A THEORETICAL STUDY OF THE SUBSTITUENT EFFECT ON THE STABILITY OF COLLAGEN

2004 ◽  
Vol 03 (02) ◽  
pp. 225-243 ◽  
Author(s):  
JUN-MIN QUAN ◽  
YUN-DONG Wu
Keyword(s):  
Electrostatic Interactions ◽  
Triple Helix ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Substituent Effects ◽  
Binding Energies ◽  
Model Studies ◽  
Collagen Triple Helix ◽  
Triple Helices ◽  
The Stability

Theoretical calculations have been carried out to investigate the effect of the 4(R)-substituents ( OH , F , NH 2, and [Formula: see text]) in proline on the stability of the collagen triple helix. A series of substituted proline models were studied first with density functional (B3LYP/6-31+G*) calculations. The solvent effect was studied using the SCIPCM method. While the F , OH and NH 2 groups increase the stability of the trans-up conformation with respect to the trans-down conformation, [Formula: see text] appears to favor the trans-down conformation in an aqueous solution. Second, the triple helices of the tripeptide models, Ac – Pro – Pro(X) – Gly – H with the two proline residues in the down/down and down/up puckering conformations, were optimized with a repeating unit approach using the HF/6-31G* method. For the Ac – Pro – Pro – Gly – H model peptide, the calculated binding energies of the two triple helices with the different puckering modes are similar. All four substituents, F , OH , NH 2, and [Formula: see text], considerably increased the binding energy of the down/up helix, but only [Formula: see text] stabilizes the down/down triple helix. Our calculations indicate that the inter-chain electrostatic interactions involving the 4(R)-substituents play an important role in stabilizing triple helical collagen models and allow the rationalization of all available experimental observations. Further model studies indicate that the substituent effects by the F , OH and NH 2 substituents are local while the effect of [Formula: see text] is long-range in nature.

Effect of N- and C-terminal functional groups on the stability of collagen triple helices

2017 ◽  
Vol 53 (80) ◽  
pp. 11036-11039 ◽  
Author(s):  
Jasmine Egli ◽  
Roman S. Erdmann ◽  
Pascal J. Schmidt ◽  
Helma Wennemers
Keyword(s):  
Functional Groups ◽  
Triple Helix ◽  
Collagen Triple Helix ◽  
Triple Helices ◽  
The Stability

The effect of chargedversusneutral N- and C-termini on the stability of the collagen triple helix was examined.

scholarly journals Nanotechnology-based approaches for targeting and delivery of drugs via Hexakis (m-PE) macrocycles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samaneh Pasban ◽  
Heidar Raissi
Keyword(s):  
Drug Delivery ◽  
Density Functional ◽  
Water Solution ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Partial Density ◽  
High Propensity ◽  
The Stability ◽  
Novel Applications

AbstractHexakis (m-phenylene ethynylene) (m-PE) macrocycles, with aromatic backbones and multiple hydrogen-bonding side chains, had a very high propensity to self-assemble via H-bond and π–π stacking interactions to form nanotubular structures with defined inner pores. Such stacking of rigid macrocycles is leading to novel applications that enable the researchers to explored mass transport in the sub-nanometer scale. Herein, we performed density functional theory (DFT) calculations to examine the drug delivery performance of the hexakis dimer as a novel carrier for doxorubicin (DOX) agent in the chloroform and water solvents. Based on the DFT results, it is found that the adsorption of DOX on the carrier surface is typically physisorption with the adsorption strength values of − 115.14 and − 83.37 kJ/mol in outside and inside complexes, respectively, and so that the essence of the drug remains intact. The negative values of the binding energies for all complexes indicate the stability of the drug molecule inside and outside the carrier's cavities. The energy decomposition analysis (EDA) has also been performed and shown that the dispersion interaction has an essential role in stabilizing the drug-hexakis dimer complexes. To further explore the electronic properties of dox, the partial density of states (PDOS and TDOS) are calculated. The atom in molecules (AIM) and Becke surface (BS) methods are also analyzed to provide an inside view of the nature and strength of the H-bonding interactions in complexes. The obtained results indicate that in all studied complexes, H-bond formation is the driving force in the stabilization of these structures, and also chloroform solvent is more favorable than the water solution. Overall, our findings offer insightful information on the efficient utilization of hexakis dimer as drug delivery systems to deliver anti-cancer drugs.

scholarly journals Stability of an RNA•DNA–DNA triple helix depends on base triplet composition and length of the RNA third strand

2019 ◽  
Vol 47 (14) ◽  
pp. 7213-7222 ◽  
Author(s):  
Charlotte N Kunkler ◽  
Jacob P Hulewicz ◽  
Sarah C Hickman ◽  
Matthew C Wang ◽  
Phillip J McCown ◽  
...  
Keyword(s):  
Relative Stability ◽  
Triple Helix ◽  
Multiple Factors ◽  
Dna And Rna ◽  
Helix Formation ◽  
Canonical Base ◽  
Triple Helix Formation ◽  
Triple Helices ◽  
Dna Triple Helix ◽  
The Stability

