to the macromolecules, such as ribosomes, lipid bilayers, or cotranslationally folded domains in multidomain proteins, representing a hallmark of <I>de novo</I> protein folding environments <I>in vivo</I>. Such linkage effects on the aggregation of endogenous polypeptides have been largely neglected, although all these macromolecules have been known to effectively and robustly solubilize their linked heterologous proteins in fusion or display technology. Thus, their roles in the aggregation of linked endogenous polypeptides need to be elucidated and incorporated into the mechanisms of <I>de novo</I> protein folding <I>in vivo</I>. In the classic hydrophobic interaction-based stabilizing mechanism underlying the molecular chaperone-assisted protein folding, it has been assumed that the macromolecules connected through a simple linkage without hydrophobic interactions and conformational changes would make no effect on the aggregation of their linked polypeptide chains. However, an increasing line of evidence indicates that the intrinsic properties of soluble macromolecules, especially their surface charges and excluded volume, could be important and universal factors for stabilizing their linked polypeptides against aggregation. Taken together, these macromolecules could act as folding helpers by keeping their linked nascent chains in a folding-competent state. The folding assistance provided by these macromolecules in the linkage context would give new insights into <I>de novo</I> protein folding inside the cell.</P>

Molecular Weight Dependent Glucose Lowering Effect of Low Molecular Weight Chitosan Oligosaccharide (GO2KA1) on Postprandial Blood Glucose Level in SD Rats Model

Jo, Sung-Hoon,Ha, Kyoung-Soo,Moon, Kyoung-Sik,Kim, Jong-Gwan,Oh, Chen-Gum,Kim, Young-Cheul,Apostolidis, Emmanouil,Kwon, Young-In Molecular Diversity Preservation International (MD 2013 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.14 No.7

<P>This research investigated the effect of enzymatically digested low molecular weight (MW) chitosan oligosaccharide on type 2 diabetes prevention. Three different chitosan oligosaccharide samples with varying MW were evaluated <I>in vitro</I> for inhibition of rat small intestinal α-glucosidase and porcine pancreatic α-amylase (GO2KA1; <1000 Da, GO2KA2; 1000–10,000 Da, GO2KA3; MW > 10,000 Da). The <I>in vitro</I> results showed that all tested samples had similar rat α-glucosidase inhibitory and porcine α-amylase inhibitory activity. Based on these observations, we decided to further investigate the effect of all three samples at a dose of 0.1 g/kg, on reducing postprandial blood glucose levels in Sprague-Dawley (SD) rat model after sucrose loading test. In the animal trial, all tested samples had postprandial blood glucose reduction effect, when compared to control, however GO2KA1 supplementation had the strongest effect. The glucose peak (C<I><SUB>max</SUB></I>) for GO2KA1 and control was 152 mg/dL and 193 mg/dL, respectively. The area under the blood glucose-time curve (AUC) for GO2KA1 and control was 262 h mg/dL and 305 h mg/dL, respectively. Furthermore, the time of peak plasma concentration of blood glucose (T<I><SUB>max</SUB></I>) for GO2KA1 was significantly delayed (0.9 h) compared to control (0.5 h). These results suggest that GO2KA1 could have a beneficial effect for blood glucose management relevant to diabetes prevention in normal and pre-diabetic individuals. The suggested mechanism of action is via inhibition of the carbohydrate hydrolysis enzyme α-glucosidase and since GO2KA1 (MW < 1000 Da) had higher <I>in vivo</I> effect, we hypothesize that it is more readily absorbed and might exert further biological effect once it is absorbed in the blood stream, relevant to blood glucose management.</P>

3D QSAR Pharmacophore Modeling, <i>in Silico</i> Screening, and Density Functional Theory (DFT) Approaches for Identification of Human Chymase Inhibitors

Arooj, Mahreen,Thangapandian, Sundarapandian,John, Shalini,Hwang, Swan,Park, Jong Keun,Lee, Keun Woo Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.12

<P>Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (<I>r</I> = 0.942) pharmacophore model (Hypo1) with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating “Hypo1”, it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high <I>GOLD</I> fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC<SUB>50</SUB>) data thus successfully validating “Hypo1” by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors.</P>

A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen <i>Porphyromonas gingivalis</i>

Kim, Dooil,Lee, Dae-Sil Molecular Diversity Preservation International (MD 2010 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.11 No.9

<P>We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from <I>Porphyromonas gingivalis</I>. The binding free energy obtained is in good agreement with the available experimental data for eight benzamidine derivatives including urea and ether linker. The calculations showed that the electrostatic energies between HRgpA and inhibitors were important in determining the relative affinities of the inhibitors to the HRgpA, with an average binding free energy of about −5 kcal/mol. The average structures of the eight complexes suggest that benzamidine inhibitors interact with Asp387, His435, and Cys468 by hydrogen bonding and with Trp508 by hydrophilic interactions that are essential for the activities of benzamidine inhibitors. It can therefore be expected that the method provides a reliable tool for the investigation of new HRgpA inhibitors. This finding could significantly benefit the future design of HRgpA inhibitors.</P>

Chaperoning Roles of Macromolecules Interacting with Proteins <i>in Vivo</i>

Choi, Seong Il,Lim, Keo-Heun,Seong, Baik L. Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.3

