FTIR and SAXS study on MBCO-saccharide amorphous systems: protein-matrix reciprocal effects

Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State

ABSTRACT: The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment …

Inhomogeneous Protein-Water-Sugar Structures of Single GFP-mut2 Proteins Caged in Trehalose-Water Matrixes

More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function

Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, …

Ab initio study on the photoisomers of a nitro-substituted spiropyran

Structural and spectroscopic properties of the photoisomers of a nitro-substituted spiropyran have been investigated by performing ab initio molecular orbital (MO) calculations both in vacuo and in hexafluoro-2-propanol solution. Full geometry optimisation of the closed form and of the transoid conformations of the open form has been carried out. Dipole moments of both photoisomers have been determined, the ratio of which agrees with recent experimental results. Net atomic charges have also been determined according to three different approaches.

Density Functional Theory Study of the Trans-Trans-Cis (TTC)→Trans-Trans-Trans (TTT) Isomerization of a Photochromic Spiropyran Merocyanine

Density Functional Theory (DFT) calculations have been performed on the TTC→TTT isomerization reaction of the open forms of the 1',3'-dihydro-8-bromo-6-nitro- 1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-(2H)indole (8-Br-6-nitro-BIPS) system. The calculations were carried out in vacuo and in methylene chloride solution at different temperatures. Results are compared with the available experimental values of free energy difference and activation energy in solution.

Bioprotection Can Be Tuned with Proper Protein/Saccharide Ratio: The Case of Solid Amorphous Matrices

Saccharides, and in particular trehalose, are well known for their high efficiency in protecting biostructures against adverse environmental conditions. The protein dynamics is known to be highly inhibited in a low-water trehalose host medium, the inhibition being markedly dependent on the amount of residual water. Besides hydration, the protein/sugar ratio is expected to affect the properties of saccharide amorphous matrices. In this work, we report an infrared spectroscopy study in dry amorphous matrices of various sugars (the disaccharides trehalose, maltose, sucrose, and lactose, and the trisaccharide raffinose) containing myoglobin, at different protein/sugar ratios. We analyze the str…

Mapping CO diffusion paths in Myoglobin with the Single Sweep Method

The pathways of diffusion and escape of a CO molecule inside and out a myoglobin protein are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent.The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. We calculate all these quantities --local minima, …

Single Molecule Study of GFP-mut2 Proteins Caged in Trehalose-Water Matrixes: Spatially Inhomogeneous Protein-Water-Sugar Structures

Interconversion among low tier substates in MbCO: an FTIR, Neutron Scattering and Molecular Dynamics simulation study

Internal dynamics and protein-matrix coupling in trehalose-coated proteins.

Abstract We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water–trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides ). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q B containing or Q B deprived reaction centre from R. sphaeroides . Experimental result…

The Role of Solvent on Protein-Matrix Coupling in MbCO Embedded in Water-Saccharide Systems

Protein Thermal Denaturation and Matrix Glass Transition in Different Protein−Trehalose−Water Systems

Biopreservation by saccharides is a widely studied issue due to its scientific and technological importance; in particular, ternary amorphous protein-saccharide-water systems are extensively exploited to model the characteristics of the in vivo biopreservation process. We present here a differential scanning calorimetry (DSC) study on amorphous trehalose-water systems with embedded different proteins (myoglobin, lysozyme, BSA, hemoglobin), which differ for charge, surface, and volume properties. In our study, the protein/trehalose molar ratio is kept constant at 1/40, while the water/sugar molar ratio is varied between 2 and 300; results are compared with those obtained for binary trehalose…

STRUCTURE-DYNAMICS COUPLING BETWEEN PROTEIN AND EXTERNAL MATRIX IN MBCO EMBEDDED IN VARIOUS SACCHARIDE MATRICES: A FTIR STUDY

Role of residual water hydrogen bonding in sugar/water/biomolecule systems: a possible explanation fortrehalose peculiarity

We report on the set of experimental and simulative evidences which enabled us to suggest how biological structures embedded in a non-liquid water–saccharide solvent are anchored to the surrounding matrix via a hydrogen bond network. Such a network, whose rigidity increases by decreasing the sample water content, couples the degrees of freedom of the biostructure to those of the matrix and gives place to protein–saccharide–water structures (protein–solvent conformational substates). In particular, the whole set of data evidences that, while the protein–sugar interaction is well described in terms of a water entrapment hypothesis, the water replacement hypothesis better describes the sugar–m…

