Measuring Hydrophobic Interactions with Three-Dimensional Nanometer Resolution

2008 ◽  
Vol 112 (26) ◽  
pp. 9769-9776 ◽  
Author(s):  
Allard J. Katan ◽  
Tjerk H. Oosterkamp
Keyword(s):  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Nanometer Resolution

scholarly journals Protein-Based Nanohydrogels for Bioactive Delivery

2021 ◽  
Vol 9 ◽  
Author(s):  
Subhash Chander ◽  
Giriraj T. Kulkarni ◽  
Neerupma Dhiman ◽  
Harsha Kharkwal
Keyword(s):  
Drug Delivery ◽  
Electrostatic Interactions ◽  
Hydrophobic Interactions ◽  
Biological Fluids ◽  
Three Dimensional ◽  
Covalent Bond ◽  
Ionic Concentration ◽  
Covalent Bonds ◽  
Encapsulation Process ◽  
Insightful Analysis

Hydrogels possess a unique three-dimensional, cross-linked network of polymers capable of absorbing large amounts of water and biological fluids without dissolving. Nanohydrogels (NGs) or nanogels are composed of diverse types of polymers of synthetic or natural origin. Their combination is bound by a chemical covalent bond or is physically cross-linked with non-covalent bonds like electrostatic interactions, hydrophobic interactions, and hydrogen bonding. Its remarkable ability to absorb water or other fluids is mainly attributed to hydrophilic groups like hydroxyl, amide, and sulphate, etc. Natural biomolecules such as protein- or peptide-based nanohydrogels are an important category of hydrogels which possess high biocompatibility and metabolic degradability. The preparation of protein nanohydrogels and the subsequent encapsulation process generally involve use of environment friendly solvents and can be fabricated using different proteins, such as fibroins, albumin, collagen, elastin, gelatin, and lipoprotein, etc. involving emulsion, electrospray, and desolvation methods to name a few. Nanohydrogels are excellent biomaterials with broad applications in the areas of regenerative medicine, tissue engineering, and drug delivery due to certain advantages like biodegradability, biocompatibility, tunable mechanical strength, molecular binding abilities, and customizable responses to certain stimuli like ionic concentration, pH, and temperature. The present review aims to provide an insightful analysis of protein/peptide nanohydrogels including their preparation, biophysiochemical aspects, and applications in diverse disciplines like in drug delivery, immunotherapy, intracellular delivery, nutraceutical delivery, cell adhesion, and wound dressing. Naturally occurring structural proteins that are being explored in protein nanohydrogels, along with their unique properties, are also discussed briefly. Further, the review also covers the advantages, limitations, overview of clinical potential, toxicity aspects, stability issues, and future perspectives of protein nanohydrogels.

Protein intrachain contact prediction with most interacting residues (MIR)

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Ruben Acuña ◽  
Zoé Lacroix ◽  
Nikolaos Papandreou ◽  
Jacques Chomilier
Keyword(s):  
Structural Changes ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Accessible Surface Area ◽  
Dimensional Structure ◽  
Closed Loops ◽  
Folding Process ◽  
Folding Nucleus ◽  
Accessible Surface ◽  
The Stability

AbstractThe transition state ensemble during the folding process of globular proteins occurs when a sufficient number of intrachain contacts are formed, mainly, but not exclusively, due to hydrophobic interactions. These contacts are related to the folding nucleus, and they contribute to the stability of the native structure, although they may disappear after the energetic barrier of transition states has been passed. A number of structure and sequence analyses, as well as protein engineering studies, have shown that the signature of the folding nucleus is surprisingly present in the native three-dimensional structure, in the form of closed loops, and also in the early folding events. These findings support the idea that the residues of the folding nucleus become buried in the very first folding events, therefore helping the formation of closed loops that act as anchor structures, speed up the process, and overcome the Levinthal paradox. We present here a review of an algorithm intended to simulate in a discrete space the early steps of the folding process. It is based on a Monte Carlo simulation where perturbations, or moves, are randomly applied to residues within a sequence. In contrast with many technically similar approaches, this model does not intend to fold the protein but to calculate the number of non-covalent neighbors of each residue, during the early steps of the folding process. Amino acids along the sequence are categorized as most interacting residues (MIRs) or least interacting residues. The MIR method can be applied under a variety of circumstances. In the cases tested thus far, MIR has successfully identified the exact residue whose mutation causes a switch in conformation. This follows with the idea that MIR identifies residues that are important in the folding process. Most MIR positions correspond to hydrophobic residues; correspondingly, MIRs have zero or very low accessible surface area. Alongside the review of the MIR method, we present a new postprocessing method called smoothed MIR (SMIR), which refines the original MIR method by exploiting the knowledge of residue hydrophobicity. We review known results and present new ones, focusing on the ability of MIR to predict structural changes, secondary structure, and the improved precision with the SMIR method.

