Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins

Gowder, Shambhu Malleshappa; Chatterjee, Jhinuk; Chaudhuri, Tuhin K.; Paul, Kusum

doi:10.1155/2014/971258

Cited by 61 publications

(42 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Therefore, those have a relative solvent accessibility (RSA) higher than 30% are defined as the "active residues" while those lower than 30% are the "passive residues" for the parameterization of HADDOCK. Here, RSA was calculated by the software NACCESS [ 76 ]. According to HADDOCK, active residues should be part of the interface while passive residues can also be at the interface, but will not be energetically penalized if they are not.…”

Section: Methodsmentioning

confidence: 99%

S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain

Khan

Zou

et al. 2018

PLoS ONE

View full text Add to dashboard Cite

Ca2+-binding human S100A1 protein is a type of S100 protein. S100A1 is a significant mediator during inflammation when Ca2+ binds to its EF-hand motifs. Receptors for advanced glycation end products (RAGE) correspond to 5 domains: the cytoplasmic, transmembrane, C2, C1, and V domains. The V domain of RAGE is one of the most important target proteins for S100A1. It binds to the hydrophobic surface and triggers signaling transduction cascades that induce cell growth, cell proliferation, and tumorigenesis. We used nuclear magnetic resonance (NMR) spectroscopy to characterize the interaction between S100A1 and the RAGE V domain. We found that S100B could interact with S100A1 via NMR 1H-15N HSQC titrations. We used the HADDOCK program to generate the following two binary complexes based on the NMR titration results: S100A1-RAGE V domain and S100A1-S100B. After overlapping these two complex structures, we found that S100B plays a crucial role in blocking the interaction site between RAGE V domain and S100A1. A cell proliferation assay WST-1 also supported our results. This report could potentially be useful for new protein development for cancer treatment.

show abstract

Section: Methodsmentioning

confidence: 99%

S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain

Khan

Zou

et al. 2018

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…Chemical modification of hydrophobic groups to proteins have not been reported to the same degree. In native proteins, the hydrophobic residues are internally situated [22,23], although these residues can be exposed to the surface if the protein is denatured by chemical or physical stress [24,25]; moreover, protein aggregation has been assumed to be due to hydrophobic interaction between denatured proteins with surface-exposed hydrophobic residues [26,27]. Furthermore, aggregation affects biological activity and causes immunogenicity, and thus must be controlled during development of biopharmaceuticals [28,29].…”

Section: Introductionmentioning

confidence: 99%

Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

et al. 2020

View full text Add to dashboard Cite

Hydrophobic interaction is important for protein conformation. Conjugation of a hydrophobic group can introduce intermolecular hydrophobic contacts that can be contained within the molecule. It is possible that a strongly folded state can be formed in solution compared with the native state. In this study, we synthesized cholesteryl conjugated lysozyme (CHLysozyme) using lysozyme and cholesterol as the model protein and hydrophobic group, respectively. Cholesteryl conjugation to lysozyme was confirmed by nuclear-magnetic resonance. Differential-scanning calorimetry suggested that CHLysozyme was folded in solution. CHLysozyme secondary structure was similar to lysozyme, although circular dichroism spectra indicated differences to the tertiary structure. Fluorescence measurements revealed a significant increase in the hydrophobic surface of CHLysozyme compared with that of lysozyme; CHLysozyme self-associated by hydrophobic interaction of the conjugated cholesterol but the hydrophobic surface of CHLysozyme decreased with time. The results suggested that hydrophobic interaction changed from intramolecular interaction to an intermolecular interaction. Furthermore, the relative activity of CHLysozyme to lysozyme increased with time. Therefore, CHLysozyme likely forms a folded state with an extended durability of activity. Moreover, lysozyme was denatured in 100% DMSO but the local environment of tryptophan in CHLysozyme was similar to that of a native lysozyme. Thus, this study suggests that protein solution stability and resistance to organic solvents may be improved by conjugation of a hydrophobic group.

show abstract

“…Protein folding and stability in aqueous solution is governed by a delicate balance of hydrogen bonding, electrostatic interaction, and hydrophobic interactions; hydrophobic interactions provide the major structural stability to the proteins 1 2 3 . Surface hydrophobic interactions are fundamental to protein-ligand interaction, molecular recognition 4 , and may influence intermolecular interactions and biological functions 5 6 .…”

mentioning

confidence: 99%

BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity

Dorh

Zhu

Dhungana

et al. 2015

Sci Rep

View full text Add to dashboard Cite

Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors can be used as a sensitive indicator of protein surface hydrophobicity. A first principle approach is used to identify the molecular level mechanism for the substantial increase in the fluorescence signal strength. Our results show that conformational change and increased molecular rigidity of the dye due to its hydrophobic interaction with protein lead to fluorescence enhancement.

show abstract

Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins

Cited by 61 publications

References 28 publications

S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain

S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain

Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity

Contact Info

Product

Resources

About