Changes In Protein Secondary Structure Research Articles

Serum albumin interaction with xanthine drugs at nano-bio interfaces: A combined multi-spectroscopic and molecular modelling approach

Theophylline (THP), theobromine (THB) and caffeine (CAF) belong to the xanthine group of drugs and are principle component of tea or coffee with important pharmacological activities and clinical applications. The interaction between these drugs and serum albumin proteins obtained from bovine and human (BSA and HSA, respectively) in the presence and absence of silver as well as gold nanoparticles (Ag and AuNP, respectively) was investigated for the first time by using a series of biophysical techniques and molecular modelling calculations. Time resolved fluorescence measurements confirm that all the drugs quench the intrinsic tryptophan fluorescence of the proteins through a static mechanism irrespective of the absence or presence of NPs. However, the binding constant of the proteins towards the drugs changes considerably in presence of NPs. Addition of drugs decreases α-helicity of the proteins both in the absence and presence of NPs; however, no substantial change in protein secondary structure is perceived only with the NPs. The results show that the drug carrying capacity of the albumins can be significantly modulated with metal NPs towards desired pharmacokinetic and therapeutic applications without compromising the basic structure; and therefore, the function of the proteins.

Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy.

While having multiple aminoacyl-tRNA synthetases implicated in Charcot-Marie-Tooth (CMT) disease suggests a common mechanism, a defect in enzymatic activity is not shared among the CMT-causing mutants. Protein misfolding is a common hypothesis underlying the development of many neurological diseases. Its process usually involves an initial reduction in protein stability and then the subsequent oligomerization and aggregation. Here, we study the structural effect of three CMT-causing mutations in tyrosyl-tRNA synthetase (TyrRS or YARS). Through various approaches, we found that the mutations do not induce changes in protein secondary structures, or shared effects on oligomerization state and stability. However, all mutations provide access to a surface masked in the wild-type enzyme, and that access correlates with protein misinteraction. With recent data on another CMT-linked tRNA synthetase, we suggest that an inherent plasticity, engendering the formation of alternative stable conformations capable of aberrant interactions, links the tRNA synthetase family to CMT.

Effect of salts and nonionic surfactants on thermal characteristics of egg white proteins

Effect of salts (Sodium chloride (NaCl), Sodium sulfate (Na2SO4), Ammonium sulfate ((NH4)2SO4), and nonionic surfactants (glycerol, tween20, tween80) on thermal properties of egg white proteins as a whole were investigated. Egg white solutions with additive (0, 0.5 and 1%) were collected after 0, 1 and 2min heat treatment. Physico-chemical properties of egg white proteins were evaluated by measuring heat coagulation time, solubility and turbidity of solution. Adding glycerol caused the most significant decrease in turbidity and increase in heat coagulation time and solubility of egg white, although Sodium Chloride had the least positive impact on physico-chemical properties of egg white under heat treatment. The Fourier transform infrared (FT-IR) spectroscopy analysis of heat treated egg white proteins as a whole with additives demonstrated changes in secondary protein structure, which are presented regarding the shape, intensity and position of FT-IR band. Meanwhile, it showed a good correlation with the physico-chemical properties consequences. Generally, the effect of nonionic surfactants were more noticeable than that of salts in preventing of egg white proteins aggregation under heat treatment. By improving thermal stability of egg white proteins, its usage in thermal processing industry can be evolved.

Evaluation of in silico ADMET analysis and human serum albumin interactions of a new lanthanum(III) complex by spectroscopic and molecular modeling studies

A new lanthanum(III) complex, [La(Phe)3(H2O)2] (Phe=phenylalanine), was synthesized. The complex was characterized by elemental analysis, conductivity measurement, FT-IR, UV/Vis and 1H NMR techniques. Drug-like properties of this complex was evaluated through in silico ADMET predictions. The reactivity of this complex to human serum albumin (HSA) under simulated physiological conditions was studied by spectroscopic and molecular docking analysis. The fluorescence quenching of protein by addition of La(III) complex was due to static quenching mechanism. The thermodynamic parameters show that the binding process was spontaneous and that hydrogen bonds and hydrophobic forces play a major role in the association of the HSA–La(III) complex. Binding parameters between La(III) complex and protein such as binding sites number (n ∼1) and binding constant (Ka ∼104M−1) were determined. The conformational changes of protein secondary structure in the presence of above complex were demonstrated by FT-IR, three-dimensional fluorescence and UV–Vis absorption techniques. Molecular docking of La(III) complex relating to HSA was investigated and confirmed the experimental results. All these experimental and computational results clarified that La(III) complex could bind with HSA effectively, which could be a useful guideline for efficient drug design.

