Effect of Molecular Dynamics and Internal Water Contact on the Photophysical Properties of Red pH-Sensitive Proteins.

The pH dependence of the absorption and (time-resolved) fluorescence of two red-shifted fluorescent proteins, mCardinal and mNeptune, was investigated. Decay-associated spectra were measured following fluorescence excitation at 470 nm in PBS buffer with a pH that ranged from 5.5 to 8.0. The fluorescence of both proteins shows two different decay components. mCardinal exhibits an increase in the long-lived fluorescence component with acidification from 1.34 ns at pH 8.0 to 1.62 ns at pH 5.5. An additional fast decay component with 0.64 ns at pH 8.0 up to 1.1 ns at pH 5.5 was found to be blue-shifted compared to the long-lived component. The fluorescence lifetime of mNeptune is insensitive to pH. DAS of mCardinal were simulated assuming a coupled two-level system to describe the 1S state of the chromophore within two different conformations of the protein. MD simulations were conducted to correlate the experimentally observed pH-induced change in the lifetime in mCardinal with its molecular properties. While the chromophores of both protein variants are stabilized by the same number of hydrogen bonds, it was found that the chromophore in mCardinal exhibits more water contacts compared to mNeptune. In mCardinal, interaction between the chromophore and Glu-145 is reduced as compared to mNeptune, but interaction with Thr-147 which is Ser-147 in mNeptune is stronger in mCardinal. Therefore, the dynamics of the excited-state proton transfer (ESPT) might be different in mCardinal and mNeptune. The pH dependency of ESPT is suggested as a key mechanism for pH sensitivity.

Real-time, label-free detection and identification of bacteria through non-invasive optical imaging.

Currently, traditional and newer molecular and mass spectrometry techniques of identifying bacteria from biological samples requires lengthy sample preparation, growth and labelling/staining assays. Thus, there is a pressing clinical need for an adjunct method that accurately identifies bacteria in real time. Here we report on the evaluation of confocal microscopy for the identification of clinically important and multi-drug resistant (MDR) bacteria in real time, using their intrinsic fluorescence features, i.e., emission spectra and fluorescence lifetime. The results demonstrate that difference in emission spectra and fluorescence lifetimes can be used as a fingerprint for identification of 12 bacterial species and MDR strains in real-time. Photostability or time-traces of bacteria demonstrated that these parameters could be used for tracking and recording without a need for labelling. Further, dilution experiments demonstrated that using intrinsic fluorescence S. aureus, Klebsiella pneumoniae and Escherichia coli bacteria can be detected and identified at clinically relevant concentrations as low as 2 × 102 CFU/mL. This non-invasive, non-labelling optical methodology may serve as the basis for development of a device that would quickly and accurately identify bacteria in biological samples. Thus, this intrinsic fluorescence technique would provide clinicians information, within minutes from sampling, to base accurate and specific treatments for patients.

Source, Synthesis, and Biological Evaluation of Natural Occurring 2,2'-Bipyridines.

Molecules containing bipyridine scaffold are fascinating and versatile compounds in the field of natural product chemistry and drug discovery, and these molecules have possible therapeutic applications due to possession of potent biological activities such as antimicrobial, immunomodulatory, antitumor, and phytotoxic. Significant efforts have been devoted to isolating various 2,2' bipyridine compounds from natural sources, with antimicrobial, anti-cancer, and immunosuppressive properties. This review describes recent developments in isolation from different microbial origins, synthesis, and investigation of different kinds of biological activities of 2,2' bipyridines, with a particular emphasis on caerulomycins, collismycins, and related derivates thereof in detail.

Detection and identification of amino acids and proteins using their intrinsic fluorescence in the visible light spectrum.