Three-dimensional Electrical Property Mapping with Nanometer Resolution

2009 ◽  
Vol 21 (48) ◽  
pp. 4915-4919 ◽  
Author(s):  
Alexander Alekseev ◽  
Anton Efimov ◽  
Kangbo Lu ◽  
Joachim Loos
Keyword(s):  
Electrical Property ◽  
Three Dimensional ◽  
Nanometer Resolution

scholarly journals Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential

2020 ◽  
Vol 21 (1) ◽  
pp. 366 ◽  
Author(s):  
Azat Vadimovich Abdullatypov
Keyword(s):  
Hydrophobic Interactions ◽  
Purple Bacteria ◽  
Three Dimensional ◽  
Small Subunit ◽  
Protein Docking ◽  
Intramolecular Interactions ◽  
Oligomeric State ◽  
E Coli ◽  
Membrane Bound ◽  
Molecular Tunnels

Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus.

Non-scanning, non-interferometric, three-dimensional optical prof ilometer with nanometer resolution

2011 ◽  
Vol 9 (10) ◽  
pp. 101202-101204 ◽  
Author(s):  
譚振台 Chen-Tai Tan ◽  
詹遠生 Yuan-Sheng Chan ◽  
陳昭安 Jhao-An Chen ◽  
廖得照 Teh-Chao Liao ◽  
邱銘宏 Ming-Hung Chiu
Keyword(s):  
Three Dimensional ◽  
Nanometer Resolution

scholarly journals Unusual quaternary structure of a homodimeric synergistic-type toxin from mamba snake venom defines its molecular evolution

2020 ◽  
Vol 477 (20) ◽  
pp. 3951-3962
Author(s):  
Narumi Aoki-Shioi ◽  
Chacko Jobichen ◽  
J. Sivaraman ◽  
R. Manjunatha Kini
Keyword(s):  
Disulfide Bond ◽  
Disulfide Bonds ◽  
Quaternary Structure ◽  
Hydrophobic Interactions ◽  
Biological Effects ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Common Structure

Snake venoms are complex mixtures of enzymes and nonenzymatic proteins that have evolved to immobilize and kill prey animals or deter predators. Among them, three-finger toxins (3FTxs) belong to the largest superfamily of nonenzymatic proteins. They share a common structure of three β-stranded loops extending like fingers from a central core containing all four conserved disulfide bonds. Most 3FTxs are monomers and through subtle changes in their amino acid sequences, they interact with different receptors, ion channels and enzymes to exhibit a wide variety of biological effects. The 3FTxs have further expanded their pharmacological space through covalent or noncovalent dimerization. Synergistic-type toxins (SynTxs) isolated from the deadly mamba venoms, although nontoxic, have been known to enhance the toxicity of other venom proteins. However, the details of three-dimensional structure and molecular mechanism of activity of this unusual class of 3FTxs are unclear. We determined the first three-dimensional structure of a SynTx isolated from Dendroaspis jamesoni jamesoni (Jameson's mamba) venom. The SynTx forms a unique homodimer that is held together by an interchain disulfide bond. The dimeric interface is elaborate and encompasses loops II and III. In addition to the inter-subunit disulfide bond, the hydrogen bonds and hydrophobic interactions between the monomers contribute to the dimer formation. Besides, two sulfate ions that mediate interactions between the monomers. This unique quaternary structure is evolved through noncovalent homodimers such as κ-bungarotoxins. This novel dimerization further enhances the diversity in structure and function of 3FTxs.

scholarly journals In Silico Screening of Novel α1-GABAA Receptor PAMs towards Schizophrenia Based on Combined Modeling Studies of Imidazo [1,2-a]-Pyridines

2021 ◽  
Vol 22 (17) ◽  
pp. 9645
Author(s):  
Xiaojiao Zheng ◽  
Chenchen Wang ◽  
Na Zhai ◽  
Xiaogang Luo ◽  
Genyan Liu ◽  
...  
Keyword(s):  
Gabaa Receptor ◽  
Rational Design ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Pharmacophore Model ◽  
3D Qsar ◽  
Md Simulations ◽  
Binding Pocket ◽  
Pharmacophore Modeling ◽  
Topomer Search