Synthesis, Characterization, Cytotoxicity and Detailed HSA Interaction of New Zinc(II) Complexes Containing Dithiocarbamate and Heterocyclic N-donor Ligands

ABSTRACT[Zn(ph-dtc)(bpy)]Cl (1) and [Zn(ph-dtc)(phen)]Cl (2) (where bpy = 2,2′-bipyridine, phen = 1,10-phenanthroline and ph-dtc = phenylacetichydrazidedithiocarbamate) were synthesized and characterized by elemental analysis and spectroscopic methods (FT–IR, UV–Vis and 1H NMR). Zn(II) complexes were examined in biological tests in vitro using MCF-7 breast cancer cell line. Both complexes showed significant cytotoxic activity against human breast cancer MCF-7 cells. The interaction of above compounds with Human Serum Albumin (HSA) was investigated by means of various spectroscopic (at pH ∼ 7.4 in Tris–HCl buffer medium) and molecular docking methods. The fluorescence data showed that 1 and 2 quench the intrinsic fluorescence of HSA through a static quenching procedure. The binding constants (Kb) and the number of binding sites (n ∼ 1) were calculated. The thermodynamic analysis suggested that hydrophobic interaction played major roles in the binding of 1 or 2 to HSA. The distance r between protein and the above-mentioned compounds was obtained according to fluorescence resonance energy transfer. The conformational changes of protein secondary structure in the presence of Zn(II) complexes were proven using UV–Vis absorption and circular dichroism techniques. Also, docking results confirmed the spectroscopic results.

Charge-transfer interactions induce surface dependent conformational changes in apolipoprotein biocorona.

Upon introduction into a biological system, engineered nanomaterials (ENMs) rapidly associate with a variety of biomolecules such as proteins and lipids to form a biocorona. The presence of "biocorona" influences nano-bio interactions considerably, and could ultimately result in altered biological responses. Apolipoprotein A-I (ApoA-I), the major constituent of high-density lipoprotein (HDL), is one of the most prevalent proteins found in ENM-biocorona irrespective of ENM nature, size, and shape. Given the importance of ApoA-I in HDL and cholesterol transport, it is necessary to understand the mechanisms of ApoA-I adsorption and the associated structural changes for assessing consequences of ENM exposure. Here, the authors used a comprehensive array of microscopic and spectroscopic tools to elucidate the interactions between ApoA-I and 100 nm Ag nanoparticles (AgNPs) with four different surface functional groups. The authors found that the protein adsorption and secondary structural changes are highly dependent on the surface functionality. Our electrochemical studies provided new evidence for charge transfer interactions that influence ApoA-I unfolding. While the unfolding of ApoA-I on AgNPs did not significantly change their uptake and short-term cytotoxicity, the authors observed that it strongly altered the ability of only some AgNPs to generate of reactive oxygen species. Our results shed new light on the importance of surface functionality and charge transfer interactions in biocorona formation.

Synthesis, spectroscopic and molecular docking studies of imidazolium and pyridinium based ionic liquids with HSA as potential antimicrobial agents

The interaction between human serum albumin (HSA) and synthesized imidazolium and pyridinium based ionic liquids (ILs), as good potential microbial growth inhibitors, was investigated by spectroscopic techniques combined with molecular docking analysis. All compounds were significant active against the tested bacterial and fungal strains. FT-IR spectroscopy indicated that the interaction of HSA with ILs generates considerable changes in protein secondary structure. The results of the molecular docking study showed that the studied ILs are able to firmly bind in the subdomain IIA of HSA with almost equal binding affinity (about −6.23 kcal/mol). Investigated HSA–ILs complex binds through hydrogen bonding or/and cation-π interactions. This study provides a better understanding of the binding of imidazolium and pyridinium based ILs to HSA and opens the way for their further biological and pharmaceutical investigations as candidates with antimicrobial properties.