Lipid Phase Transition in Saccharide-Coated Cholate-Containing Liposomes: Coupling to the Surrounding Matrix

Acceleration of the AChBP conformational transition using Temperarure Accelerated Molecular Dynamics

The water association band as a marker of hydrogen bonds in trehalose amorphous matrices

The relevant role played by residual water in modulating the dynamics and structure of a protein, a matrix and their coupling has been thoroughly studied in bioprotective amorphous saccharide matrices via experiments and simulations. In order to better characterize this residual water and the hydrogen bond structures in which it is involved, in this work infrared spectroscopy experiments are conducted on trehalose-water systems. The properties of water are inferred from the study of a peculiar infrared band, the water association band, which we exploited as a marker of the hydrogen bonds in which water is involved. Our aim was the identification of populations of water molecules, which give…

Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection

Bioprotection by sugars, and in particular trehalose peculiarity, is a relevant topic due to the implications in several fields. The underlying mechanisms are not yet clearly elucidated, and remain the focus of current investigations. Here we revisit data obtained at our lab on binary sugar/water and ternary protein/sugar/water systems, in wide ranges of water content and temperature, in the light of the current literature. The data here discussed come from complementary techniques (Infrared Spectroscopy, Molecular Dynamics simulations, Small Angle X-ray Scattering and Calorimetry), which provided a consistent description of the bioprotection by sugars from the atomistic to the macroscopic …

A calorimetric study of ternary protein-trehalose-water systems: matrix glass transition and protein thermal denaturation

Protein-solvent coupling in carboxy-myoglobin/sugar/water systems by molecular dynamics simulations

Hepatitis B protein HBx binds the DLEU2 lncRNA to sustain cccDNA and host cancer-related gene transcription.

Objective: The HBV HBx regulatory protein is required for transcription from the covalently closed circular DNA (cccDNA) minichromosome and affects the epigenetic control of both viral and host cellular chromatin. Design: We explored, in relevant cellular models of HBV replication, the functional consequences of HBx interaction with DLEU2, a long non-coding RNA (lncRNA) expressed in the liver and increased in human hepatocellular carcinoma (HCC), in the regulation of host target genes and the HBV cccDNA. Results: We show that HBx binds the promoter region, enhances the transcription and induces the accumulation of DLEU2 in infected hepatocytes. We found that nuclear DLEU2 directly binds HBx…

Protein-solvent coupling in carboxy-myoglobin--sugar-water systems by Molecular Dynamics Simulation

Molecular Dynamics simulation of carboxy-myoglobin in trehalose and sucrose-water systems

Mapping the network of pathways of CO diffusion in myoglobin.

The pathways of diffusion of a CO molecule inside a myoglobin protein and toward the solvent are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent. The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. Here, all the local minima of the PMF, the MF…

Observing myoglobin proteinquake with an X-ray free-electron laser

The events following the photodissociation of the bond be- tween myoglobin and its ligand have been extensively studied with a variety of experimental, theoretical and computational methods [1]. The results of these investigations have been rationalized in terms of a model that implies a protein quake- like motion [2], i.e. the propagation of the strain released upon photoexcitation through the protein similar to the prop- agation of acoustic waves during an earthquake. The exper- imental investigations performed so far have been based on spectroscopic measurements or did not have sufficient time- resolution to measure the timescale of such “proteinquake”. We have obtained direct experiment…

Protein Bioprotection in disaccharides: a multiscale approach

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Immobilization of proteins and other biomolecules in saccharide matrices leads to a series of peculiar properties that are relevant from the point of view of both biochemistry and biophysics, and have important implications on related fields such as food industry, pharmaceutics, and medicine. In the last years, the properties of biomolecules embedded into glassy matrices and/or highly concentrated solutions of saccharides have been thoroughly investigated, at the molecular level, through in vivo, in vitro, and in silico studies. These systems show an outstanding ability to protect biostructures against stress conditions; various mechanisms appear to be at the basis of such bioprotection, th…

Effect of protein net charge and steric hindrance on the glass transition of Protein-Trehalose-Water systems and on protein thermal denaturation

GFP-mut2 proteins in trehalose-water matrixes: spatially heterogeneous protein-water-sugar structure

