Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (R-g), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrirner as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).

Ultrafast Chemical Dynamics in Time Domain Through Fluorescence Spectroscopy

While absorption and emission spectroscopy have always been used to detect and characterize molecules and molecular complexes, the availability of ultrashort laser pulses and associated computer-aided optical detection techniques allowed study of chemical processes directly in the time domain at unprecedented time scales, through appearance and disappearance of fluorescence from participating chemical species. Application of such techniques to chemical dynamics in liquids, where many processes occur with picosecond and femtosecond time scales lead to the discovery of a host of new phenomena that in turn led to the development of many new theories. Experiment and theory together provided new and valuable insight into many fundamental chemical processes, like isomerization dynamics, electron and proton transfer reactions, vibrational energy and phase relaxation, photosynthesis, to name just a few. In this article, we shall review a few of such discoveries in attempt to provide a glimpse of the fascinating research employing fluorescence spectroscopy that changed the field of chemical dynamics forever.

Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

Differential dynamics of the serotonin(1A) receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation

The serotonin(1A) receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin(1A) receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3s, to analyze the effect of cholesterol on the structure and dynamics of the serotonin(1A) receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin(1A) receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.

Modulation of Buckling Dynamics in Nanoparticle Laden Droplets Using External Heating

Dynamics of contact free (levitated) drying of nanofluid droplets is ubiquitous in many application domains ranging from spray drying to pharmaceutics. Controlling the final morphology (macro to micro scales) of the dried out sample poses some serious challenges. Evaporation of solvent and agglomeration of particles leads to porous shell formation in acoustically levitated nanosilica droplets. The capillary pressure due to evaporation across the menisci at the nanoscale pores causes buckling of the shell which leads to ring and bowl shaped final structures. Acoustics plays a crucial role in flattening of droplets which is a prerequisite for initiation of buckling in the shell: Introduction of mixed nanocolloids (sodium dodecyl sulfate + nanosilica) reduces evaporation rate, disrupts formation of porous shell, and enhances mechanical strength of the shell, all of which restricts the process of buckling. Although buckling is completely arrested in such surfactant added droplets, controlled external heating using laser enhances evaporation through the pores in the shell due to thermally induced structural changes and rearrangement of SDS aggregates which reinitializes buckling in such droplets, Furthermore, inclusion of anilinium hydrochloride into the nanoparticle laden droplets produces ions which adsorb and modify the morphology of sodium dodecyl sulfate crystals and reinitializes buckling in the shell (irrespective of external heating conditions). The kinetics of buckling is determined by the combined effect of morphology of the colloidal particles, particle/aggregate diffusion rate within the droplet, and the rate of evaporation of water. The buckling dynamics leads to cavity formation which grows subsequently to yield final structures with drastically different morphological features. The cavity growth is controlled by evaporation through the nanoscate pores and exhibits a universal trend irrespective of heating rate and nanoparticle type.

Molecular Dynamics Simulation of Microstructure of Nanocrystalline Copper

The microstructure of computer generated nanocrystalline coppers is simulated by using molecular dynamics with the Finnis-Sinclair potential, analysed by means of radial distribution functions, coordination number, atomic energy and local crystalline order. The influence of the grain size on the nanocrystalline structure is studied. The results reveal that as the grain size is reduced, the grain boundary shows no significant structural difference, but the grain interior becomes more disordered, and their structural difference diminishes gradually; however, the density and the atomic average energy of the grain boundary present different tendencies from those of the grain interior.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Forced extension of P-selectin construct using steered molecular dynamics

P-selectin, a 70-nm-long cellular adhesive molecule, possesses elastic and extensible properties when neutrophils roll over the activated endotheliam of blood vessel in inflammatory reaction. Transient formation and dissociation of P-selectin/ligand bond on applied force of blood flow induces the extension of P-selectin and relevant ligands. Steered molecular dynamics simulations were performed to stretch a single P-selectin construct consisting of a lectin (Lec) domain and an epithelial growth factor (EGF)-like domain, where P-selectin construct was forced to extend in water with pulling velocities of 0.005-0.05 nm/ps and with constant forces of 1000-2500 pN respectively. Resulting force-extension profiles exhibited a dual-peak pattern on various velocities, while both plateaus and shoulders appeared in the extension-time profiles on various forces. The force or extension profiles along stretching pathways were correlated to the conformational changes, suggesting that the structural collapses of P-selectin Lec/EGF domains were mainly attributed to the burst of hydrogen bonds within the major beta sheet of EGF domain and the disruptions of two hydrophobic cores of Lee domain. This work furthers the understanding of forced dissociation of P-selectin/ligand bond.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Capturing protein dynamics with time-resolved luminescence spectroscopy