Binding interaction of sodium-N-dodecanoyl sarcosinate with hemoglobin and myoglobin: Physicochemical and spectroscopic studies with molecular docking analysis

The interaction of an amino acid surfactant, sodium-N-dodecanoyl sarcosinate (SDDS), with two heme proteins, hemoglobin (Hb) and myoglobin (Mb), has been studied employing various physicochemical and spectroscopic techniques like tensiometry, UV–Vis spectroscopy, steady-state fluorometry, time-resolved fluorometry, circular dichroism (CD) spectroscopy, calorimetry and stopped flow kinetics at physiological pH of 7.2 and 298K. Tensiometric and fluorometric analysis suggest that the interaction between SDDS and protein starts with the monomer form of the surfactant which produces small induced micelles. The micelles bind to protein backbone causing denaturation of the protein structure, and finally free micelles are formed on further addition of surfactant. Life-time measurements have been performed to shed light on the binding of surfactant around the tryptophan moieties present in the heme proteins. The changes in protein secondary structure induced by AAS collected from CD measurements reveals that the proteins are quite perturbed upon action of SDDS. The enthalpy change values of each stepwise interaction process have been found from isothermal titration calorimetry (ITC). The kinetics of the protein-surfactant interaction process has been studied using stopped flow technique. Quantum mechanical calculations involving density functional theory (DFT) and molecular docking analysis have been performed to highlight the interactive phenomenon between the surfactant and heme proteins. Thus the entire study shows a total inspection of an amino acid surfactant–heme protein interaction.

Molecular forces involved in heat-induced freshwater surimi gel: Effects of various bond disrupting agents on the gel properties and protein conformation changes

Urea, sodium dodecyl sulfate (SDS) and N-ethylmaleimide (NEM) were employed to monitor the contributions of hydrogen bonds, hydrophobic interactions and disulfide bonds in heat-induced surimi gel. Surimi gels were prepared with the bond disrupting agents followed by texture profile, gel strength, rheological and Raman analysis. The rheological analysis demonstrated that remarkable changes of storage moduli (G′) were presented below the critical temperature, especially for SDS treatments. Gel strength significantly decreased as the concentration of urea and NEM increased, while it was slightly improved by 1% SDS. With the involvement of bond disrupting agents, hardness and gumminess of surimi gel presented a dramatical decrease. The Raman results indicated that protein secondary structure tended to transform to random coil, with content of α-helix and β-sheet decreasing. Textural properties were in correlation with protein conformation. Less of random coil led to improvement of gel strength, and springiness was mainly contributed by β-sheet and β-turn. The results suggested that different bond disrupting agents induced various changes in surimi gel properties and protein secondary structure.

Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study

The interaction between losartan and human serum albumin (HSA), as well as its glycated form (gHSA) was studied by multiple spectroscopic techniques and molecular dynamics simulation under physiological conditions. The binding information, including the binding constants, effective quenching constant and number of binding sites showed that the binding partiality of losartan to HSA was higher than to gHSA. The findings of three-dimensional fluorescence spectra demonstrated that the binding of losartan to HSA and gHSA would alter the protein conformation. The distances between Trp residue and the binding sites of the drug were evaluated on the basis of the Förster theory, and it was indicated that non-radiative energy transfer from HSA and gHSA to the losartan happened with a high possibility. According to molecular dynamics simulation, the protein secondary and tertiary structure changes were compared in HSA and gHSA for clarifying the obtained results.

Biospectroscopy of Nanodiamond-Induced Alterations in Conformation of Intra- and Extracellular Proteins: A Nanoscale IR Study.

The toxicity of nanomaterials raises major concerns because of the impact that nanomaterials may have on health, which remains poorly understood. We need to explore the fate of individual nanoparticles in cells at nano and molecular levels to establish their safety. Conformational changes in secondary protein structures are one of the main indicators of impaired biological function, and hence, the ability to identify these changes at a nanoscale level offers unique insights into the nanotoxicity of materials. Here, we used nanoscale infrared spectroscopy and demonstrated for the first time that nanodiamond-induced alterations in both extra- and intracellular secondary protein structures lead to the formation of antiparallel β-sheet, β-turns, intermolecular β-sheet, and aggregation of proteins. These conformational changes of the protein structure may result in the loss of functionality of proteins and in turn lead to adverse effects.

In vivosubsite classification and diagnosis of oral cancers using Raman spectroscopy

