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Observation of Biomolecules and Their Dynamics in SERS
Published in Marc Lamy de la Chapelle, Nordin Felidj, Plasmonics in Chemistry and Biology, 2019
Jean Emmanuel Clément, Thibault Brulé, Aymeric Leray, Eric Finot
Biomolecules include both small molecules such as metabolites, vitamins, and hormones and large macromolecules such as amino acids and proteins. In the case of proteins of high molecular weight, their three-dimensional arrangements enable them to fold into one or more specific spatial conformations driven by noncovalent interactions. The structural biology is a new transverse topic of molecular biochemistry and biophysics that is concerned with the protein conformations linked to its biological functions. There is then a clear call for developing new physical tools to determine the protein structure and its dynamics with the final goal of our better understanding of the function of biomolecule or the design of new protein. From a biological point of view, the protein has three main levels of structure. The primary structure consists of a sequence of 20 natural amino acids connected to each other by peptide bonds. The secondary structure describes the local folding of the main protein chain. At this level, there are two main structures: the α-helix and β-sheet. The third structure is the result of complex interactions relevant for the three-dimensional conformation of proteins. To put it more bluntly, the protein might be seen as a sentence in which amino acids are the letters, the secondary structures are the word and finally the third structure is the sentence. From a physicochemical point of view, the protein is a linear polymer having thermodynamic stability. Phase transitions between unfolded and native states are activated by a difference in free energy of few kcal/mol) and driven also by surface properties, including surface charge, surface free energy, and hydrophilicity.
Intermolecular Force Parameters
Published in Mihai V. Putz, New Frontiers in Nanochemistry, 2020
Bogdan Bumbăcilă, Mihai V. Putz
The intermolecular forces are particularly important to assess in order to design and discover new drugs. The biological activity of most of the present therapeutic agents is based on the process of ligand-receptor interaction. In order to bind to the receptor, the drug molecule has to fit its specific site on the receptor but also to establish some non-covalent interactions at the spot: hydrogen bonds, electrostatic interactions, van der Waals interactions, π-interactions. The parameters which express the potency of these interactions are useful in QSAR studies because they can show the best candidate in a series of molecules for the best fit on their biological receptor.
Bionanocomposites, Their Processing, and Environmental Applications
Published in Shakeel Ahmed, Saiqa Ikram, Suvardhan Kanchi, Krishna Bisetty, Biocomposites, 2018
Sagar Roy, Chaudhery Mustansar Hussain
Proteins are natural biopolymers that have found several applications in their native form, such as wool, silk, and collagen. The three-dimensional structure of these proteins is stabilized mainly by non-covalent interactions. The unit structure of proteins forms through regular arrangements of various types of amino acids. Structural heterogeneity, thermal sensitivity, and hydrophilic behavior of proteins control the functional properties of specific protein. The degradation of proteins by enzymes occurs via amide hydrolysis reaction. Various vegetable and animal proteins are commonly used as biodegradable polymers, some of which are as follows:
Purification and characterization of a highly-stable fungal xylanase from Aspergillus tubingensis cultivated on palm wastes through combined solid-state and submerged fermentation
Published in Preparative Biochemistry & Biotechnology, 2022
Rawitsara Intasit, Benjamas Cheirsilp, Wasana Suyotha, Piyarat Boonsawang
Figure 3f shows half-life of crude and purified xylanases. One of common parameter used in the characterization of enzyme stability is its half-life. Assuming that the thermal deactivation is a first order process, half-life of xylanase can be calculated from rate constant of thermal deactivation reaction.[12] It was found that purified xylanase gave 2–8 folds longer half-life than crude xylanase. Temperature can affect the conformational stability of protein as the three dimension of protein structure contains large number of weak/non-covalent interactions like hydrogen bonds, van der Waal bonds and others.[22] The results clearly indicate that the purified fungal xylanase is suitable for industrial application at temperature in the range of 30 − 60 °C. The fungal xylanase is considered as an environmental friendly biocatalyst that can be applied in various industrial processes such as modifying cereal-based food, improving digestibility of animal feed, converting lignocellulosic wastes to bioproducts and prebleaching of paper pulps.[2,16,17]
Spectrophotometric and physicochemical studies on the interaction of a new platinum(IV) complex containing the drug pregabalin with calf thymus DNA
Published in Journal of Coordination Chemistry, 2020
Nahid Shahabadi, Sara Amiri, Hossein Zhaleh
Fluorescence is widely used in studying the mode of the interaction between a bio system and drug molecules. Various types of non-covalent interactions can play a role in the binding of a small molecule to a biomolecule including hydrogen bonds, van der Waals forces, electrostatic and hydrophobic interactions. According to the data of enthalpy changes (ΔH) and entropy changes (ΔS), the model of interaction can be concluded [42]: (a) ΔH > 0 and ΔS > 0, hydrophobic forces; (b) ΔH < 0 and ΔS < 0, van der Waals interactions and hydrogen bonds; and (c) ΔH < 0 and ΔS > 0, electrostatic interactions [43]. When there is little change of temperature, the enthalpy change (ΔH) can be seen as a constant, and then its value and that of entropy changes (ΔS) can be determined from the van’t Hoff equation (eq. (4)): where K is the binding constant at the corresponding temperature and R is gas constant. The values of ΔH and ΔS were obtained from the slope and intercept of the linear plot based on LnK versus 1/T. The values of ΔG were evaluated from the following equation (eq. (5)):
Tuning of non-covalent interactions involving a halogen atom that plays the role of Lewis acid and base simultaneously
Published in Molecular Physics, 2018
The formation of molecular complexes is a phenomenon which has attracted much attention over the last decades [1–5]. Molecular complexes are defined as systems whose individual fragments (most often simply molecules) are held together by non-covalent (in other words intermolecular) interactions. Non-covalent interactions are a broad category of interactions and in the most general sense, they actually span everything except for covalent interactions, i.e. interactions associated with the overlap of electronic density in the bonding region between interacting fragments with unfilled electronic shells, which lead to the formation of a chemical bond and a new molecule [6]. Among non-covalent interactions, hydrogen bonding (HB) and halogen bonding (XB) have received probably most of the attention due to the fact that these interactions play an important role in many areas of chemistry and physics [7,8], e.g. in biochemical processes [9–12], crystal engineering [12–16] and material science [12,17,18]. They have also become one of the main topics in computational chemistry and physics in recent years [12,19,20].