AbstractRecent studies suggest noncoding RNAs interact with genomic DNA, forming an RNA•DNA–DNA triple helix that regulates gene expression. However, base triplet composition of pyrimidine motif RNA•DNA–DNA triple helices is not well understood beyond the canonical U•A–T and C•G–C base triplets. Using native gel-shift assays, the relative stability of 16 different base triplets at a single position, Z•X–Y (where Z = C, U, A, G and X–Y = A–T, G–C, T–A, C–G), in an RNA•DNA–DNA triple helix was determined. The canonical U•A–T and C•G–C base triplets were the most stable, while three non-canonical base triplets completely disrupted triple-helix formation. We further show that our RNA•DNA–DNA triple helix can tolerate up to two consecutive non-canonical A•G–C base triplets. Additionally, the RNA third strand must be at least 19 nucleotides to form an RNA•DNA–DNA triple helix but increasing the length to 27 nucleotides does not increase stability. The relative stability of 16 different base triplets in DNA•DNA–DNA and RNA•RNA–RNA triple helices was distinctly different from those in RNA•DNA–DNA triple helices, showing that base triplet stability depends on strand composition being DNA and/or RNA. Multiple factors influence the stability of triple helices, emphasizing the importance of experimentally validating formation of computationally predicted triple helices.

scholarly journals A Theoretical Study of the Adsorption Process of B-aflatoxins Using Pyracantha koidzumii (Hayata) Rehder Biomasses

Toxins ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 283
Author(s):  
Abraham Méndez-Albores ◽  
René Escobedo-González ◽  
Juan Manuel Aceves-Hernández ◽  
Perla García-Casillas ◽  
María Inés Nicolás-Vázquez ◽  
...  
Keyword(s):  
Functional Groups ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Ph Value ◽  
Theoretical Calculations ◽  
Basis Set ◽  
Hydroxyl Group ◽  
Biosorption Process

Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) functional and basis set, the interaction of the aflatoxin B1 (AFB1) molecule and the functional groups present in the Pyracantha koidzumii biosorbent was investigated. Dissociation free energy and acidity equilibrium constant values were obtained theoretically both in solution (water) and gas phases. Additionally, the molecular electrostatic potential for the protonated molecules was calculated to verify the reactivity. Thus, methanol (hydroxyl group), methylammonium ion (amino group), acetate ion (carboxyl group), and acetone (carbonyl group), were used as representatives of the substrates present in the biomass; these references were considered using the corresponding protonated or unprotonated forms at a pH value of 5. The experimental infrared spectrophotometric data suggested the participation of these functional groups in the AFB1 biosorption process, indicating that the mechanism was dominated by electrostatic interactions between the charged functional groups and the positively charged AFB1 molecule. The theoretical determination indicated that the carboxylate ion provided the highest interaction energy with the AFB1 molecule. Consequently, an enriched biosorbent with compounds containing carboxyl groups could improve the yield of the AFB1 adsorption when using in vitro and in vivo trials.

Different Effects of 4-Hydroxyproline and 4-Fluoroproline on the Stability of Collagen Triple Helix

Biochemistry ◽  
2005 ◽  
Vol 44 (16) ◽  
pp. 6034-6042 ◽  
Author(s):  
Yoshinori Nishi ◽  
Susumu Uchiyama ◽  
Masamitsu Doi ◽  
Yuji Nishiuchi ◽  
Takashi Nakazawa ◽  
...  
Keyword(s):  
Triple Helix ◽  
Collagen Triple Helix ◽  
The Stability

Mindo-Forces Study on the Keto-Enol Tautomerism of α-Substituted Acetaldehydes XCH2CH=O (X = H, F, Oh, Cn, NH2, NO2, CH3, CF3, OCH3): Comparison with Acetyl Derivatives

2004 ◽  
Vol 59 (12) ◽  
pp. 980-986
Author(s):  
Wasim F. Al-Halasah ◽  
Salim M. Khalil
Keyword(s):  
Theoretical Calculations ◽  
Geometry Optimization ◽  
Substituent Effects ◽  
Geometrical Parameters ◽  
Free Energies ◽  
Electron Densities ◽  
The Stability ◽  
Complete Geometry Optimization

MINDO-Forces calculations with complete geometry optimization have been performed on α- substituted acetaldehydes XCH2CH=O and their enols (X = H, F, OH, CN, NH2, NO2, CH3, CF3, OCH3). All substituents were found to decrease the stability of the acetaldehyde and mostly in the case of electron withdrawing capacity (e. g NO2 and CF3). This agrees with theoretical calculations, except in the case of F. The substituent effects on the stabilities in this study are compared with results obtained from our previous theoretical calculations on acetyl derivatives. Geometrical parameters, electron densities, and Gibbs free energies are reported.

scholarly journals Contribution of dipole-dipole interactions to the stability of the collagen triple helix

2008 ◽  
Vol 17 (5) ◽  
pp. 955-961 ◽  
Author(s):  
Roberto Improta ◽  
Rita Berisio ◽  
Luigi Vitagliano
Keyword(s):  
Triple Helix ◽  
Collagen Triple Helix ◽  
Dipole Interactions ◽  
The Stability
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