Oral cancers suffer from poor disease-free survival rates due to delayed diagnosis. Noninvasive, rapid, objective approaches as adjuncts to visual inspection can help in better management of oral cancers. Raman spectroscopy (RS) has shown potential in identification of oral premalignant and malignant conditions and also in the detection of early cancer changes like cancer-field-effects (CFE) at buccal mucosa subsite. Anatomic differences between different oral subsites have also been reported using RS. In this study, anatomical differences between subsites and their possible influence on healthy vs pathological classification were evaluated on 85 oral cancer and 72 healthy subjects. Spectra were acquired from buccal mucosa, lip and tongue in healthy, contralateral (internal healthy control), premalignant and cancer conditions using fiber-optic Raman spectrometer. Mean spectra indicate predominance of lipids in healthy buccal mucosa, contribution of both lipids and proteins in lip while major dominance of protein in tongue spectra. From healthy to tumor, changes in protein secondary-structure, DNA and heme-related features were observed. Principal component linear discriminant analysis (PC-LDA) followed by leave-one-out-cross-validation (LOOCV) was used for data analysis. Findings indicate buccal mucosa and tongue are distinct entities, while lip misclassifies with both these subsites. Additionally, the diagnostic algorithm for individual subsites gave improved classification efficiencies with respect to the pooled subsites model. However, as the pooled subsites model yielded 98% specificity and 100% sensitivity, this model may be more useful for preliminary screening applications. Large-scale validation studies are a pre-requisite before envisaging future clinical applications.

Assessing physio-macromolecular effects of lactic acid on Zygosaccharomyces bailii cells during microaerobic fermentation.

The ability of Zygosaccharomyces bailii to grow at low pH and in the presence of considerable amounts of weak organic acids, at lethal condition for Saccharomyces cerevisiae, increased the interest in the biotechnological potential of the yeast. To understand the mechanism of tolerance and growth effect of weak acids on Z. bailii, we evaluated the physiological and macromolecular changes of the yeast exposed to sub lethal concentrations of lactic acid. Lactic acid represents one of the important commodity chemical which can be produced by microbial fermentation. We assessed physiological effect of lactic acid by bioreactor fermentation using synthetic media at low pH in the presence of lactic acid. Samples collected from bioreactors were stained with propidium iodide (PI) which revealed that, despite lactic acid negatively influence the growth rate, the number of PI positive cells is similar to that of the control. Moreover, we have performed Fourier Transform Infra-Red (FTIR) microspectroscopy analysis on intact cells of the same samples. This technique has been never applied before to study Z. bailii under this condition. The analyses revealed lactic acid induced macromolecular changes in the overall cellular protein secondary structures, and alterations of cell wall and membrane physico-chemical properties.

The physicochemical properties of membranes correlate with the NADPH oxidase activity

BackgroundPhagocytes kill ingested microbes by exposure to high concentrations of toxic reactive species generated by NADPH-oxidases. This membrane-bound electron-transferring enzyme is tightly regulated by cellular signaling cascades. So far, molecular and biophysical studies of the NADPH-oxidase were performed over limited temperature ranges, which weaken our understanding of immune response or inflammatory events. In this work, we have inspected the influence of temperature and lipid membrane properties on the NADPH-oxidase activity using a system free of cell complexity. MethodsWe have extended the experimental conditions of the accepted model for NADPH-oxidase activity, the so-called cell-free assay, to a large temperature range (10–40°C) using different membrane compositions (subcellular compartments or liposomes). ResultsA remarkable increase of superoxide production rate was observed with rising temperature. Synchrotron radiation circular dichroism data showed that this is not correlated with protein secondary structure changes. When lipid bilayers are in fluid phase, Arrhenius plots of the oxidase activity showed linear relationships with small activation energy (Ea), while when in solid phase, high Ea was found. The sterol content modulates kinetic and thermodynamic parameters. ConclusionHigh temperature promotes the rate of superoxide production. The key element of this enhancement is related to membrane properties such as thickness and viscosity and not to protein structural changes. Membrane viscosity that can be driven by sterols is a paramount parameter of Ea of NADPH oxidase activity. The membrane bilayer state modulated by its sterol content may be considered locally as an enzyme regulator.This article is part of a Special Issue entitled “Science for Life” Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

Effects of power ultrasound on oxidation and structure of beef proteins during curing processing

The aim of this study was to evaluate the effects of power ultrasound intensity (PUS, 2.39, 6.23, 11.32 and 20.96Wcm−2) and treatment time (30, 60, 90 and 120min) on the oxidation and structure of beef proteins during the brining procedure with 6% NaCl concentration. The investigation was conducted with an ultrasonic generator with the frequency of 20kHz and fresh beef at 48h after slaughter. Analysis of TBARS (Thiobarbituric acid reactive substances) contents showed that PUS treatment significantly increased the extent of lipid oxidation compared to static brining (P<0.05). As indicators of protein oxidation, the carbonyl contents were significantly affected by PUS (P<0.05). SDS–PAGE analysis showed that PUS treatment increased protein aggregation through disulfide cross-linking, indicated by the decreasing content of total sulfhydryl groups which would contribute to protein oxidation. In addition, changes in protein structure after PUS treatment are suggested by the increases in free sulfhydryl residues and protein surface hydrophobicity. Fourier transformed infrared spectroscopy (FTIR) provided further information about the changes in protein secondary structures with increases in β-sheet and decreases in α-helix contents after PUS processing. These results indicate that PUS leads to changes in structures and oxidation of beef proteins caused by mechanical effects of cavitation and the resultant generation of free radicals.

