STUDY OF TWO BIOACTIVE PEPTIDES IN VACUUM AND SOLVENT BY MOLECULAR MODELING

2006 ◽  
Vol 17 (06) ◽  
pp. 825-839
Author(s):  
F. YAŞAR ◽  
K. DEMIR
Keyword(s):  
Molecular Modeling ◽  
Three Dimensional ◽  
Helical Structures ◽  
Surface Areas ◽  
Solvent Model ◽  
Letter Code ◽  
End Distance ◽  
Accessible Surface ◽  
High Level ◽  
Ramachandran Plots

The thermodynamic and structural properties of Tyrosine-Glycine-Leusine-Phenylalanine (YGLF, in a one letter code) and Lysine-Valine-Leusine-Proline-Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of β-turn, γ-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of γ-turns and low level of β-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model.

MOLECULAR MODELING OF TWO HEXAPEPTIDE REPEAT MOTIFS OF HMW GLUTENIN SUBUNITS

2001 ◽  
Vol 12 (02) ◽  
pp. 281-292 ◽  
Author(s):  
HANDAN ARKIN ◽  
FATİH YAŞAR ◽  
TARIK ÇELİK ◽  
SÜEDA ÇELİK ◽  
HAMİT KÖKSEL
Keyword(s):  
Three Dimensional ◽  
Glutenin Subunits ◽  
Central Domain ◽  
Hmw Glutenin Subunits ◽  
Simulation Procedure ◽  
Helical State ◽  
Letter Code ◽  
Hmw Glutenin ◽  
High Level ◽  
Ramachandran Plots

The three-dimensional structures of two hexapeptide repeat motifs (PGQGQQ and SGQGQQ, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of β-turn and γ-turn structures and helical state. Structural predictions of PGQGQQ repeat motif indicated the presence of high level of β-turns and considerable level of γ-turns. Simulations of the repeat motifs in the repetitive central domain of HMW glutenin subunits indicated that these structures take important part in the three-dimensional structures of repeat motifs.

MULTICANONICAL SIMULATIONS OF FIVE TETRAPEPTIDE SEQUENCES IN THE CENTRAL DOMAIN OF HMW GLUTENIN

2000 ◽  
Vol 11 (08) ◽  
pp. 1595-1606 ◽  
Author(s):  
HANDAN ARKIN ◽  
FATİH YAŞAR ◽  
TARIK ÇELİK ◽  
SÜEDA ÇELİK ◽  
HAMİT KÖKSEL
Keyword(s):  
Three Dimensional ◽  
Simulation Method ◽  
Glutenin Subunits ◽  
Central Domain ◽  
Small Proteins ◽  
Letter Code ◽  
Hmw Glutenin ◽  
High Level ◽  
Ramachandran Plots ◽  
Proteins And Peptides

The application of the multicanonical simulation method to small proteins and peptides seems to be feasible and should be undertaken. In this work, the three-dimensional structures of five common tetrapeptide sequences (QPGQ, QSGQ, YPTS, SPQQ and QPGY, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of β-turn and γ-turn structures and helical states. Structural predictions of the five tetrapeptide sequences indicated the presence of high level of β-turns and considerable level of γ-turns. It was also possible to distinguish different type of turns and their occurrence probabilities.

Guided surgery with 3D printed device: a case report

2020 ◽  
Author(s):  
Michelle Carvalho de Sales ◽  
Rafael Maluza Flores ◽  
Julianny da Silva Guimaraes ◽  
Gustavo Vargas da Silva Salomao ◽  
Tamara Kerber Tedesco ◽  
...  
Keyword(s):  
Operating Time ◽  
Three Dimensional ◽  
Conventional Technique ◽  
Cervical Region ◽  
Mean Deviation ◽  
Apical Region ◽  
Virtual Planning ◽  
Surgical Guide ◽  
Surgical Guides ◽  
High Level