The detection and identification of biomolecules are essential in the modern era of medical diagnostics. Several approaches have been established, but they have significant limitations such as laborious and time-consuming sample preparation, analysis, and the need to use external probes which provide adequate but not desired levels of accuracy and sensitivity. Herein, we have explored successfully a non-invasive technique to detect and identifybiomolecules such as amino acids and proteins by utilizing their intrinsic fluorescence. The developed confocal microscopy method revealed high and photostable emission counts of these biomolecules including amino acids (tryptophan, phenylalanine, tyrosine, proline, histidine, cysteine, aspartic acid, asparagine, isoleucine, lysine, glutamic acid, arginine) and proteins (HSA, BSA) when they are excited with a green laser. The fluorescence lifetime of the samples enabled the identification and distinction of known and blind samples of biomolecules from each other. The developed optical technique is straightforward, non-destructive and does not require laborious labeling to identify specific proteins, and may serve as the basis for the development of a device that would quickly and accurately identify proteins at an amino acid level. Therefore, this approach would open an avenue for precise detection in imaging and at the same time increases our understanding of chemical dynamics at the molecular level.

Synthesis and Characterization of Highly Crystalline Bi-Functional Mn-Doped Zn2SiO4 Nanostructures by Low-Cost Sol-Gel Process.

Herein, we demonstrate a process for the synthesis of a highly crystalline bi-functional manganese (Mn)-doped zinc silicate (Zn2SiO4) nanostructures using a low-cost sol-gel route followed by solid state reaction method. Structural and morphological characterizations of Mn-doped Zn2SiO4 with variable doping concentration of 0.03, 0.05, 0.1, 0.2, 0.5, 1.0, and 2.0 wt% were investigated by using X-ray diffraction and high-resolution transmission electron microscopy (HR-TEM) techniques. HR-TEM-assisted elemental mapping of the as-grown sample was conducted to confirm the presence of Mn in Zn2SiO4. Photoluminescence (PL) spectra indicated that the Mn-doped Zn2SiO4 nanostructures exhibited strong green emission at 521 nm under 259 nm excitation wavelengths. It was observed that PL intensity increased with the increase of Mn-doping concentration in Zn2SiO4 nanostructures, with no change in emission peak position. Furthermore, magnetism in doped Zn2SiO4 nanostructures was probed by static DC magnetization measurement. The observed photoluminescence and magnetic properties in Mn-doped Zn2SiO4 nanostructures are discussed in terms of structural defect/lattice strain caused by Mn doping and the Jahn-Teller effect. These bi-functional properties of as-synthesized Zn2SiO4 nanostructures provide a new platform for their potential applications towards magneto-optical and spintronic and devices areas.

Facile synthesized zinc oxide nanorod film humidity sensor based on variation in optical transmissivity.

Variation in the transmitted light intensity from metal oxide thin films with moisture content provides a great opportunity to use them for humidity sensing. Herein, we have developed a novel and simple humidity sensor based on ZnO nanorod (ZNR) thin films which work as transmission-based sensing elements in an in-house fabricated sensing setup. The ZNR sensing element shows excellent linear sensing performance in the relative humidity (RH) range 10-90% and does not show any hysteresis. A maximum change in optical power of ∼95 µW is observed with the change in RH in the range 10-90%, for the sample with the smallest crystallite size (ZNR1) and highest pore diameter of the ZNR film. Also, a maximum sensitivity of 1.104 µW/% RH is observed for the ZNR1 sample which drops to 0.604 µW/% RH for the highest crystallite size sample (ZNR4). The presence of oxygen vacancies and the micro-porous nature of the film allow the absorption of water vapour on the film which deflects light at different angles that vary with the moisture content. The experimental results suggest that the ZNR film with a smaller crystallite size and larger pore diameter is more sensitive for humidity measurements. Further, an improved sensing performance is perceived in ZNRs because of the larger surface area of the nanorods. The ZNR based sensing elements do not suffer from ageing effects and exhibit high repeatability (88.74%). Further, the humidity sensor has a response time of 62 seconds and recovery time of 100 seconds which can be considered as a fairly quick response.

Self-Assembly and Micellar Transition in CTAB Solutions Triggered by 1-Octanol.