Enhanced ubiquitination and proteasomal degradation of catalytically deficient human choline acetyltransferase mutants.

Choline acetyltransferase (ChAT) is essential for cholinergic neuron function as it mediates synthesis of the neurotransmitter acetylcholine. ChAT mutations have been linked to the neuromuscular disorder congenital myasthenic syndrome (CMS). One CMS-related ChAT mutation, V18M, reduces enzyme activity and cellular protein levels, and is positioned within a highly conserved proline-rich motif with the sequence 14 PKLPVPP20 . We demonstrate that N-terminal truncation that includes this proline-rich motif, as well as mutation of prolines-17/19 together to alanine (P17A/P19A), dramatically reduces ChAT steady-state protein levels and cellular activity when expressed in cholinergic SN56 neural cells. The invitro activity of bacterially expressed recombinant P17A/P19A-ChAT is also reduced, although this is not caused by changes in protein secondary structure or thermal stability. Treatment of SN56 cells with the proteasome inhibitor MG132 increases cellular P17A/P19A-ChAT steady-state protein levels, and by immunoprecipitation we found that ChAT is ubiquitinated and that polyubiquitination of P17A/P19A-ChAT is increased compared to wild-type (WT) ChAT. Using a novel fluorescent-biorthogonal pulse-chase protocol in SN56 cells, we determined that the protein half-life of P17A/P19A-ChAT (2.2h) is substantially reduced compared to WT-ChAT (19.7h). Lastly, we show that two CMS-related ChAT mutants (V18M and A513T) have enhanced ubiquitination, and that treatment with MG132 can partially restore both the steady-state protein levels as well as cellular activity of some CMS-mutant ChAT. These results identify a novel mechanism for regulation of ChAT through the ubiquitin-proteasome system that is influenced by the conserved N-terminal proline-rich motif of ChAT and may be implicated in CMS pathology. Choline acetyltransferase (ChAT) synthesizes acetylcholine in cholinergic neurons. In this study we find that steady-state protein levels of human 69-kDa ChAT are regulated by the ubiquitin-proteasome system. Mutation of a highly conserved N-terminal proline-rich motif in human 69-kDa ChAT reduces both cellular ChAT protein levels, through enhanced ubiquitination and proteasomal degradation, and enzyme activity. Ubiquitination of catalytically deficient congenital myasthenic syndrome (CMS)-mutant ChAT is increased in cells, and importantly proteasome inhibition partially restores steady-state protein levels as well as cellular activity of some CMS-mutant ChAT proteins.

Conjugation of cytochrome c with ferrocene-terminated hyperbranched polymer and its influence on protein structure, conformation and function

Interaction mechanism of a new hyperbranched polyurethane-based ferrocene (HPU-Fc) with cytochrome c (cyt c) and cyt c structure and conformation change induced by HPU-Fc were investigated using cyclic voltammogram(CV), differential pulse voltammetry (DPV), circular dichroism (CD), fluorescence, synchronous fluorescence and absorbance spectroscopy technique. The peroxidase activity of cyt c in the presence of HPU-Fc was also studied. The structure and conformation of protein are relatively stable at moderate concentration of HPU-Fc without obvious perturbation of the heme pocket and significant changes in protein secondary structure. Conjugation of cyt c with excessive HPU-Fc (over about 3 times of cyt c) slightly changed the α-helix structure in protein, disturbed the microenvironment around heme as well as away from the heme crevice, which caused the changes of the electrochemical behavior and the absorption spectra. Reasonable amount of HPU-Fc has no significant influence on the protein enzymatic activity, while excess HPU-Fc may cause a conformation not suitable for H2O2 activation and guaiacol oxidation. The interaction of HPU-Fc with cyt c and the conservation of protein function at suitable HPU-Fc amount make prepared complex promising for the synergistic anticancer therapy.

Fourier transform infrared spectroscopic analysis of sperm chromatin structure and DNA stability.