Coupling between the Thermal Evolution of the Heme Pocket and the External Matrix Structure in Trehalose Coated Carboxymyoglobin

Proteins can assume a very large number of conformations (conformational substates), all concurring to its function. We present experimental evidence for the existence, in trehalose coated carboxymyoglobin, of a structured environment of the protein, tightly coupled to the heme pocket structure, as experienced by the bound CO molecule. This was evidenced by the strict correlation observed between the thermal evolution (300−20 K) of the CO stretching and of the water association bands in samples of carboxymyoglobin embedded in trehalose matrixes of different hydration. This observation put forward the coupling between the degrees of freedom of the matrix and those of the protein. In the drie…

MOLECULAR DYNAMICS SIMULATIONS COMPLEMENT EXPERIMENTAL DATA ON PROTEIN EMBEDDED IN SUGAR-WATER SYSTEMS

Atomic mean square displacements in proteins by Molecular Dynamics: a case for analysis of variance

Structure-dynamics-function of proteins: Molecular Dynamics simulations of myoglobin in water and complex solvents

Thermal evolution of heme pocket structure in trehalose coated carboxy-myoglobin probed by FTIR measurements

Water effects on saccharide matrices studied with molecular dynamics

Relationship between the Glass Transition of Myoglobin-Water-Disaccharide systems and Protein Thermal Denaturation

Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamicscottone

Microscopic aspects of solute-solute interactions induced by the solvent

Nous presentons les plus importants resultats que nous ayons obtenus par des simulations etendues de dynamique moleculaire de solutions aqueuses contenant des modeles de solute hydrophiles et hydrophobes. Ces simulations determinent les forces induites par le solvant sur les solutes (SIFs) en fonction du type de solute, de la separation solute-solute et de leur orientation mutuelle. Les proprietes structurales et dynamiques du solvant autour des solutes ont ete analysees pour comprendre leur relation avec les SIFs. les presents resultats sont compares a des observations experimentales et precedentes stimulations sur des solutions aqueuses de biomolecules.

Matrix glass transition and embedded protein denaturation: effect of trehalose on different proteins

MbCo in Saccharide Solid Amorphous Systems: A Combined FTIR and SAXS Study

Saccharides, and in particular trehalose, are known for their efficiency in protecting biostructures against environmental stress [1], although the preservation mechanism is still debated. Experiments and simulations [2,3] on carboxy-myoglobin (MbCO) showed that the protein dynamics is highly inhibited in dry trehalose matrices, the inhibition being dependent on the water content. In these conditions, a mutual protein-matrix structural and dynamic influence is observed.Here we report a combined FTIR and SAXS study on MbCO embedded in dry amorphous matrices of trehalose and sucrose. FTIR measurements were performed at different protein/sugar ratios, focussing on the stretching band of the bo…

A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation.

Results from room-temperature molecular dynamics simulation on a system containing carboxy-myoglobin, water, and maltose molecules are reported. Protein atomic fluctuations, protein−solvent and solvent−solvent hydrogen bonding have been analyzed and compared to the ones in trehalose−water and sucrose−water systems (Proteins 2005, 59, 291−302). Results help in rationalizing, at a molecular level, the effects of homologues disaccharides on protein structure/dynamics experimentally observed. Furthermore, the effectiveness of disaccharides in bioprotection in terms of peculiar protein−matrix coupling is also discussed.

Water effects on trehalose matrices studied through Molecular Dynamics

Exploring the dynamics of AChBP unbound and bound to the Lobeline partial agonist

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both confo…

MAPPING THE FREE ENERGY LANDSCAPE OF CO DIFFUSION IN MYOGLOBIN

Myoglobin embedded in saccharide amorphous matrices: water-dependent domains evidenced by small angle X-ray scattering

We report Small Angle X-ray Scattering (SAXS) measurements performed on samples of carboxy-myoglobin (MbCO) embedded in low-water trehalose glasses. Results showed that, in such samples, "low-protein" trehalose-water domains are present, surrounded by a protein-trehalose-water background; such finding is supported by Infrared Spectroscopy (FTIR) measurements. These domains, which do not appear in the absence of the protein and in analogous sucrose systems, preferentially incorporate the incoming water at the onset of rehydration, and disappear following large hydration. This observation suggests that, in organisms under anhydrobiosis, analogous domains could play a buffering role against th…