This study exploits higher-order micellar transition ranging from ellipsoidal to rodlike to wormlike induced by 1-octanol (C8OH) in an aqueous solution of cetyltrimethylammonium bromide (CTAB), characterizing phase behavior, rheology, and small-angle neutron scattering (SANS). The phase diagram for the ternary system CTAB-C8OH-water was constructed, which depicted the varied solution behavior. Such performance was further inferred from the rheology study (oscillatory-shear frequency sweep (ω) and viscosity (η)) that displayed an interesting solution behavior of CTAB solutions as a function of C8OH. It was observed that at low C8OH concentrations, the solutions appeared viscous/viscoelastic fluids that changed to an elastic gel with an infinite relaxation time at higher concentrations of C8OH, thereby confirming the existence of distinct micelle morphologies. Small-angle neutron scattering (SANS) provided various micellar parameters such as aggregation numbers (Nagg) and micellar size/shape. The experimental results were further validated with a computational simulation approach. The molecular dynamic (MD) study offered an insight into the molecular interactions and aggregation behavior through different analyses, including radial distribution function (RDF), radius of gyration (Rg), and solvent-accessible surface area (SASA).

Emerging Prospects of Nanozymes for Antibacterial and Anticancer Applications.

The ability of some nanoparticles to mimic the activity of certain enzymes paves the way for several attractive biomedical applications which bolster the already impressive arsenal of nanomaterials to combat deadly diseases. A key feature of such 'nanozymes' is the duplication of activities of enzymes or classes of enzymes, such as catalase, superoxide dismutase, oxidase, and peroxidase which are known to modulate the oxidative balance of treated cells for facilitating a particular biological process such as cellular apoptosis. Several nanoparticles that include those of metals, metal oxides/sulfides, metal-organic frameworks, carbon-based materials, etc., have shown the ability to behave as one or more of such enzymes. As compared to natural enzymes, these artificial nanozymes are safer, less expensive, and more stable. Moreover, their catalytic activity can be tuned by changing their size, shape, surface properties, etc. In addition, they can also be engineered to demonstrate additional features, such as photoactivated hyperthermia, or be loaded with active agents for multimodal action. Several researchers have explored the nanozyme-mediated oxidative modulation for therapeutic purposes, often in combination with other diagnostic and/or therapeutic modalities, using a single probe. It has been observed that such synergistic action can effectively by-pass the various defense mechanisms adapted by rogue cells such as hypoxia, evasion of immuno-recognition, drug-rejection, etc. The emerging prospects of using several such nanoparticle platforms for the treatment of bacterial infections/diseases and cancer, along with various related challenges and opportunities, are discussed in this review.

Occurrence of urinary tract infection and preventive strategies practiced by female students at a tertiary care teaching institution.

BACKGROUND: Urinary tract infections (UTIs) are more common in females than males and predominantly based on their unhealthy practices in their day to day lives. This study is trying to assess the occurrence of UTI and strategies used by female student to prevent UTI. MATERIALS AND METHODS: A cross-sectional descriptive study carried out in a tertiary care teaching institute. A total of 338 conveniently selected B. Sc. Nursing and MBBS Medical students were surveyed. The data were collected by using a pretested, a self-structured questionnaire related to occurrence and practices to prevent UTI along with necessary demographic details. Descriptive (frequency, percentage, mean and standard deviation) and inferential (Chi-square test) statistics was used to compute the data. RESULTS: The result of this study shows that 10.05% female students reported of having UTI. The proportion was higher in nursing students (67.6%) than medical (32.4%) but did not show a significance difference (P = 0.61). Age, duration of hostel life, and marital status were significantly associated with the status of UTI (P = 0.001). To prevent UTI, students were using commercial product with Tea Tree Oil, soap, drinking 3-4 l water/day, increased frequency of peri-wash during menstruation period, and use of Citrus Fruits. The use of western toilet was also significantly associated with status of UTI (P = 0.04). CONCLUSION: The occurrence of UTI was more among nursing students. Most of the perineal hygienic practices by the female students were associated with occurrence of UTI; hence, it is necessary to emphasize on preventive practices to minimize re-occurrence.

Facile Synthesis, Static, and Dynamic Magnetic Characteristics of Varying Size Double-Surfactant-Coated Mesoscopic Magnetic Nanoparticles Dispersed Stable Aqueous Magnetic Fluids.

