Membrane organization and dynamics of "inner pair" and "outer pair" tryptophan residues in gramicidin channels

The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation

Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.

Delving into Membrane Heterogeneity Utilizing Fluorescence Lifetime Distribution Analysis

Lipid bilayer membranes are indispensable parts of cellular architecture. One of the integral properties of bilayer membranes is the environmental heterogeneity over a wide range of spatiotemporal scales. The environmental heterogeneity is a manifestation of the dynamic and compositional anisotropy in the plane of the membrane as well as along the bilayer normal. Fluorescence lifetime distribution analysis provides a spectroscopic tool to quantitatively characterize such heterogeneities. The review discusses recent applications of fluorescence lifetime distribution analysis utilizing the maximum entropy method to characterize horizontal and vertical heterogeneities in membranes.

Measuring Membrane Penetration Depths and Conformational Changes in Membrane Peptides and Proteins

The structural organization and dynamic nature of the biomembrane components are important determinants for numerous cellular functions. Particularly, membrane proteins are critically important for various physiological functions and are important drug targets. The mechanistic insights on the complex functionality of membrane lipids and proteins can be elucidated by understanding the interplay between structure and dynamics. In this regard, membrane penetration depth represents an important parameter to obtain the precise depth of membrane-embedded molecules that often define the conformation and topology of membrane probes and proteins. In this review, we discuss about the widely used fluorescence quenching-based methods (parallax method, distribution analysis, and dual-quencher analysis) to accurately determine the membrane penetration depths of fluorescent probes that are either membrane-embedded or attached to lipids and proteins. Further, we also discuss a relatively novel fluorescence quenching method that utilizes tryptophan residue as the quencher, namely the tryptophan-induced quenching, which is sensitive to monitor small-scale conformational changes (short distances of < 15 Å) and useful in mapping distances in proteins. We have provided numerous examples for the benefit of readers to appreciate the importance and applicability of these simple yet powerful methods to study membrane proteins.

A multi-spectroscopic approach to investigate the interactions between Gramicidin A and silver nanoparticles

The comprehension and control of the interactions between nanoparticles and proteins at a molecular level are crucial to improve biomedical applications of nanomaterials and to develop nanosystems able to influence and regulate the conformational changes in proteins. In this work, we explore the interactions between Gramicidin A peptide (GramA) and dodecanethiol-stabilized small silver nanoparticles (D-AgNPs), paying particular attention to the effect on GramA conformation in POPC bilayers. D-AgNPs have been prepared to have dimensions (5 nm) and a hydrophobic nature compatible with the POPC lipid bilayer. Fluorescence, Raman and IR spectroscopies have been used to investigate both peptide conformation and its position inside the phospholipid bilayer. Results are discussed in terms of solvent exposure and conformation of GramA peptide.

Design, synthesis, and biological evaluation of stable β6.3-Helices: Discovery of non-hemolytic antibacterial peptides

Gramicidin A, a topical antibiotic made from alternating L and D amino acids, is characterized by its wide central pore; upon insertion into membranes, it forms channels that disrupts ion gradients. We present helical peptidomimetics with this characteristic wide central pore that have been designed to mimic gramicidin A channels. Mimetics were designed using molecular modeling focused on oligomers of heterochiral dipeptides of proline analogs, in particular azaproline (AzPro). Molecular Dynamics simulations in water confirmed the stability of the designed helices. A sixteen-residue Formyl-(AzPro-Pro)₈-NHCH₂CH₂OH helix was synthesized as well as a full thirty-two residue Cbz-(AzPro-Pro)₁₆-O^tBu channels. No liposomal lysis activity was observed suggesting lack of channel formation, possibly due to inappropriate hydrogen-bonding interactions in the membrane. These peptidomimetics also did not hemolyze red blood cells, unlike gramicidin A.

Depth-Dependent Organization and Dynamics of Archaeal and Eukaryotic Membranes: Development of Membrane Anisotropy Gradient with Natural Evolution

The lipid composition of archaea is unique and has been correlated with increased stability under extreme environmental conditions. In this article, we have focused on the evolution of membrane organization and dynamics with natural evolution. Dynamic anisotropy along the membrane normal (i.e., gradients of mobility, polarity, and heterogeneity) is a hallmark of fluid phase diester or diether phospholipid membranes. We monitored gradients of mobility, polarity, and heterogeneity along the membrane normal in membranes made of a representative archaeal lipid using a series of membrane depth-dependent fluorescent probes, and compared them to membranes prepared from a typical diether lipid from higher organisms (eukaryotes). Our results show that the representative dynamic anisotropy gradient along the membrane normal is absent in membranes made from archaeal lipids. We hypothesize that the dynamic gradient observed in membranes of diester and diether phospholipids is a consequence of natural evolution of membrane lipids in response to the requirement of carrying out complex cellular functions by membrane proteins.

Gramicidin conformational changes during riboflavin photosensitized oxidation in solution and the effect of N-methylation of tryptophan residues

During riboflavin mediated photo-oxidation, gramicidin changes from intertwined to monomeric conformation (disaggregation), while the methylated derivative is not photo-oxidized.