The ionotropic GABAA receptor (GABAAR) has been proven to be an important target of atypical antipsychotics. A novel series of imidazo [1,2-a]-pyridine derivatives, as selective positive allosteric modulators (PAMs) of α1-containing GABAARs with potent antipsychotic activities, have been reported recently. To better clarify the pharmacological essentiality of these PAMs and explore novel antipsychotics hits, three-dimensional quantitative structure–activity relationships (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) were performed on 33 imidazo [1,2-a]-pyridines. The constructed 3D-QSAR models exhibited good predictive abilities. The dockings results and MD simulations demonstrated that hydrogen bonds, π–π stackings, and hydrophobic interactions play essential roles in the binding of these novel PAMs in the GABAAR binding pocket. Four hit compounds (DS01–04) were then screened out by the combination of the constructed models and computations, including the pharmacophore model, Topomer Search, molecular dockings, ADME/T predictions, and MD simulations. The compounds DS03 and DS04, with higher docking scores and better predicted activities, were also found to be relatively stable in the binding pocket by MD simulations. These results might provide a significant theoretical direction or information for the rational design and development of novel α1-GABAAR PAMs with antipsychotic activities.

Techniques and Applications for Non-Planar Lithography

2002 ◽  
Vol 739 ◽  
Author(s):  
John A. Rogers
Keyword(s):  
High Resolution ◽  
Microcontact Printing ◽  
Three Dimensional ◽  
Contact Printing ◽  
Nanometer Resolution ◽  
Replica Molding ◽  
Flat Surfaces ◽  
Operational Characteristics ◽  
Printing Technique

ABSTRACTCertain classes of three dimensional nanostructures can be fabricated by contact printing patterns onto curved or non-flat surfaces. This paper reviews some of our work that demonstrates this approach by using microcontact printing to form a range of three dimensional structures with feature sizes as small as 1–2 microns and it demonstrates their use in a variety of functional devices. We also describe a nanotransfer printing technique with operational characteristics that are similar to those of microcontact printing but which enables nanometer resolution. High resolution replica molding techniques provide a method for producing copies of some of these printed structures.

scholarly journals Analysis of the Thermostability Determinants of Hyperthermophilic Esterase EstE1 Based on Its Predicted Three-Dimensional Structure

2006 ◽  
Vol 72 (4) ◽  
pp. 3021-3025 ◽  
Author(s):  
Jin-Kyu Rhee ◽  
Do-Yun Kim ◽  
Dae-Gyun Ahn ◽  
Jung-Hyuk Yun ◽  
Seung-Hwan Jang ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Hydrophobic Interactions ◽  
3D Structure ◽  
Three Dimensional ◽  
Ion Pair ◽  
Archaeoglobus Fulgidus ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Structure Relationship

ABSTRACT The three-dimensional (3D) structure of the hyperthermophilic esterase EstE1 was constructed by homology modeling using Archaeoglobus fulgidus esterase as a reference, and the thermostability-structure relationship was analyzed. Our results verified the predicted 3D structure of EstE1 and identified the ion pair networks and hydrophobic interactions that are critical determinants for the thermostability of EstE1.

scholarly journals The insertion of human apolipoprotein H into phospholipid membranes: a monolayer study

1998 ◽  
Vol 335 (2) ◽  
pp. 225-232 ◽  
Author(s):  
Shao-Xiong WANG ◽  
Guo-ping CAI ◽  
Sen-fang SUI
Keyword(s):  
Lipid Membrane ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Heat Inactivation ◽  
Sequence Motif ◽  
Phospholipid Membranes ◽  
Human Apolipoprotein ◽  
Stable Domain ◽  
Apolipoprotein H

Apolipoprotein H (ApoH) is a plasma glycoprotein isolated from human serum. The interactions of ApoH with lipid membrane were reported to be essential for its physiological and pathogenic roles. In this paper we studied the ability of ApoH to insert into phospholipid membranes using the monolayer approach. The results show that ApoH is surface active and can insert into the lipid monolayers. The insertion ability of ApoH is stronger when a higher content of negatively charged lipids is present in the membrane. The acidic-pH and low-ionic-strength conditions will also enhance ApoH insertion, but these factors may not have much influence on the final insertion ability of ApoH, suggesting that, in the mechanism of ApoH insertion, not only electrostatic forces, but also hydrophobic interactions, are evidently involved. Modification by heat inactivation and reduction/alkylation does not change the critical insertion pressure (πc) of ApoH, suggesting a stable domain, maybe a linear sequence motif, but not the native three-dimensional structure of ApoH, is responsible for its insertion. The extent to which insertion of ApoH into phospholipid membranes may facilitate the ‘immune cleaning ’ of plasma liposomes is discussed.

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