The present work reports the synthesis of a stable aqueous magnetic fluid (AMF) by dispersing double-surfactant-coated Fe3O4 magnetic nanoparticles (MNPs) in water using a facile ambient scalable wet chemical route. MNPs do not disperse well in water, resulting in low stability. This was improved by dispersing double-surfactant (oleic acid and sodium oleate)-coated MNPs in water, where cross-linking between the surfactants improves the stability of the AMFs. The stability was probed by rheological measurements and all the AMF samples showed a good long-term stability and stability against a gradient magnetic field. Further, the microwave spin resonance behavior of AMFs was studied in detail by corroborating the experimental results obtained from the ferromagnetic resonance (FMR) technique to theoretical predictions by appropriate fittings. A broad spectrum was perceived for AMFs which indicates strong ferromagnetic characteristics. The resonance field shifted to higher magnetic field values with the decrease in particle size as larger-size MNPs magnetize and demagnetize more easily since their magnetic spins can align in the field direction more definitely. The FMR spectra was fitted to obtain various spin resonance parameters. The asymmetric shapes of the FMR spectra were observed with a decrease in particle sizes, which indicates an increase in relaxation time. The relaxation time increased with a decrease in particle sizes (sample A to D) from 37.2779 ps to 42.8301 ps. Further, a detailed investigation of the structural, morphological, and dc magnetic properties of the AMF samples was performed. Room temperature dc magnetic measurements confirmed the superparamagnetic (SPM) characteristics of the AMF and the M-H plot for each sample was fitted with a Langevin function to obtain the domain magnetization, permeability, and hydrodynamic diameter of the MNPs. The saturation magnetization and coercivity of the AMF samples increased with the increase in dispersed MNPs' size of the samples. The improvement in the stability and magnetic characteristics makes AMFs suitable candidates for various biomedical applications such as drug delivery, magnetic fluid hyperthermia, and biomedicines.

Medication adherence and quality of life among type-2 diabetes mellitus patients in India.

BACKGROUND: Diabetes mellitus (DM) is a progressively increasing metabolic disorder and a significant public health burden that demands immediate global attention. However, there is a paucity of data about adherence to antidiabetic drugs among patients with type-2 (T2)DM in Uttarakhand, India. Outpatient research reported that more than 50% of patients do not adhere to the correct administration and appropriate medicine dosage. It has been reported that patients with chronic diseases who adhere to treatment may experience improvement in quality of life (QoL) and vice versa. AIM: To assess the adherence to antidiabetic medication and QoL among patients with T2DM. METHODS: This cross-sectional descriptive study was conducted at a tertiary care hospital in Uttarakhand, India. The Medication Adherence Rating Scale and World Health Organization QoL-BREF scale were used to assess medication adherence and QoL. RESULTS: Two hundred seventy-seven patients suffering from T2DM participated in the study. Their mean age was 50.80 (± 10.6) years, 155 (56%) had a poor adherence level and 122 (44%) had a good adherence level to antidiabetic medications. After adjusting for sociodemographic factors, multiple linear regression analysis found patients who were adherent to antidiabetic medications had significantly higher mean overall perception of QoL and overall perception of health, with beta scores of 0.36 and 0.34, respectively (both P = 0.000) points compared with nonadherent patients. CONCLUSION: There was an association between medication adherence and QoL in patients with T2DM. Hence, there is a need to plan awareness and counseling programs followed by regular follow-up to motivate patient adherence to recommended treatment and lifestyle regimens.

Contrasting effect of 1-butanol and 1,4-butanediol on the triggered micellar self-assemblies of C16-type cationic surfactants.

The self-assembly in aqueous solutions of three quaternary salt-based C16-type cationic surfactants with different polar head groups and identical carbon alkyl chain viz., cetylpyridinium bromide (CPB), cetyltrimethylammonium tosylate (CTAT), and cetyltriphenylphosphonium bromide (CTPPB) in the presence of 1-butanol (BuOH) and 1,4-butanediol (BTD) was investigated using tensiometry, 2D-nuclear Overhauser enhancement spectroscopy (2D-NOESY) and small angle neutron scattering (SANS) techniques. The adsorption parameters and micellar characteristics evaluated at 303.15 K distinctly showed that BuOH promotes the mixed micelle formation while BTD interfered with the micellization phenomenon. The SANS data fitted using an ellipsoid (as derived by Hayter and Penfold using the Ornstein-Zernike equation and the mean spherical approximation) and wormlike micellar models offered an insight into the micelle size/shape and aggregation number (Nagg) in the examined systems. The evaluated descriptors presented a clear indication of the morphology transition in cationic micelles as induced by the addition of the two alcohols. We also offer an investigation into the acceptable molecular interactions governing the differences in micelle morphologies, using the non-invasive 2D-NOESY technique and molecular modeling. The experimental observations elucidated from computational simulation add novelty to this work. Giving an account to the structural complexity in the three cationic surfactants, the molecular dynamics (MD) simulation was performed for CPB micelles in an aqueous solution of alcohols that highlighted the micelle solvation and structural transition, which is further complemented in terms of critical packing parameter (PP) for the examined systems.

