Swagata Dasgupta

Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers.

A survey was compiled of several characteristics of the intersubunit contacts in 58 oligomeric proteins, and of the intermolecular contacts in the lattice for 223 protein crystal structures. The total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contact patches are frequently smaller than patches involved in oligomer interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acids at oligomer interfaces. Arginine is the only amino acid prominent in both types of interfaces. Potentials of mean force for residue–residue contacts at both crystal and oligomer interfaces were derived from comparison of the number of observed residue–residue interactions with the number expected by mass action. They show that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. They also suggest that complex salt bridges with certain amino acid compositions might be important in oligomer formation. For a protein that is recalcitrant to crystallization, substitution of lysine residues with arginine or glutamine is a recommended strategy. Proteins 28:494–514, 1997.

Studies on the interaction of copper complexes of (-)-epicatechin gallate and (-)-epigallocatechin gallate with calf thymus DNA.

The interaction of copper complexes of (-)-epicatechin gallate (ECG) and (-)-epigallocatechin gallate (EGCG) with calf thymus DNA (ct-DNA) was investigated by UV-visible (UV-Vis), fluorescence and circular dichroism along with melting studies. It was observed that both copper complexes quench the fluorescence intensity of ethidium bromide bound ct-DNA upon binding, resulting in a ground state complex formation by a static quenching process. The binding constants evaluated from fluorescence data were supported by the UV-Vis study. The values ranged from 0.84 to 1.07x10(5)M(-1) and 1.14 to 1.04x10(5)M(-1) for Cu(II)-ECG and Cu(II)-EGCG, respectively for the temperature range 21-42 degrees C with two binding sites. Thermodynamic parameters obtained are suggestive of the involvement of different modes of interaction during binding for each complex although both were found to be intercalating in nature. Circular dichroism studies and variations in the melting temperature reveal unwinding of the ct-DNA helix with conformational changes due to binding.

Fibrillation in Human Serum Albumin Is Enhanced in the Presence of Copper(II)

The aggregation process in proteins is governed by several factors such as temperature, pH, presence of electrolytes, denaturants, and metal ions. Here, we report the role of Cu(II) in inducing rapid fibrillation in human serum albumin. We have monitored this process via UV-vis spectroscopy, fluorescence spectroscopy, circular dichroism, zeta-potential measurements, electron paramagnetic resonance studies, fluorescence microscopy, and field emission scanning electron microscopy. Images show a fibrillar network of human serum albumin in the presence of Cu(II) in 60% ethanol incubated at 65 degrees C at physiological pH. All other studies also support the enhanced fibrillation in presence of Cu(II).

Magnetic Field Effect Corroborated with Docking Study to Explore Photoinduced Electron Transfer in Drug-Protein Interaction

Conventional spectroscopic tools such as absorption, fluorescence, and circular dichroism spectroscopy used in the study of photoinduced drug-protein interactions can yield useful information about ground-state and excited-state phenomena. However, photoinduced electron transfer (PET) may be a possible phenomenon in the drug-protein interaction, which may go unnoticed if only conventional spectroscopic observations are taken into account. Laser flash photolysis coupled with an external magnetic field can be utilized to confirm the occurrence of PET and authenticate the spin states of the radicals/radical ions formed. In the study of interaction of the model protein human serum albumin (HSA) with acridine derivatives, acridine yellow (AY) and proflavin (PF(+)), conventional spectroscopic tools along with docking study have been used to decipher the binding mechanism, and laser flash photolysis technique with an associated magnetic field (MF) has been used to explore PET. The results of fluorescence study indicate that fluorescence resonance energy transfer takes place from the protein to the acridine-based drugs. Docking study unveils the crucial role of Ser 232 residue of HSA in explaining the differential behavior of the two drugs towards the model protein. Laser flash photolysis experiments help to identify the radicals/radical ions formed in the due course of PET (PF(•), AY(•-), TrpH(•+), Trp(•)), and the application of an external MF has been used to characterize their initial spin-state. Owing to its distance dependence, MF effect gives an idea about the proximity of the radicals/radical ions during interaction in the system and also helps to elucidate the reaction mechanisms. A prominent MF effect is observed in homogeneous buffer medium owing to the pseudoconfinement of the radicals/radical ions provided by the complex structure of the protein.

