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An Efficient Protein Structure Prediction Using Genetic Algorithm
Published in Abdel-Badeeh M. Salem, Innovative Smart Healthcare and Bio-Medical Systems, 2020
Mohamad Yousef, Tamer Abdelkader, Khaled El-Bahnasy
These local structures are classified into two major classes: alpha helix and beta sheet. Alpha helix structures are the most occurring local structures. It has 3.6 amino acids per turn. In beta sheets, the polypeptide does not form a spiral coil. Instead, it zig-zags in an extended shape (see Figure 4.1).
Introduction to Oral and Craniofacial Tissue Engineering
Published in Vincenzo Guarino, Marco Antonio Alvarez-Pérez, Current Advances in Oral and Craniofacial Tissue Engineering, 2020
María Verónica Cuevas González, Eduardo Villarreal-Ramírez, Adriana Pérez-Soria, Pedro Alberto López Reynoso, Vincenzo Guarino, Marco Antonio Alvarez-Pérez
All collagen members share common features. The collagen proteins have at least one triple alpha helix collagenous domain (COL), which is a rod-like structure to provide stiffness and the content or number of repetitions of this COL domain depends on the specific type of the collagen. The alpha helix chains are supercoiled to form a triple helix. The COL domain frequently has a triplet sequence Gly-X-Y, where Gly corresponds to the glycine residues and generally by steric constraints occupies the central positions in the triple helix. Meanwhile, X and Y can be any amino acid but frequently are found in these positions to proline and hydroxyproline, respectively. Hydroxyproline residues are essential to triple helix stability (Birk and Brückner 2011).
Disease Prediction and Drug Development
Published in Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam, Introduction to Computational Health Informatics, 2019
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam
There are two types of secondary structures: α-helix and β-sheet. Alpha-helix is a right-handed helical structure that is maintained using a hydrogen-bond between N–H group and C=O group of four amino-acid residue occurring earlier. Beta-sheet is pleated and consists of three to ten polypeptides-strands. A strand in a β-sheet is connected to the adjacent strand in a lateral direction using hydrogen-bonds.
Flavonoids and Acid-Hydrolysis derivatives of Neo-Clerodane diterpenes from Teucrium flavum subsp. glaucum as inhibitors of the HIV-1 reverse transcriptase–associated RNase H function
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2021
Benedetta Fois, Angela Corona, Enzo Tramontano, Simona Distinto, Elias Maccioni, Rita Meleddu, Pierluigi Caboni, Costantino Floris, Filippo Cottiglia
The next mutation involved the residue A502 located in the alpha helix, close to the second identified allosteric binding pocket. This pocket is located in the RNase H domain, between the RNase H active site and the primer grip region, close to the interface of subunits p66 and p51. A502 residue was replaced by a phenylalanine with the aim to provoke a shift of alpha helix that might reduce the space between the two subunits p51 and p66 and therefore hinder the entrance of the compound in the pocket. Also in this case, flavuglaucin B showed a moderate loss in potency (3.5-fold). Conversely, flavuglaucin B showed a significant loss in potency in the case of R448A (5.5-fold), R557A (6.5-fold) and, especially, A508V that totally impaired the RNase H inhibition by flavuglaucin B (IC50 >100 µM). All together these data suggested that flavuglaucin B established strong interactions within the allosteric pocket located between the RNase H active site and the primer grip region, close to the interface of subunits p66 and p51, previously investigated for other allosteric RNase H inhibitors20.
A novel CRYGC E128* mutation underlying an autosomal dominant nuclear cataract in a south Indian kindred
Published in Ophthalmic Genetics, 2020
Dinesh Kumar Kandaswamy, K. Vasantha, Jochen Graw, Sathiyaveedu Thyagarajan Santhiya
The mutated nucleotide is highly conserved across species which is evident by the high scores of PhyloP (Score- 5.44) and PhastCons (1). This mutation leads to a truncated protein with a complete loss of 47 amino acids including the last amino acid of Greek key motif 3 and the complete Greek key motif 4. This makes a dysfunction of the γC-crystallin very likely. To investigate the molecular mechanism underlying cataract formation caused by the p.E128* mutation, homology modeling were conducted using SWISS-MODEL (10) with the NMR structures of human γC-crystallin (PDB ID: 2nbr1.a) (11) as the template structures. There was decrease in the Q mean (Qualitative model energy analysis) score of the mutant compared to that of wild-type structure. Structures like beta strands (amino acid 122–128, 130–135, 139–145, 147–150, 165–168) and alpha helix (between amino acid 153–156) and turns formed between amino acid 136–138, were eventually lost in the mutant protein (Figure 5).
Aiming at the heart: the capsid protein of dengue virus as a vaccine candidate
Published in Expert Review of Vaccines, 2019
Laura Lazo, Iris Valdes, Gerardo Guillén, Lisset Hermida, Lázaro Gil
The DENV capsid protein was found to be composed of four alpha helices. Each protein monomer presents a three alpha helix core (α1-α3) [11]. The longest helix, α4 extends out from the 3-alpha helix core and has little intramolecular contact. Two pairs of antiparallel helices, α2-α2ʹ and α4-α4ʹ, form the majority of the dimer contact surface with both interfaces being stabilized by extensive hydrophobic interaction. The dimer net charge is +46. There are 26 basic amino acids and only three acidic residues per 100-residue subunit. The spatial charge distribution is not uniform. While the surface α4-α4ʹ presents a high number of basic residues, the opposite face (α2-α2ʹ and α1-α1ʹ) is largely lacking of charge [11]. Based on the asymmetric charge distribution the α4-α4ʹ region could be assumed to interact with RNA, whereas the apolar α2-α2ʹ region would interact with the viral membrane (for recent reviews see [14,15]). The alpha helix 4 (α4) is located at the C terminus while α1 is located at the N terminus. The latter was found to be unstructured and could be removed without disrupting the structural integrity of the protein [13].