MbCO↔matrix reciprocal effects in low hydration amorphous saccharide systems: a FTIR study

Role of Solvent on Protein-Matrix Coupling in MbCO Embedded in Water-Saccharide Systems: A Fourier Transform Infrared Spectroscopy Study

AbstractEmbedding protein in sugar systems of low water content enables one to investigate the protein dynamic-structure function in matrixes whose rigidity is modulated by varying the content of residual water. Accordingly, studying the dynamics and structure thermal evolution of a protein in sugar systems of different hydration constitutes a tool for disentangling solvent rigidity from temperature effects. Furthermore, studies performed using different sugars may give information on how the detailed composition of the surrounding solvent affects the internal protein dynamics and structural evolution. In this work, we compare Fourier transform infrared spectroscopy measurements (300–20K) o…

Atomistic MD simulation of proteins in complex solvents

Molecular Dynamics simulation of carboxy-myoglobin in trehalose and sucrose-water systems

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation

International audience; Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukary- otic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is du…

“Water Association” Band in Saccharide Amorphous Matrices: Role of Residual Water on Bioprotection

Saccharides protect biostructures against adverse environmental conditions mainly by preventing large scale motions leading to unfolding. The efficiency of this molecular mechanism, which is higher in trehalose with respect to other sugars, strongly depends on hydration and sugar/protein ratio. Here we report an Infrared Spectroscopy study on dry amorphous matrices of the disaccharides trehalose, maltose, sucrose and lactose, and the trisaccharide raffinose. Samples with and without embedded protein (Myoglobin) are investigated at different sugar/protein ratios, and compared. To inspect matrix properties we analyse the Water Association Band (WAB), and carefully decompose it into sub-bands,…

Water association band : anuseful tool for studying the water structure in samples of low water content

Thermodynamics and kinetics of ion permeation in wild-type and mutated open active conformation of the human α7 nicotinic receptor

Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven role in a wide spectrum of disorders including schizophrenia and Alzheimer's disease. By exploiting an all-atom structural model of the full (transmembrane and extracellular) protein in the open, agonist-bound conformation we recently developed, we evaluate the free energy and the mean first passage time of single-ion permeation using …

In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification

International audience; Although botulinum neurotoxins (BoNTs) are among the most toxic compounds found in nature, their molecular mechanism of action is far from being elucidated. A key event is the conformational transition due to acidification of the interior of synaptic vesicles, leading to translocation of the BoNT catalytic domain into the neuronal cytosol. To investigate these conformational variations, homology modeling and atomistic simulations are combined to explore the internal dynamics of the sub-types BoNT/A1 (the most-used sub-type in medical applications) and BoNT/E1 (the most kinetically efficient sub-type). This first simulation study of di-chain BoNTs in closed and open s…

Protein-solvent coupling in myoglobin-sugar-water systems: a Molecular Dynamics study

Water Association Band as marker of the matrix structure in amorphous saccharide and saccharide–protein samples

Computational Modeling of Geminate Recombination and Energy Relaxation of Nitric Oxide in Myoglobin under Constant Illumination,

Thermal Behavior of dry and hydrated MbCO crowded systems

Molecular dynamics simulations of a new model of human a7 nicotinic receptor

Protein-Matrix Coupling in MbCO embedded in saccharide matrices

Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study

International audience; Nicotinic acetylcholine receptors, belonging to the Cys-loop super-family of ligand-gated ion channels (LGICs), are membrane proteins present in neurons and at neuromuscular junctions. They are responsible for signal transmission, and their function is regulated by neurotransmitters, agonists and antagonists drugs. A detailed knowledge of their conformational transition in response to ligand binding is critical to understand the basis of ligand-receptor interaction, in view of new pharmacological approaches to control receptor activity. However, the scarcity of experimentally derived structures of human channels makes this perspective extremely challenging. To contri…

A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group

An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directl…

Cosolutes affect structure and dynamics of myoglobin-trehalose amorphous systems: a FTIR and MD study

Ricostruzione del panorama di energia libera per il processo di diffusione del CO all'interno della mioglobina IES08, Maggio 08.