A spectroscopic investigation into the interactions of 3′-O-carboxy esters of thymidine with bovine serum albumin

Binding studies of 3′‐O‐carboxy esters of thymidine, reported inhibitors of ribonucleases, with bovine serum albumin (BSA) have been explored in this report. Fluorescence spectroscopy in combination with Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy have been used to determine the nature and mode of binding. The binding and quenching parameters were determined from tryptophan fluorescence quenching by Scatchard plots and modified Stern–Volmer plots. The association constants are of the order of 104 M−1 for both the ligands. Thermodynamic parameters suggest that apart from an initial hydrophobic association, hydrogen bonding and van der Waals interactions play a decisive role during protein‐ligand complex formation. Minor changes were observed in the secondary structures of human serum albumin (HSA) as revealed by FTIR and CD. Docking studies suggest that the ligands are close to Trp 213, which causes fluorescence quenching.

Evidence of conformational changes in adsorbed lysozyme molecule on silver colloids

In this article, we discuss metal-protein interactions in the Ag-lysozyme complex by spectroscopic measurements. The analysis of the variation in relative intensities of SERS bands reveals the orientation and the change in conformation of the protein molecules on the Ag surface with time. The interaction kinetics of metal-protein complexes has been analyzed over a period of 3h via Raman measurements. Our analysis indicates that the Ag nanoparticles most likely interact with Trp123 which is in close proximity to Phe34 of the lysozyme molecule.

(-)-Epicatechin gallate prevents alkali-salt mediated fibrillogenesis of hen egg white lysozyme.

Green tea polyphenols (GTPs) are found to be potent inhibitors of amyloid fibril formation. We report the effective inhibitory property of (-)-epicatechin gallate (ECG) during the alkali-salt induced fibrillogenesis of hen egg white lysozyme (HEWL) at 37 °C. Spectroscopic techniques such as fluorescence, circular dichroism and microscopic images show that (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECG), and (-)-epigallocatechin gallate (EGCG) show moderate inhibition of fibrillation with ECG as the most potent polyphenol. Aromatic interactions, hydrophobic interactions, the radical scavenging activity and autoxidation of polyphenols are likely to be the major reasons for ECG being the most effective inhibitor.

Copper complexes of ( )-epicatechin gallate and ( )-epigallocatechin gallate act as inhibitors of Ribonuclease A

Green tea polyphenols, which have the ability to inhibit angiogenesis, form complexes with Cu(II), a known potent stimulator of blood vessel proliferation. Copper complexes of (−)‐epicatechin gallate and (−)‐epigallocatechin gallate were found to inhibit the enzymatic activity of Ribonuclease A (RNase A) as revealed by an agarose gel based assay and urea denatured gel electrophoresis. The copper complexes were found to be non‐competitive inhibitors of RNase A with inhibition constants in the micromolar range. Changes in the secondary structure of the protein are found to occur due to the interaction as revealed from Fourier transform infrared and circular dichroism studies.

Effect of green tea polyphenols on angiogenesis induced by an angiogenin-like protein

Angiogenesis is a fundamental process by which new blood vessels are formed. The angiogenesis process is induced by several growth factors. Among them angiogenin is the most potent blood vessel inducer known. In this paper, we have investigated the effect of green tea polyphenols, mainly the catechins, on an angiogenin-like protein induced angiogenesis process. The angiogenin-like protein was isolated from goat serum and the effect of green tea components was tested by the chicken chorioallantoic membrane (CAM) assay. The results show that green tea components are capable of reducing the vascularization on CAM that is induced by the angiogenin-like protein.

Molecular recognition: Connection and disconnection of hydrogen bonds, a case study with dimeric and highly associated monocarboxylic acids with simple receptors

Abstract The new receptor (5) having mixed diamide moieties is a simple synthetic model which binds carboxylic acids by three point hydrogen bonds involving pyridine nitrogen, pyridine amide as well as the flexible aliphatic amide moieties. This is in contrast to the receptor (6) which makes only two point hydrogen bonds. Binding studies of the simple pyridine amide (3) making two hydrogen bonds with a number of dimeric and highly associated monocarboxylic acids are also reported. Receptor (9) shows higher binding constant with ibuprofen compared to (3).