Tuning Cationic Micelle Properties with an Antioxidant Additive: A Molecular Perspective.

In this work, we characterize the micellization and morphology transition induced in aqueous cetyltrimethylammonium bromide (CTAB) solution by the addition of the antioxidant propyl gallate (PG) using tensiometry, rheology, and small-angle neutron scattering (SANS) techniques combined with the molecular dynamics (MD) simulation approach. The adsorption of CTAB at the air-water interface in the presence of varying [PG] revealed a progressive decrease in the critical micelle concentration (CMC), while the changes in different interfacial parameters indicated enhancement of the hydrophobicity induced by PG in the CTAB micellar system. The dynamic rheology behavior indicated an increase in the flow viscosity (η) as a function of [PG]. Moreover, the rheological components (storage modulus, G', and loss modulus, G″) depicted the viscoelastic features. SANS measurements depicted the existence of ellipsoidal micelles with varying sizes and aggregation number (Nagg) as a function of [PG] and temperature. Computational simulation performed using density functional theory (DFT) calculations and molecular dynamics (MD) provided an insight into the atomic composition of the examined system. The molecular electrostatic potential (MEP) analysis depicted a close proximity of CTAB, i.e., emphasized favorable interactions between the quaternary nitrogen of CTAB and the hydroxyl group of the PG monomer, further validated by the two-dimensional nuclear Overhauser enhancement spectroscopy (2D-NOESY), which showed the penetration of PG inside the CTAB micelles. In addition, various dynamic properties, viz., the radial distribution function (RDF), the radius of gyration (Rg), and solvent-accessible surface area (SASA), showed a significant microstructural evolution of the ellipsoidal micelles in the examined CTAB-PG system, where the changes in the micellar morphology with a more elongated hydrophobic chain and the increased Rg and SASA values indicated the notable intercalation of PG in the CTAB micelles.

Silk Fibroin Coated Magnesium Oxide Nanospheres: A Biocompatible and Biodegradable Tool for Noninvasive Bioimaging Applications.

Fluorescent nanoparticles (NPs) have been increasingly studied as contrast agents for better understanding of biological processes at the cellular and molecular level. However, their use as bioimaging tools is strongly dependent on their optical emission as well as their biocompatibility. This work reports the fabrication and characterization of silk fibroin (SF) coated magnesium oxide (MgO) nanospheres, containing oxygen, Cr3+ and V2+ related optical defects, as a nontoxic and biodegradable hybrid platform for bioimaging applications. The MgO-SF spheres demonstrated enhanced emission efficiency compared to noncoated MgO NPs. Furthermore, SF sphere coating was found to overcome agglomeration limitations of the MgO NPs. The hybrid nanospheres were investigated as an in vitro bioimaging tool by recording their cellular uptake, trajectories, and mobility in human skin keratinocytes cells (HaCaT), human glioma cells (U87MG) and breast cancer cells (MCF7). Enhanced cellular uptake and improved intracellular mobilities of MgO-SF spheres compared to MgO NPs was demonstrated in three different cell lines. Validated infrared and bright emission of MgO-SF NP indicate their prospects for in vivo imaging. The results identify the potential of the hybrid MgO-SF nanospheres for bioimaging. This study may also open new avenues to optimize drug delivery through biodegradable silk and provide noninvasive functional imaging feedback on the therapeutic processes through fluorescent MgO.

Interface chemistry of two-dimensional heterostructures - fundamentals to applications.