Protein-solvent coupling in carboxymyoglobin/sugar/water systems by molecular dynamics simulation

Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations

The structure and interactions of proteins play a critical role in determining the quality attributes of many foods, beverages, and pharmaceutical products. Incorporating a multiscale understanding of the structure–function relationships of proteins can provide greater insight into, and control of, the relevant processes at play. Combining data from experimental measurements, human sensory panels, and computer simulations through machine learning allows the construction of statistical models relating nanoscale properties of proteins to the physicochemical properties, physiological outcomes, and tastes of foods. This review highlights several examples of advanced computer simulations at mol…

Protein-solvent coupling in carboxy-myoglobin-sugar-water systems Molecular Dynamics Simulations and Experiments

Multiphoton Absorption of Myoglobin-Nitric Oxide Complex: Relaxation by D-NEMD of a Stationary State

Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.

Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…

Structure and Dynamics in Glassy and Plasticized Amorphous Disaccharide-Water Samples: A FTIR Study

The electric properties of ionic solutions: a molecular dynamics (preliminary) study

Biopreservation of Myoglobin in Crowded Environment: A Comparison between Gelatin and Trehalose Matrixes.

Biopreservation by sugar and/or polymeric matrixes is a thoroughly studied research topic with wide technological relevance. Ternary amorphous systems containing both saccharides and proteins are extensively exploited to model the in vivo biopreservation process. With the aim of disentangling the effect of saccharides and polypeptidic crowders (such as gelatin) on the preservation of a model protein, we present here a combined differential scanning calorimetry and UV-vis spectrophotometry study on samples of myoglobin embedded in amorphous gelatin and trehalose + gelatin matrixes at different hydrations, and compare them with amorphous myoglobin-only and myoglobin-Trehalose samples. The res…

Thermal denaturation of myoglobin in water--disaccharide matrixes: relation with the glass transition of the system.

Proteins embedded in glassy saccharide systems are protected against adverse environmental conditions [Crowe et al. Annu. Rev. Physiol. 1998, 60, 73-103]. To further characterize this process, we studied the relationship between the glass transition temperature of the protein-containing saccharide system (T(g)) and the temperature of thermal denaturation of the embedded protein (T(den)). To this end, we studied by differential scanning calorimetry the thermal denaturation of ferric myoglobin in water/disaccharide mixtures containing nonreducing (trehalose, sucrose) or reducing (maltose, lactose) disaccharides. All the samples studied are, at room temperature, liquid systems whose viscosity …

Thermal evolution of the CO stretching band in carboxy-myoglobin in the light of neutron scattering and molecular dynamics simulations

Abstract As it is well known, the thermal behaviour of the CO stretching band in MbCO reflects the interconversion among protein’s taxonomic and lower tier substates. We compare here FTIR data on the thermal behaviour of the CO stretching band in MbCO embedded in non-liquid, water–trehalose matrixes, and neutron scattering data on dry and hydrated proteins and nucleic acids. The comparison, also in the light of simulative data, gives relevant information on the relationship between the mean square displacements of hydrogen atoms and the heme pocket thermal rearrangements in MbCO, as experienced by the bound CO, in the temperature region 100–200 K, and at higher temperature when large scale …

Theoretical study of spiropyran-merocyanine thermal isomerization.

Abstract Quantum mechanical computations at DFT level were carried out on the processes involved in the thermal reaction SP ⇆ ME, where SP is the nitro-substituted spirobenzopyran (1 ′ ,3 ′ -dihydro-1 ′ ,3 ′ ,3 ′ -trimethyl-6-nitro-spiro[2H-1-benzopyran-2,2 ′ - [2H]indole]) in the closed form and ME is the corresponding open form. A detailed theoretical description of the overall reaction is reported along with the thermodynamic parameters for all intermediates and transition states. The obtained activation energy value is in agreement with the available experimental data in solution.