Dental surgeons need in-depth knowledge of the bone tissue status and gingival morphology of atrophic maxillae. The aim of this study is to describe preoperative virtual planning of placement of five implants and to compare the plan with the actual surgical results. Three-dimensional planning of rehabilitation using software programs enables surgical guides to be specially designed for the implant site and manufactured using 3D printing. A patient with five teeth missing was selected for this study. The patient’s maxillary region was scanned with CBCT and a cast model was produced. After virtual planning using ImplantViewer, five implants were placed using a printed surgical guide. Two weeks after the surgical procedure, the patient underwent another CBCT scan of the maxilla. Statistically significant differences were detected between the virtually planned positions and the actual positions of the implants, with a mean deviation of 0.36 mm in the cervical region and 0.7 mm in the apical region. The surgical technique used enables more accurate procedures when compared to the conventional technique. Implants can be better positioned, with a high level of predictability, reducing both operating time and patient discomfort.

scholarly journals Pairwise calculation of protein solvent-accessible surface areas

1998 ◽  
Vol 3 (4) ◽  
pp. 253-258 ◽  
Author(s):  
Arthur G. Street ◽  
Stephen L. Mayo
Keyword(s):  
Surface Areas ◽  
Accessible Surface ◽  
Solvent Accessible Surface

Urban network of China from the perspective of population mobility: Three-dimensional co-occurrence of nodes and links

2021 ◽  
pp. 0308518X2199781
Author(s):  
Xinyue Luo ◽  
Mingxing Chen
Keyword(s):  
Three Dimensional ◽  
Geographical Distance ◽  
Two Dimensional ◽  
Population Mobility ◽  
Urban Network ◽  
Urban Networks ◽  
Low Level ◽  
Medium Level ◽  
High Level ◽  
External Connections

The nodes and links in urban networks are usually presented in a two-dimensional(2D) view. The co-occurrence of nodes and links can also be realized from a three-dimensional(3D) perspective to make the characteristics of urban network more intuitively revealed. Our result shows that the external connections of high-level cities are mainly affected by the level of cities(nodes) and less affected by geographical distance, while medium-level cities are affected by the interaction of the level of cities(nodes) and geographical distance. The external connections of low-level cities are greatly restricted by geographical distance.

Three-Dimensional Computerized Anthropometry of the Nose: Landmark Representation Compared to Surface Analysis

2007 ◽  
Vol 44 (3) ◽  
pp. 278-285 ◽  
Author(s):  
Virgilio F. Ferrario ◽  
Fabrizio Mian ◽  
Redento Peretta ◽  
Riccardo Rosati ◽  
Chiarella Sforza
Keyword(s):  
Three Dimensional ◽  
Digital Data ◽  
Limits Of Agreement ◽  
B Splines ◽  
Surface Areas ◽  
Using Data ◽  
Difference Volume ◽  
T Values ◽  
Plaster Models ◽  
Plaster Casts

Objective: To compare three-dimensional nasal measurements directly made on subjects to those made on plaster casts, and nasal dimensions obtained with a surface-based approach to values obtained with a landmark representation. Methods: Soft-tissue nasal landmarks were directly digitized on 20 healthy adults. Stone casts of their noses were digitized and mathematically reconstructed using nonuniform rational B-splines (NURBS) curves. Linear distances, angles, volumes and surface areas were computed using facial landmarks and NURBS-reconstructed models (surface-based approach). Results: Measurements on the stone casts were somewhat smaller than values obtained directly from subjects (differences between −0.05 and −1.58 mm). Dahlberg's statistic ranged between 0.73 and 1.47 mm. Significant (p < .05) t values were found for 4 of 15 measurements. The surface-based approach gave values 3.5 (volumes) and 2.1 (surface area) times larger than those computed with the landmark-based method. The two values were significantly related (volume, r = 0.881; surface, r = 0.924; p < .001), the resulting equations estimated actual values well (mean difference, volume −0.01 mm3, SD 1.47, area 0.05 cm2, SD 1.44); limits of agreement between −2.89 and 2.87 mm3 (volume); −2.88 and 2.78 cm2 (area). Conclusions: Considering the characteristics of the two methods, and for practical purposes, nasal distances and angles obtained on plaster models were comparable to digital data obtained directly from subjects. Surface areas and volumes were best obtained using a surface-based approach, but could be estimated using data provided by the landmark representation.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 311
Author(s):  
Yang Li ◽  
Wang Li ◽  
Zhengshuang Xu
Keyword(s):  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Three Dimensional ◽  
Conformational Space ◽  
Cell Permeability ◽  
Relative Importance ◽  
Intrinsic Properties ◽  
Surface Areas ◽  
Synthetic Methodologies ◽  
Three Dimensional Configuration

Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.

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