Dynamic insight into protein structure utilizing red edge excitation shift

Proteins are considered the workhorses in the cellular machinery. They are often organized in a highly ordered conformation in the crowded cellular environment. These conformations display characteristic dynamics over a range of time scales. An emerging consensus is that protein function is critically dependent on its dynamics. The subtle interplay between structure and dynamics is a hallmark of protein organization and is essential for its function. Depending on the environmental context, proteins can adopt a range of conformations such as native, molten globule, unfolded (denatured), and misfolded states. Although protein crystallography is a well established technique, it is not always possible to characterize various protein conformations by X-ray crystallography due to transient nature of these states. Even in cases where structural characterization is possible, the information obtained lacks dynamic component, which is needed to understand protein function. In this overall scenario, approaches that reveal information on protein dynamics are much appreciated. Dynamics of confined water has interesting implications in protein folding. Interfacial hydration combines the motion of water molecules with the slow moving protein molecules. The red edge excitation shift (REES) approach becomes relevant in this context. REES is defined as the shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of absorption spectrum. REES arises due to slow rates (relative to fluorescence lifetime) of solvent relaxation (reorientation) around an excited state fluorophore in organized assemblies such as proteins. Consequently, REES depends on the environment-induced motional restriction imposed on the solvent molecules in the immediate vicinity of the fluorophore. In the case of a protein, the confined water in the protein creates a dipolar field that acts as the solvent for a fluorophore in the protein. In this Account, we focus on REES to monitor organization and dynamics of soluble and membrane proteins utilizing intrinsic protein fluorescence. We discuss here the application of REES in various conformations of proteins. While application of REES to proteins in native conformation has been in use for a long time, our work highlights the potential of this approach in case of molten globule and denatured conformations. For example, we have demonstrated the presence of residual structure, that could not be detected using other methods, by REES of denatured spectrin. Given the functional relevance of such residual structures, these results are very far reaching. We discuss here the application of REES to molten globule conformation and to the green fluorescent protein (GFP). The case of GFP is particularly interesting since the dipolar field in this case is provided by the protein matrix itself and not confined water. We envision that future applications of REES in proteins will involve generating a dynamic hydration map of the protein, which would allow us to explore protein function in terms of local dynamics and hydration.

Importance of indole N-H hydrogen bonding in the organization and dynamics of gramicidin channels

The linear ion channel peptide gramicidin represents an excellent model for exploring the principles underlying membrane protein structure and function, especially with respect to tryptophan residues. The tryptophan residues in gramicidin channels are crucial for the structure and function of the channel. In order to test the importance of indole hydrogen bonding for the biophysical properties of gramicidin channels, we monitored the effect of N-methylation of gramicidin tryptophans, using a combination of steady state and time-resolved fluorescence approaches along with circular dichroism spectroscopy. We show here that in the absence of the hydrogen bonding ability of tryptophans, tetramethyltryptophan gramicidin (TM-gramicidin) is unable to maintain the single stranded, head-to-head dimeric channel conformation in membranes. Our results show that TM-gramicidin displays a red-shifted fluorescence emission maximum, lower red edge excitation shift (REES), and higher fluorescence intensity and lifetime, consistent with its nonchannel conformation. This is in agreement with the measured location (average depth) of the 1-methyltryptophans in TM-gramicidin using the parallax method. These results bring out the usefulness of 1-methyltryptophan as a fluorescent tool to examine the hydrogen bonding ability of tryptophans in proteins and peptides. We conclude that changes in the hydrogen bonding ability of tryptophans, along with coupled changes in peptide backbone structure induce the loss of single stranded β(6.3) helical dimer conformation. These results agree with earlier results from size-exclusion chromatography and single-channel measurements for TM-gramicidin, and confirm the importance of indole hydrogen bonding for the conformation and function of ion channels and membrane proteins.

Organization and dynamics of the N-terminal domain of chemokine receptor CXCR1 in reverse micelles: effect of graded hydration

Water plays a fundamental role in the folding, structure, dynamics, and function of proteins and peptides. The extracellular N-terminal domain of chemokine receptors is crucial in mediating binding affinity, receptor selectivity, and regulating function. The flexible N-terminal domain becomes ordered in membranes and membrane-mimetic assemblies, thereby indicating that the membrane could play an important role in regulating CXC chemokine receptor 1 (CXCR1) function. In view of the role of hydration in lipid-protein interactions in membranes, we explored the organization and dynamics of a 34-mer peptide of the CXCR1 N-terminal domain in reverse micelles by utilizing a combination of fluorescence-based approaches and circular dichroism spectroscopy. Our results show that the secondary structure adopted by the CXCR1 N-domain is critically dependent on hydration. The tryptophan residues of the CXCR1 N-domain experience motional restriction and exhibit red edge excitation shift (REES) upon incorporation in reverse micelles. REES and fluorescence lifetime exhibit reduction with increasing reverse micellar hydration. Time-resolved fluorescence anisotropy measurements reveal the effect of hydration on peptide rotational dynamics. Taken together, these results constitute the first report demonstrating modulation in the organization and dynamics of the N-terminal domain of a chemokine receptor in a membrane-like environment of varying hydration. We envisage that these results are relevant in the context of hydration in the function of G protein-coupled receptors.