The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes---one that exhibits two-state folding (cytochrome cb₅₆₂) and one that has both a kinetic refolding intermediate ensemble and a distinct equilibrium unfolding intermediate (cytochrome c₅₅₂). Our data reveal that the distinct structural features of cytochrome c₅₅₂ contribute to its thermostability.

We have also investigated intrachain contact dynamics in unfolded cytochrome cb₅₆₂ by monitoring electron transfer, which occurs as the heme collides with a ruthenium photosensitizer, covalently bound to residues along the polypeptide. Intrachain diffusion for chemically denatured proteins proceeds on the microsecond timescale with an upper limit of 0.1 microseconds. The power-law dependence (slope = -1.5) of the rate constants on the number of peptide bonds between the heme and Ru complex indicate that cytochrome cb₅₆₂ is minimally frustrated.

In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome b₅₆₂ to a c-type cytochrome with the porphyrin covalently bound to cysteine sidechains. We have investigated the effects of the changes to the protein structure (i.e., increased rigidity and potential new equatorial tunneling pathways) on the electron transfer rates, measured by transient absorption, in a series of ruthenium photosensitizer-modified proteins.

Rate and Microstructure Effects on the Dynamics of Carbon Nanotube Foams

Soft hierarchical materials often present unique functional properties that are sensitive to the geometry and organization of their micro- and nano-structural features across different lengthscales. Carbon Nanotube (CNT) foams are hierarchical materials with fibrous morphology that are known for their remarkable physical, chemical and electrical properties. Their complex microstructure has led them to exhibit intriguing mechanical responses at different length-scales and in different loading regimes. Even though these materials have been studied for mechanical behavior over the past few years, their response at high-rate finite deformations and the influence of their microstructure on bulk mechanical behavior and energy dissipative characteristics remain elusive.

In this dissertation, we study the response of aligned CNT foams at the high strain-rate regime of 10² - 10⁴ s^-1. We investigate their bulk dynamic response and the fundamental deformation mechanisms at different lengthscales, and correlate them to the microstructural characteristics of the foams. We develop an experimental platform, with which to study the mechanics of CNT foams in high-rate deformations, that includes direct measurements of the strain and transmitted forces, and allows for a full field visualization of the sample’s deformation through high-speed microscopy.

We synthesize various CNT foams (e.g., vertically aligned CNT (VACNT) foams, helical CNT foams, micro-architectured VACNT foams and VACNT foams with microscale heterogeneities) and show that the bulk functional properties of these materials are highly tunable either by tailoring their microstructure during synthesis or by designing micro-architectures that exploit the principles of structural mechanics. We also develop numerical models to describe the bulk dynamic response using multiscale mass-spring models and identify the mechanical properties at length scales that are smaller than the sample height.

The ability to control the geometry of microstructural features, and their local interactions, allows the creation of novel hierarchical materials with desired functional properties. The fundamental understanding provided by this work on the key structure-function relations that govern the bulk response of CNT foams can be extended to other fibrous, soft and hierarchical materials. The findings can be used to design materials with tailored properties for different engineering applications, like vibration damping, impact mitigation and packaging.

Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MSCL)

The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.

It has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 °C – 60 °C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.

Extensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.

MscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.

Defect and structural imperfection effects on the electronic properties of BiTeI surfaces

The surface electronic structure of the narrow-gap seminconductor BiTeI exhibits a large Rashba-splitting which strongly depends on the surface termination. Here we report on a detailed investigation of the surface morphology and electronic properties of cleaved BiTeI single crystals by scanning tunneling microscopy, photoelectron spectroscopy (ARPES, XPS), electron diffraction (SPA-LEED) and density functional theory calculations. Our measurements confirm a previously reported coexistence of Te- and I-terminated surface areas

Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.