Sperm chromatin structure and condensation determine accessibility for damage, and hence success of fertilization and development. The aim of this study was to reveal characteristic spectral features coinciding with abnormal sperm chromatin packing (i.e., DNA-protein interactions) and decreased fertility, using Fourier transform infrared spectroscopy. Chromatin structure in spermatozoa obtained from different stallions was investigated. Furthermore, spermatozoa were exposed to oxidative stress, or treated with thiol-oxidizing and disulfide-reducing agents, to alter chromatin structure and packing. Spectroscopic studies were corroborated with flow cytometric analyses using the DNA-intercalating fluorescent dye acridine orange. Decreased fertility of individuals correlated with increased abnormal sperm morphology and decreased stability toward induced DNA damage. Treatment with the disulfide reducing agent dithiothreitol resulted in increased sperm chromatin decondensation and DNA accessibility, similar as found for less mature epididymal spermatozoa. In situ infrared spectroscopic analysis revealed that characteristic bands arising from the DNA backbone (ν1230, ν1086, ν1051cm(-1) ) changed in response to induced oxidative damage, water removal, and decondensation. This coincided with changes in the amide-I region (intensity at ν1620 vs. ν1640cm(-1) ) denoting concomitant changes in protein secondary structure. Reduction in protein disulfide bonds resulted in a decreased value of the asymmetric to symmetric phosphate band intensity (ν1230/ν1086cm(-1) ), suggesting that this band ratio is sensitive for the degree of chromatin condensation. Moreover, when analyzing spermatozoa from different individuals, it was found that the asymmetric/symmetric phosphate band ratio negatively correlated with the percentage of morphologically abnormal spermatozoa.

Structural effects of simvastatin on liver rat [corrected] tissue: Fourier transform infrared and Raman microspectroscopic studies.

Simvastatin is one of the most frequently prescribed statins because of its efficacy in the treatment of hypercholesterolemia, reducing cardiovascular risk and related mortality. Determination of its side effects on different tissues is mandatory to improve safe use of this drug. In the present study, the effects of simvastatin on molecular composition and structure of healthy rat livers were investigated by Fourier transform infrared and Raman imaging. Simvastatin-treated groups received 50 mg/kg/day simvastatin for 30 days. The ratio of the area and/or intensity of the bands assigned to lipids, proteins, and nucleic acids were calculated to get information about the drug-induced changes in tissues. Loss of unsaturation, accumulation of end products of lipid peroxidation, and alterations in lipid-to-protein ratio were observed in the treated group. Protein secondary structure studies revealed significant decrease in α-helix and increase in random coil, while native β-sheet decreases and aggregated β-sheet increases in treated group implying simvastatin-induced protein denaturation. Moreover, groups were successfully discriminated using principal component analysis. Consequently, high-dose simvastatin treatment induces hepatic lipid peroxidation and changes in molecular content and protein secondary structure, implying the risk of liver disorders in drug therapy.

Fluctuating Finite Element Analysis: Development and Applications to Cytoplasmic Dynein

The number of structures in the Electron Microscopy Database (EMDB) is growing rapidly due to improvements in cryo-electron microscopy and tomography [1]. This database is complementary to the Protein Data Base (PDB), in that it contains volumetric information about the overall shape of a biomolecule, rather than fully atomistic structures. Fluctuating Finite Element Analysis (FFEA) [2] is a new computer simulation technique that simulates the dynamic behaviour of bio-molecular structures in the EMDB, in an analogous manner to the use of atomistic molecular dynamics trajectories based on structures deposited in the PDB. As FFEA uses a continuum representation of biomolecules it has no upper length-scale limit, and provides access to mesoscopic regimes (50-1000nm) inaccessible to more detailed modelling techniques.To model the action of molecular motors using FFEA, we account for atomistic processes such as ATP binding, hydrolysis and changes in protein secondary structure by including them as instantaneous events occurring at a given rate. Coupling the temperature driven dynamics of the motor with the probability that a transition will occur ensures that the internal strain energy influences the rate of the chemical processes driving the action of the motor. We are currently applying this coupled simulation to cytoplasmic dynein, which is a dimeric molecular motor involved in intracellular cargo transport, to study how mechanical communication and gating between the two subunits enables the motor to walk without moving backwards, stalling or releasing from the microtubule completely.[1] Kuehlbrandt, W., The Resolution Revolution, Science. 2014, 343(6178), 1443-4.[2] Oliver, R. C., Read, D. J., Harlen, O. G. And Harris, S. A., A stochastic finite element model for the dynamics of globular macromolecules, J. Comp. Phys. 2013, 239, 147-65.