A new approach in protein folding studies revealed the potential site for nucleation center

A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone

Molecular dynamics study of the structure, flexibility and dynamics of thermostable L1 lipase at high temperatures.

Molecular Dynamics (MD) simulations have been used to understand how protein structure, dynamics, and flexibility are affected by adaptation to high temperature for several years. We report here the results of the high temperature MD simulations of Bacillus stearothermophilus L1 (L1 lipase). We found that the N-terminal moiety of the enzyme showed a high flexibility and dynamics during high temperature simulations which preceded and followed by clear structural changes in two specific regions; the small domain and the main catalytic domain or core domain of the enzyme. These two domains interact with each other through a Zn(2+)-binding coordination with Asp-61 and Asp-238 from the core domain and His-81 and His-87 from the small domain. Interestingly, the His-81 and His-87 were among the highly fluctuated and mobile residues at high temperatures. The results appear to suggest that tight interactions of Zn(2+)-binding coordination with specified residues became weak at high temperature which suggests the contribution of this region to the thermostability of the enzyme

Deciphering the flexibility and dynamics of Geobacillus zalihae strain T1 lipase at high temperatures by molecular dynamics simulation

The stability of biocatalysts is an important criterion for a sustainable industrial operation economically. T1 lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1 (T1 lipase) that was isolated from palm oil mill effluent (POME) in Malaysia. We report here the results of high temperatures molecular dynamics (MD) simulations of T1 lipase in explicit solvent. We found that the N-terminal moiety of this enzyme was accompanied by a large flexibility and dynamics during temperature-induced unfolding simulations which preceded and followed by clear structural changes in two specific regions; the small domain (consisting of helices alpha3 and alpha5, strands beta1 and beta2, and connecting loops) and the main catalytic domain or core domain (consisting of helices alpha6- alpha9 and connecting loops which located above the active site) of the enzyme. The results suggest that the small domain of model enzyme is a critical region to the thermostability of this organism

Deciphering the flexibility and dynamics of Geobacillus zalihae strain T1 lipase at high temperatures by molecular dynamics simulation

The stability of biocatalysts is an important criterion for a sustainable industrial operation economically. T1 lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1 (T1 lipase) that was isolated from palm oil mill effluent (POME) in Malaysia. We report here the results of high temperatures molecular dynamics (MD) simulations of T1 lipase in explicit solvent. We found that the N-terminal moiety of this enzyme was accompanied by a large flexibility and dynamics during temperature-induced unfolding simulations which preceded and followed by clear structural changes in two specific regions; the small domain (consisting of helices alpha3 and alpha5, strands beta1 and beta2, and connecting loops) and the main catalytic domain or core domain (consisting of helices alpha6- alpha9 and connecting loops which located above the active site) of the enzyme. The results suggest that the small domain of model enzyme is a critical region to the thermostability of this organism

In vitro evaluation of porcupine bezoar extracts as anticancer agent on A549 -A preliminary study

Porcupine bezoar (PB) was reported to possess medicinal properties in old medical manuscript. However, its potential as anticancer agent on human lung cancer cells (A549) is not yet studied. In present study, porcupine bezoar was tested to observe its ability in inhibiting cell growth of cancer cell (A549) and its cytotoxicity on Normal Human Gingival Fibroblast Cell (HGF-1). A549 cells morphology was observed after treated with bezoars for 72 hours. The ability of bezoars to induce DNA damage and apoptosis was analyzed by staining cells with Hoechst 33428(nucleus) and Rhodamine Phalloidin (f-actin). The A549 IC50 is 13.6±1.58μg/ml A549 growths was inhibited in dose-dependent pattern, but no inhibition found on normal HGF-1 cells. Treated A549 morphology shows sign of apoptosis such as DNA fragmentation, cytoplasm shrunk and vacuolation. The finding in this study suggests PB extracts able to inhibit cell growth, induce DNA damage and apoptosis, further analysis need to be done to verify the mechanism

Design of novel semisynethetic metalloenzyme from thermolysin

Initial applications of biocatalysis involved the used of naturally occurring enzyme. With new challenges in green chemical reaction, biocatalyst that shed the light is metalloenzyme,which function as enzyme and contain metal that are tightly attached and always isolated with the protein[1]. In recent years, enzyme engineering has proven to be an invaluable tool for elucidating biocatalytic mechanisms as well as producing enzymes for industrial purposes.Approaches developed for in vivo chemical modification and in silico computational methods promise to increase the scope and have already been used successfully to alter existing protein so that they have better stability and functionality [2]. This task might be good to address in designing a new biocatalyst with improved properties

2-Bromo-4-(3,4-dimethyl-5-phenyl-1,3-oxazolidin-2-yl)-6-meth­oxy­phenol

In the title compound, C18H20BrNO3, the oxazolidine ring adopts an envelope conformation with the N atom at the flap position. The mean plane of oxazolidine ring makes dihedral angles of 82.96 (13) and 70.97 (12)°, respectively, with the phenyl and benzene rings. In the crystal, adjacent mol­ecules are connected via O—H⋯O and C—H⋯O hydrogen bonds and C—H⋯π inter­actions into a zigzag chain along the b axis

Ethyl 1-(2-hy­droxy­eth­yl)-2-p-tolyl-1H-benzimidazole-5-carboxyl­ate

The asymmetric unit of the title compound, C19H20N2O3, contains two mol­ecules (A and B) with slightly different orientations of the ethyl groups with respect to the attached carboxyl­ate groups. Intra­molecular C—H⋯O hydrogen bonds generate S(8) ring motifs in both mol­ecules A and B. In each mol­ecule, the benzimidazole ring system is essentially planar, with maximum deviations of 0.023 (1) and 0.020 (1) Å, respectively, for mol­ecules A and B. The dihedral angle between the benzimidazole ring system and the phenyl ring is 37.34 (5)° for mol­ecule A and 42.42 (5)° for mol­ecule B. In the crystal, O—H⋯N and C—H⋯O hydrogen bonds link the mol­ecules into [100] columns with a cross-section of two-mol­ecule by two-mol­ecule wide, and further stabilization is provided by weak C—H⋯π and π–π inter­actions [centroid separations = 3.5207 (7) and 3.6314 (8) Å]

Insights into the neuropathology of cerebral ischemia and its mechanisms

Cerebral ischemia is a result of insufficient blood flow to the brain. It leads to limited supply of oxygen and other nutrients to meet metabolic demands. These phenomena lead to brain damage. There are two types of cerebral ischemia: focal and global ischemia. This condition has significant impact on patient's health and health care system requirements. Animal models such as transient occlusion of the middle cerebral artery and permanent occlusion of extracranial vessels have been established to mimic the conditions of the respective type of cerebral ischemia and to further understand pathophysiological mechanisms of these ischemic conditions. It is important to understand the pathophysiology of cerebral ischemia in order to identify therapeutic strategies for prevention and treatment. Here, we review the neuropathologies that are caused by cerebral ischemia and discuss the mechanisms that occur in cerebral ischemia such as reduction of cerebral blood flow, hippocampal damage, white matter lesions, neuronal cell death, cholinergic dysfunction, excitotoxicity, calcium overload, cytotoxic oedema, a decline in adenosine triphosphate (ATP), malfunctioning of Na+/K+-ATPase, and the blood-brain barrier breakdown. Altogether, the information provided can be used to guide therapeutic strategies for cerebral ischemia