<P>The principles obtained from studies on molecular chaperones have provided explanations for the assisted protein folding <I>in vivo</I>. However, the majority of proteins can fold without the assistance of the known molecular chaperones, and little attention has been paid to the potential chaperoning roles of other macromolecules. During protein biogenesis and folding, newly synthesized polypeptide chains interact with a variety of macromolecules, including ribosomes, RNAs, cytoskeleton, lipid bilayer, proteolytic system, <I>etc</I>. In general, the hydrophobic interactions between molecular chaperones and their substrates have been widely believed to be mainly responsible for the substrate stabilization against aggregation. Emerging evidence now indicates that other features of macromolecules such as their surface charges, probably resulting in electrostatic repulsions, and steric hindrance, could play a key role in the stabilization of their linked proteins against aggregation. Such stabilizing mechanisms are expected to give new insights into our understanding of the chaperoning functions for <I>de novo</I> protein folding. In this review, we will discuss the possible chaperoning roles of these macromolecules in <I>de novo</I> folding, based on their charge and steric features.</P>

Wild and Hatchery Populations of Korean Starry Flounder ( <i>Platichthys stellatus</i> ) Compared Using Microsatellite DNA Markers

An, Hye Suck,Byun, Soon Gyu,Kim, Yi Cheong,Lee, Jang Wook,Myeong, Jeong-In Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.12

<P>Starry flounder (<I>Platichthys stellatus</I>) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (<I>F</I><SUB>ST</SUB> = 0.043, <I>P</I> < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity.</P>

The Influence of Light Quality, Circadian Rhythm, and Photoperiod on the CBF-Mediated Freezing Tolerance

Maibam, Punyakishore,Nawkar, Ganesh M.,Park, Joung Hun,Sahi, Vaidurya Pratap,Lee, Sang Yeol,Kang, Chang Ho Molecular Diversity Preservation International (MD 2013 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.14 No.6

<P>Low temperature adversely affects crop yields by restraining plant growth and productivity. Most temperate plants have the potential to increase their freezing tolerance upon exposure to low but nonfreezing temperatures, a process known as cold acclimation. Various physiological, molecular, and metabolic changes occur during cold acclimation, which suggests that the plant cold stress response is a complex, vital phenomenon that involves more than one pathway. The C-Repeat Binding Factor (CBF) pathway is the most important and well-studied cold regulatory pathway that imparts freezing tolerance to plants. The regulation of freezing tolerance involves the action of phytochromes, which play an important role in light-mediated signalling to activate cold-induced gene expression through the CBF pathway. Under normal temperature conditions, CBF expression is regulated by the circadian clock through the action of a central oscillator and also day length (photoperiod). The phytochrome and phytochrome interacting factor are involved in the repression of the CBF expression under long day (LD) conditions. Apart from the CBF regulon, a novel pathway involving the Z-box element also mediates the cold acclimation response in a light-dependent manner. This review provides insights into the progress of cold acclimation in relation to light quality, circadian regulation, and photoperiodic regulation and also explains the underlying molecular mechanisms of cold acclimation for introducing the engineering of economically important, cold-tolerant plants.</P>

Isolation and Characterization of 13 Microsatellite Loci from a Korean Endemic Species, <i>Sophora koreensis</i> (Fabaceae)

Lee, Ji-Yeon,Lee, Dong-Hyuk,Choi, Byoung-Hee Molecular Diversity Preservation International (MD 2012 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.13 No.9

<P>To evaluate the population genetics structure as a means of devising conservation strategies, we developed microsatellite primers for <I>Sophora koreensis</I>, a narrowly endemic and endangered species in Korea. Thirteen polymorphic microsatellite markers were developed in Korean populations of <I>S. koreensis</I>. Genetic diversity was analyzed in 40 individuals from two populations. The number of alleles per locus ranged from 4 to 14, with observed and expected heterozygosities ranging from 0.200 to 1.000 and from 0.189 to 0.864, respectively. The microsatellite markers described here are valuable tools for the population genetics research of <I>S. koreensis</I>. They can be used to obtain information for creating suitable management strategies to conserve this endemic and endangered species.</P>

Identification of Important Chemical Features of 11β-Hydroxysteroid Dehydrogenase Type1 Inhibitors: Application of Ligand Based Virtual Screening and Density Functional Theory

Sakkiah, Sugunadevi,Meganathan, Chandrasekaran,Sohn, Young-Sik,Namadevan, Sundaraganesan,Lee, Keun Woo Molecular Diversity Preservation International (MD 2012 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.13 No.4

<P>11β-Hydroxysteroid dehydrogenase type1 (11βHSD1) regulates the conversion from inactive cortisone to active cortisol. Increased cortisol results in diabetes, hence quelling the activity of 11βHSD1 has been thought of as an effective approach for the treatment of diabetes. Quantitative hypotheses were developed and validated to identify the critical chemical features with reliable geometric constraints that contribute to the inhibition of 11βHSD1 function. The best hypothesis, Hypo1, which contains one-HBA; one-Hy-Ali, and two-RA features, was validated using Fischer’s randomization method, a test and a decoy set. The well validated, Hypo1, was used as 3D query to perform a virtual screening of three different chemical databases. Compounds selected by Hypo1 in the virtual screening were filtered by applying Lipinski’s rule of five, ADMET, and molecular docking. Finally, five hit compounds were selected as virtual novel hit molecules for 11βHSD1 based on their electronic properties calculated by Density functional theory.</P>

Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers

Koedrith, Preeyaporn,Seo, Young Rok Molecular Diversity Preservation International (MD 2011 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.12 No.12

<P>Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-κB, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression.</P>