A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study

International audience; The determination of the conformational states corresponding to diverse functional roles of ligand gated ion channels is subject of intense investigation with various techniques, from X-rays structure determination to electrophysiology and computational modeling. Even with a certain number of structures becoming recently available, only few major structural features distinguishing conductive open channel from the non conductive resting protein have been highlighted, while high-resolution details are still missing. The characterization of the desensitized conformation(s) is even more complex, and only few specific characteristics have been identified. Furthermore, exp…

SAXS and FTIR study on MbCO-Saccharide amorphous systems

A FTIR study on low hydration saccharide amorphous matrices: Thermal behaviour of the Water Association Band

Abstract We report a study on the thermal behaviour of the infrared Water Association Band (WAB) in dry binary saccharide–water systems (containing trehalose, sucrose, maltose, and raffinose). This is a follow-up of preceding studies on analogous carboxymyoglobin-saccharide–water ternary systems, which pointed out a mutual protein-matrix influence (coupling). A comparison between binary and ternary systems, for all the saccharides studied, evidences a reduction in the residual water content in the latter and, except for trehalose, a sizable modification in the thermal behaviour, which is discussed in terms of structure and hydrogen bonding properties of the sugars. The study allowed us also…

GFP-mut2 Proteins in Trehalose-Water Matrixes: Spatially Heterogeneous Protein-Water-Sugar Structures

We report investigations on the properties of nanoenvironments around single-GFP-mut2 proteins in trehalose-water matrixes. Single-GFPmut2 molecules embedded in thin trehalose-water films were characterized in terms of their fluorescence brightness, bleaching dynamics, excited state lifetime, and fluorescence polarization. For each property, sets of approximately 100-150 single molecules have been investigated as a function of trehalose content and hydration. Three distinct and interconverting families of proteins have been found which differ widely in terms of bleaching dynamics, brightness, and fluorescence polarization, whose relative populations sizably depend on sample hydration. The r…

Molecular dynamics simulation of carboxy-myoglobin embedded in a trehalose-water matrix

AbstractWe report on a molecular dynamics (MD) simulation of carboxy-myoglobin (MbCO) embedded in a water-trehalose system. The mean square fluctuations of protein atoms, calculated at different temperatures in the 100–300K range, are compared with those from a previous MD simulation on an H2O-solvated MbCO and with experimental data from Mössbauer spectroscopy and incoherent elastic neutron scattering on trehalose-coated MbCO. The results show that, for almost all the atomic classes, the amplitude of the nonharmonic motions stemming from the interconversion among the protein’s conformational substates is reduced with respect to the H2O-solvated system, and their onset is shifted toward hig…

Thermal Denaturation of Myoglobin in Water–Sugar Matrices and Relationship with the Glass Transition of the System

Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin

We performed a room temperature molecular dynamics (MD) simulation on a system containing 1 carboxy-myoglobin (MbCO) molecule in a sucrose–water matrix of identical composition (89% [sucrose/(sucrose + water)] w/w) as for a previous trehalose–water–MbCO simulation (Cottone et al., Biophys J 2001;80:931–938). Results show that, as for trehalose, the amplitude of protein atomic mean-square fluctuations, on the nanosecond timescale, is reduced with respect to aqueous solutions also in sucrose. A detailed comparison as a function of residue number evidences mobility differences along the protein backbone, which can be related to a different efficacy in bioprotection. Different heme pocket struc…

Proteins in amorphous disaccharides: insights on bioprotection from Molecular Dynamics simulations and FTIR experiments

FTIR Study on Reciprocal Protein↔Matrix effects in dry amorphous saccharide systems

Role of Solvent on Protein-Matrix Coupling in MbCO Embedded in Water-Saccharide Systems: an FTIR study.

Embedding protein in sugar systems of low water content enables one to investigate the protein dynamicstructure function in matrixes whose rigidity is modulated by varying the content of residual water. Accordingly, studying the dynamics and structure thermal evolution of a protein in sugar systems of different hydration constitutes a tool for disentangling solvent rigidity from temperature effects. Furthermore, studies performed using different sugars may give information on how the detailed composition of the surrounding solvent affects the internal protein dynamics and structural evolution. In this work, we compare Fourier transform infrared spectroscopy measurements (300–20 K) on MbCO e…

Water association band as a marker of the matrix structure in amorphous saccharide and saccharide-protein samples

Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance

AbstractInformation on protein internal motions is usually obtained through the analysis of atomic mean-square displacements, which are a measure of variability of the atomic positions distribution functions. We report a statistical approach to analyze molecular dynamics data on these displacements that is based on probability distribution functions. Using a technique inspired by the analysis of variance, we compute unbiased, reliable mean-square displacements of the atoms and analyze them statistically. We applied this procedure to characterize protein thermostability by comparing the results for a thermophilic enzyme and a mesophilic homolog. In agreement with previous experimental observ…