Two-dimensional heterostructures (2D HSs) have emerged as a new class of materials where dissimilar 2D materials are combined to synergise their advantages and alleviate shortcomings. Such a combination of dissimilar components into 2D HSs offers fascinating properties and intriguing functionalities attributed to the newly formed heterointerface of constituent components. Understanding the nature of the surface and the complex heterointerface of HSs at the atomic level is crucial for realising the desired properties, designing innovative 2D HSs, and ultimately unlocking their full potential for practical applications. Therefore, this review provides the recent progress in the field of 2D HSs with a focus on the discussion of the fundamentals and the chemistry of heterointerfaces based on van der Waals (vdW) and covalent interactions. It also explains the challenges associated with the scalable synthesis and introduces possible methodologies to produce large quantities with good control over the heterointerface. Subsequently, it highlights the specialised characterisation techniques to reveal the heterointerface formation, chemistry and nature. Afterwards, we give an overview of the role of 2D HSs in various emerging applications, particularly in high-power batteries, bifunctional catalysts, electronics, and sensors. In the end, we present conclusions with the possible solutions to the associated challenges with the heterointerfaces and potential opportunities that can be adopted for innovative applications.

Spin dynamics investigations of multifunctional ambient scalable Fe3O4 surface decorated ZnO magnetic nanocomposite using FMR.

Microwave spin resonance behavior of the Fe3O4 surface decorated ZnO nanocomposites (FZNC) has been investigated by ferromagnetic resonance (FMR). Modified hydrothermal method has been adopted to fabricate FZNC samples with Fe3O4 nanoparticles chains were used as seeds in the uniform magnetic field to decorate them on the surface of the ZnO nanoparticles in a unique configuration. Spin dynamics investigation confirms the transition of ZnO from diamagnetic to ferromagnetic as the sharp FMR spectra converts to the broad spectra with Fe3O4 nanoparticles incorporation. A single broad FMR spectra confirms that no isolated Fe3+ or Zn2+ ions exist which is also in agreement with XRD confirming suitable composite formation. Further, the increase in Fe3O4 concentration leads to decrease in g-value which is resulting from the internal field enhancement due to magnetic ordering. Also, various spin resonance parameters were calculated for the FZNC which provides a detail information about the magnetic ordering, exchange coupling and anisotropy. Elemental analysis confirms the presence of Fe and Zn simultaneously and transmission electron microscopy (TEM) image show the presence of Fe3O4 on the grain boundaries of ZnO which has been confirmed by taking high-resolution TEM and electron diffraction patterns on both sides of the interface. These unique structural configuration of the FZNC has tremendous potential in various magneto-optoelectronic, spintronics and electro-chemical applications.

Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase.

YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The ensemble of NADPH-bound monomers has a narrower average interdomain space resulting in more hydrogen bonds and rigid cofactor binding. NADP-bound YqhD fluctuates between open and closed conformations, while it was observed that NADPH-bound YqhD had slower opening/closing dynamics of the cofactor-binding cleft. In the light of enzyme kinetics and structural data, simulation findings have led us to postulate that the frequently sampled open conformation of the cofactor binding cleft with NADP leads to the more facile release of NADP while increased closed conformation sampling during NADPH binding enhances cofactor binding affinity and the aldehyde reductase activity of the enzyme.

Graphene Quantum Dot-Sensitized ZnO-Nanorod/GaN-Nanotower Heterostructure-Based High-Performance UV Photodetectors.

The fabrication of a superior-performance ultraviolet (UV) photodetector utilizing graphene quantum dots (GQDs) as a sensitization agent on a ZnO-nanorod/GaN-nanotower heterostructure has been realized. GQD sensitization displays substantial impact on the electrical as well as the optical performance of a heterojunction UV photodetector. The GQD sensitization stimulates charge carriers in both ZnO and GaN and allows energy band alignment, which is realized by a spontaneous time-correlated transient response. The fabricated device demonstrates an excellent responsivity of 3.2 × 103 A/W at -6 V and displays an enhancement of ∼265% compared to its bare counterpart. In addition, the fabricated heterostructure UV photodetector exhibits a very high external quantum efficiency of 1.2 × 106%, better switching speed, and signal detection capability as low as ∼50 fW.

In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function.

Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent.

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.