Mm Of Endoglucanases
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The document discusses molecular modeling of endoglucanases from Pyrococcus horikoshii. A homology model of the endoglucanase EGPh was generated based on the crystal structure of a related endoglucanase. Molecular dynamics simulations were performed to refine the model. Analysis of the simulations provided insights into structural features that contribute to the thermostability of EGPh compared to related enzymes.
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Metagenomics is the study of genomic material obtained directly from environmental samples rather than from isolated cultures. It allows researchers to study the 99% of microorganisms that cannot be cultured using traditional methods. There are two main approaches - sequence-driven metagenomics sequences environmental DNA and compares taxonomic relationships, while function-driven metagenomics expresses cloned genes to compare metabolic relationships and discover new enzymes/chemicals. Metagenomics has been applied to study microbes in ocean water, human gut, acid mine drainage and more extreme habitats, identifying novel genes and furthering understanding of microbial communities. Future applications include discovering new antibiotics and enzymes, studying human microbiomes and antibiotic resistance.
Metagenomics and it’s applications
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
Metagenomics newer approach in understanding Microbes
Metagenomics is the study of genetic material recovered directly from environmental samples. It provides a new approach to studying microbes that are not easily cultured in a laboratory and enables investigation of microbial communities in their natural habitats. Metagenomics involves directly extracting DNA from samples, sequencing it, and analyzing the genetic information obtained from entire communities of organisms simultaneously. This provides insights into uncultured microbes and their roles in various environments.
Metagenomics
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples without culturing. This field enables research on uncultured organisms and microbial communities. There are three main metagenomic approaches: biochemical, whole genome shotgun sequencing, and 16s rRNA sequencing. Metagenomics is being applied to study human microbiomes, discover new genes and enzymes, monitor environmental impacts, and characterize uncultured microbes. Future directions include identifying more novel products from uncultured bacteria and improving culture methods and bioinformatics tools.
Introduction to Metagenomics Data Analysis - UEB-VHIR - 2013
UEB-VHIR's Metagenomics Training. Session 1. 2013/08/26. An Introduction to Metagenomics Data Analysis. Ferran Briansó (ferran.brianso@vhir.org)
Bioremediation
This document provides an overview of bioremediation. Some key points:
- Bioremediation uses microorganisms like bacteria and fungi to remove or break down pollutants in the environment. It can be used to treat contamination in soil, water, and solid waste.
- There are different types of bioremediation including biostimulation, bioaugmentation, and intrinsic bioremediation. Genetically engineered microbes are also used.
- The microbes degrade pollutants through redox reactions and metabolic pathways. Bioremediation can be done on-site (in situ) or by removing contaminated material to another location (ex situ).
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- 1. Molecular Modeling Of Endoglucanases August, 2007
- 2. INTRODUCTION
- 13. METHODS
- 16. Part 1 Homology Modeling
- 21. Structural-based Multiple Sequence Alignment
- 23. Alignment of the endoglucanases sequences from Acidothermus cellulolyticus (1ece) [358 residues] and Pyrococcus horikoshii (EGPh) [458 residues] with ClustalW. Extra loop?
- 25. EGPh Model loop loop
- 26. Alignment from MODELLER (Align2d method)
- 28. Secondary Structure Prediction by PSIDPRED
- 34. Z-score: -8.48 EGAc crystal structure (pdb code:1ece) EGPh model Z-score: -8.17
- 35. https://prosa.services.came.sbg.ac.at/prosa.php EGAc crystal structure (pdb code:1ece) EGPh model
- 36. Z-score (68.pdb) -8.17
- 37. Z-score (after 2ns MD) -9.1
- 38. Z-score(after 2ns&Bmin) -9.32
- 39. DOPE profile before and after MD
- 41. 100% 314 Total 37+23+2 Gly+Pro+end residues 85.4% 2 68 Most favored regions 12.1% 35 Additional allowed regions 1.6% 5 Generously allowed regions 1.0% 3 Disallowed regions % # Residues in
- 44. Y 264 W 233 W 337 F 29 EGPh Y 245 W 213 W 319 F 29 EGAc
- 45. -2 -1 +1 +2
- 46. Nucleophile -E 282 E 162 – proton donor
- 49. Part 2 MD simulations of EGPh & EGAc
- 51. Preparation Obtain pdb file Step 1 Check pKa & add H atoms accordingly Step 2 Solvate the protein in a water box Step 3 Add ions (Na + or Cl - )
- 54. EGPh EGAc
- 60. Comparison of Amino Acids Composition in EGAc and EGPh Charged residues: 55 vs. 80 3.99 15 5.87 21 Ala (A) 5.85 22 6.42 23 Val (V) 6.65 25 5.31 19 Ile (I) 7.18 27 8.38 30 Leu (L) 1.86 7 1.40 5 Met (M) 6.12 23 5.87 21 Pro (P) Hydrophobic 4.79 18 3.35 12 Phe (F) 9.84 37 9.22 33 Gly (G) Residues Mol% # Mol% # EGPh (total 376aa) EGAc (total 358aa)
- 61. # 80 7.18 27 7.26 26 Asp (D) Charged 5.05 19 1.96 7 Glu (E) 2.66 10 3.63 13 Arg (R) 6.38 24 2.51 9 Lys (K) 6.12 23 6.70 24 Asn (N) 1.86 7 5.59 20 Gln (Q) 1.06 4 1.12 4 Cys (C) 4.79 18 7.26 26 Ser (S) 5.32 20 5.31 19 Tyr (Y) Polar 5.05 19 5.03 18 Trp (W) 5.32 20 6.15 22 Thr (T) 2.93 11 1.68 6 His (H) Residues Mol% # Mol% # EGPh (total 376aa) EGAc (total 358aa) # 55
- 63. Salt Bridges
- 65. References
- 66. Extras
- 69. 12 Families with endoglucanse activity Asp (experimental) Not known Glu Asp (experimental) Not known Glu (experimental) Glu (experimental) Glu (experimental) Glu (experimental) Glu (experimental) Asp (experimental) Glu (experimental) Catalytic Proton Donor Fold 7-fold β -propeller --- Fold ( α / α ) 6 --- Not available Fold ( β / α ) 8 Fold -jelly roll Fold ( α / α ) 6 Fold ( α / α ) 6 Fold -jelly roll --- Fold ( β / α ) 8 Fold Asp (experimental) I endoglucanase; etc 74 Not known -- endoglucanase 61 Not known I endoglucanase; cellobiohydrolase. 48 Clan M Asp (experimental) I endoglucanase. 45 Not known I endoglucanase; xyloglucanase 44 Glu (experimental) R mannanase; -1,3-xylanase 26 Clan A Glu (experimental) R endoglucanase; xyloglucan hydrolase ; -1,3-1,4-glucanase 12 Clan C Asp (experimental) I endoglucanase; cellobiohydrolase; -glucosidase 9 Asp (inferred) I Chitosanase; Cellulase; Licheninase; Endo-1,4--xylanase 8 Clan M Glu (experimental) R endoglucanase; reducing end-acting cellobiohydrolase 7 Clan B Asp (experimental) I Endoglucanase;cellobiohydrolase 6 Glu (experimental) R Cellulase (EC 3.2.1.4); Glucan 1,3--glucosidase (EC 3.2.1.58); Endo-1,4--xylanase (EC 3.2.1.8); Cellulose 1,4--cellobiosidase (EC 3.2.1.91), etc 5 Clan A Catalytic Nucleophile/Base Mechanism Known Activity CAZY Family
- 70. Ligand: cellutetraose Catalytic Site