Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

Rienzo, Lorenzo Di; Miotto, Mattia; Bò, Leonardo; Ruocco, G.; Raimondo, Domenico; Milanetti, Edoardo

doi:10.3389/fmolb.2021.626837

Cited by 33 publications

(43 citation statements)

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“…They defined four groups of amino acids by applying a principal component analysis and distinguish between negatively charged, positively charged, polar, and nonpolar amino acids. Accordingly, comparing the amino acid content of investigated proteins in this study, it is confirmed that hemoglobin and AFP III consists mainly out of hydrophobic amino acids whereas in BSA and Lysozyme most prevalent amino acids belong to the charged group (Di Rienzo et al, 2021).…”

Section: A N Na Nsupporting

confidence: 67%

Isoelectric Point of Proteins at Hydrophobic Interfaces

2021

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Structural and colloidal stability of proteins at different surfaces and interfaces is of great importance in many fields including medical, pharmaceutical, or material science. Due to their flexibility, proteins tend to respond to their environmental conditions and can undergo structural and conformational changes. For instance, alterations in physiological factors such as temperature, ions concentration, or pH as well as the adsorption to an interface can initiate protein aggregation. Therefore, at different surfaces and interfaces the characterization of the structural and colloidal stability of proteins, which is mainly influenced by their electrostatic and hydrophobic interactions, is of fundamental importance. In this study, we utilized sum frequency generation (SFG) spectroscopy to assess the role of solution pH on the polarity and magnitude of the electric field within the hydration shell of selected model proteins adsorbed to a hydrophobic surface. We used polystyrene (PS) as a model hydrophobic surface and determined the isoelectric point (IEP) of four structurally different model proteins. Comparing the measured IEP of proteins at the PS/solution or air/solution interface with that determined in the bulk solution via zeta potential measurement, we found significant similarities between the IEP of surface adsorbed proteins and those in the bulk aqueous phase. The pH dependence behavior of proteins was correlated to their amino acid composition and degree of hydrophobicity.

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Section: A N Na Nsupporting

confidence: 67%

Isoelectric Point of Proteins at Hydrophobic Interfaces

2021

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“…As exhibited in Figure , compared with the bare GCE and AuNPs/PEDOT/GCE, pep1/AuNPs/PEDOT/GCE showed much less DPV signal suppression associated with nonspecific protein adsorption in all of the tested single protein solutions, including negatively charged BSA (Figure , a0–a3), positively charged Lyz (Figure , b0–b3), and electrically neutral protein Mb (Figure , c0–c3). This result illustrated the superior ability of pep1/AuNPs/PEDOT/GCE to resist nonspecific protein adsorption, thanks to the presence of the designed peptide, which is neutral in charge and has good hydrophilicity , as shown in Figure S1C.…”

Section: Resultsmentioning

confidence: 73%

“…Hydrophilicity and neutral charge are two key parameters for the designed peptides to possess the antifouling property. ,, Hence, the hydrophilicity of the designed peptide was investigated by the peptide property calculator and water contact angle test, as presented in Figure S1. The hydropathy distribution image (Figure S1A) clearly shows that most of the amino acids of pep1 (chemical formula shown in Figure S1B) are hydrophilic. The measured water contact angles of bare GCE and the AuNPs/PEDOT and pep1/AuNPs/PEDOT modified electrode surfaces (Figure S1C) are 61.92, 66.43, and 28.54°, respectively, which indicated that modification of the peptide can significantly enhance the hydrophilicity of the electrode surface, proving the strong hydrophilicity of the designed peptide.…”

Section: Resultsmentioning

confidence: 99%

Antifouling Aptasensor Based on Self-Assembled Loop-Closed Peptides with Enhanced Stability for CA125 Assay in Complex Biofluids

et al. 2021

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A brief and universal ultralow fouling sensing platform capable of assaying targets in complex biofluids was developed based on designed antifouling peptides that could form a loop-closed structure with enhanced stability. The newly designed peptide with thiol groups in its two terminals self-assembled onto a gold nanoparticle (AuNP)-modified electrode surface to form a stable loop structure, which displayed excellent antifouling performance, outstanding stability under enzymatic hydrolysis, and satisfactory long-term antifouling capability in complex biofluids (clinical human serum). The antifouling and highly sensitive electrochemical aptasensor was constructed via one-step co-immobilization of the designed peptides and aptamers onto the electrode surface modified with electrodeposited poly(3,4-ethylenedioxythiophene) (PEDOT) and AuNPs. The developed peptide-based aptasensor exhibited a decent response for the analysis of the cancer antigen 125 (CA125), with a relatively wide linear range (0.1−1000 U mL −1 ) and a low limit of detection (0.027 U mL −1 ), and was capable of detecting CA125 in clinical serum samples with acceptable accuracy. This antifouling strategy-based self-assembled peptide with a loop-closed structure provided a potential path for the development of various low-fouling biosensors for application in complex biological fluids.

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“…This is at the core of the development of the 2D Zernike polynomial expansion [ 8 ] as a method to find the protein-protein binding regions. This method could in principle be adapted to other properties (such as electrostatics or hydrophobicity) besides curvature since they can be described with numerical values that can be assigned to each surface point [ 25 , 26 ], and the Zernike expansion can be applied to any function. Nonetheless, in this work the algorithm is used to maximize the information concerning only the overall shape of the molecule.…”

Section: Introductionmentioning

confidence: 99%

A novel computational strategy for defining the minimal protein molecular surface representation

et al. 2022

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Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing local features of the molecular surface, that can potentially be involved in the interaction with other molecules, represents a step forward in the investigation of the mechanisms of recognition and binding between molecules. Predictive methods often rely on extensive samplings of molecular patches with the aim to identify hot spots on the surface. In this framework, analysis of large proteins and/or many molecular dynamics frames is often unfeasible due to the high computational cost. Thus, finding optimal ways to reduce the number of points to be sampled maintaining the biological information (including the surface shape) carried by the molecular surface is pivotal. In this perspective, we here present a new theoretical and computational algorithm with the aim of defining a set of molecular surfaces composed of points not uniformly distributed in space, in such a way as to maximize the information of the overall shape of the molecule by minimizing the number of total points. We test our procedure’s ability in recognizing hot-spots by describing the local shape properties of portions of molecular surfaces through a recently developed method based on the formalism of 2D Zernike polynomials. The results of this work show the ability of the proposed algorithm to preserve the key information of the molecular surface using a reduced number of points compared to the complete surface, where all points of the surface are used for the description. In fact, the methodology shows a significant gain of the information stored in the sampling procedure compared to uniform random sampling.

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Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

Cited by 33 publications

References 50 publications

Isoelectric Point of Proteins at Hydrophobic Interfaces

Isoelectric Point of Proteins at Hydrophobic Interfaces

Antifouling Aptasensor Based on Self-Assembled Loop-Closed Peptides with Enhanced Stability for CA125 Assay in Complex Biofluids

A novel computational strategy for defining the minimal protein molecular surface representation

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