Search

A lot of literature sources discuss diseases associated with the hemoglobin protein [1-2]. In the modern world, more than 800 million people suffer from anemia [3]. Assessing the level of hemoglobin in the circulatory system is one of the ways to diagnose anemia. Hemoglobin protein is also a promising source of bioactive peptides [4]. The aim of the work was to identify the reasons leading to conformation changes of this protein. It still remains unclear what exactly causes disruption of its functionality. Human hemoglobin from Sigma H7379 was studied in the work; all experiments were conducted on a dynamic light scattering spectrometer—Photocor Complex. Experimental data were obtained using optical methods of static and dynamic light scattering. The work included an analysis of the behaviour of hemoglobin protein molecules in aqueous and aqueous-saline solutions with changes in solution parameters (pH, addition of iron chloride III). At values of pH and pH , the hemoglobin molecule underwent conformational changes, resulting in the disintegration of the quaternary structure into -dimers and individual - and -globules. As a result of the study, it was found that the addition of FeCl to aqueous solutions of hemoglobin increases the size and mass of scattering particles, which can be explained by the adsorption of Fe ions on the protein surface. However, upon reaching a certain concentration of FeCl , the pH of the solution was lowered to such an extent that it caused conformational changes in hemoglobin, leading to the disintegration of its quaternary structure. These results can be taken into account when creating medicinal drugs for the treatment of anemia and other diseases associated with the hemoglobin protein. [ABSTRACT FROM AUTHOR]

A true native protein state is realized in a water solution where proteins exhibit their dynamic properties important for the functioning. This is way we have analyzed the dynamics of α-helices inside ribosomal protein L25 from Escherichia coli in a water solution. The dynamics of only main chain Cα-atoms have been simulated along the five independent trajectories at a total time 200ns. Superposed average dynamics picture of L25 structure coincides very well with the NMR protein structure in a water solution. Dynamic shifts of Cα-atoms of the α-helices are related with a restraint status of the residue side chain. In contrast, Cα-atoms of the β-sheet, which form a hydrophobic core, show very low dynamic motion and higher stability. Dynamic specificity of the main chain of protein L25 could explain its particular features in the complex with 5S rRNA and in the structure of the ribosome.

The impact of denaturing and stabilizing osmolytes on protein conformational dynamics has been extensively explored due to the significant contribution of protein solvation to the stability, function, malfunction and regulation of globular proteins. We studied the effect of two nonspecific organic molecules, urea, which is a conventional denaturant, and dimethyl sulfoxide (DMSO), which is a multilateral organic solvent, on the stability and conformational dynamics of a non-inhibitory serpin, ovalbumin (OVA). A differential scanning microcalorimetry (DSC) experimental series conducted in the phosphate buffer solutions containing 0–30% of additives revealed the destabilizing impact of both urea and DMSO in a mild acidic media, manifested in the gradual decrease of thermal unfolding enthalpy and transition temperature. These findings differ from the results observed in our study of the mild alkaline DMSO buffered solutions of OVA, where the moderate stabilization of OVA was observed in presence of 5–10% of DMSO. However, the overall OVA interaction patterns with urea and DMSO are consistent with our previous findings on the stability and conformational flexibility of another model globular protein, α-chymotrypsin, in similar medium conditions. The obtained results could be explained by preferential solvation patterns. Positive preferential solvation of protein by urea in urea/water mixtures mainly weakens the hydrophobic interactions of the protein globule and eventually leads to the disruption of the tertiary structure within the whole range of urea concentrations. Alternatively, under certain experimental conditions in DMSO/water mixtures, positive preferential solvation by water molecules can be observed. We assume that the switch to the positive preferential solvation by DMSO, which is shown to have a soft maximum around 20–30% DMSO, could be shifted towards lower additive concentrations due to the intrinsic capability of ovalbumin OVA to convert into a heat-stable, yet flexible set of conformations that have increased the surface hydrophobicity, characteristic to molten-globule-like states.

The impact of denaturing and stabilizing osmolytes on protein conformational dynamics has been extensively explored due to the significant contribution of protein solvation to the stability, function, malfunction and regulation of globular proteins. We studied the effect of two nonspecific organic molecules, urea, which is a conventional denaturant, and dimethyl sulfoxide (DMSO), which is a multilateral organic solvent, on the stability and conformational dynamics of a non-inhibitory serpin, ovalbumin (OVA). A differential scanning microcalorimetry (DSC) experimental series conducted in the phosphate buffer solutions containing 0-30 % of additives revealed the destabilizing impact of both urea and DMSO in a mild acidic media, manifested in the gradual decrease of thermal unfolding enthalpy and transition temperature. These findings differ from the results observed in our study of the mild alkaline DMSO buffered solutions of OVA, where the moderate stabilization of OVA was observed in presence of 5-10% of DMSO. However, the overall OVA interaction patterns with urea and DMSO are consistent with our previous findings on the stability and conformational flexibility of another model globular protein, α-chymotrypsin, in similar medium conditions. The obtained results could be explained by preferential solvation patterns. Positive preferential solvation of protein by urea in urea/water mixtures mainly weakens the hydrophobic interactions of the protein globule and eventually leads to the disruption of the tertiary structure within the whole range of urea concentrations. Alternatively, under certain experimental conditions in DMSO/water mixtures, positive preferential solvation by water molecules can be observed. We assume that the switch to the positive preferential solvation by DMSO, which is shown to have a soft maximum around 20-30% DMSO, could be shifted towards lower additive concentrations due to the intrinsic capability of ovalbumin OVA to convert into a heat-stable, yet flexible set of conformations that have increased the surface hydrophobicity, characteristic to molten-globule-like states. [ABSTRACT FROM AUTHOR]

It is of fundamental importance in pharmacology and theoretical biology to analyze the binding of ligands to receptors. A better understanding of this process and its outcomes can help predict the following: how the protein interacts with ligands; whether the ligand acts as an activator, inhibitor, or substrate; in which areas the ligand interacts best with the receptor. This article describes the potential of using a software pipeline for finding the most probable position of the ligand in the receptor. Such a pipeline involves a complex algorithm, from predicting the structure of the receptor to searching and analyzing the interaction of ligands with the receptor. The advantage of the software pipeline is that it allows numerous combinations of ligands and receptors to be analyzed at once. Possible interactions of the receptor–ligand complex are studied based on certain parameters: the energy of the affinity of the ligand for the receptor; the length and energy of the bond between the receptor and the ligand, both in the whole complex and between individual atoms. All characteristics can be automatically calculated by default under the specified optimal parameters. Alternatively, they can be set by the user, depending on the task. To illustrate how the software pipeline works, we analyzed the interaction of ligands with human acetylcholinesterase, a protein with the most studied active center. We confirmed that the software pipeline works correctly by comparing the obtained results with the experimental data on the binding of various ligands to human acetylcholinesterase. The pipeline code was published on GitHub (https://github.com/NastiaKozlova/stabilisation complex-receptor-ligand).

In this paper, we show, discuss, and compare the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model, a coarse-grained model of density of hydrophobicity in proteins. In the FOD model, an input structure is enclosed in an axis-aligned ellipsoid called a drop. Two profiles of hydrophobicity are then calculated for its residues: theoretical (based on the 3D Gauss function) and observed (based on pairwise hydrophobic interactions). Condition of the hydrophobic core is revealed by comparing those profiles through relative entropy, while analysis of their local differences allows, in particular, determination of the starting location for the search for protein–protein and protein–ligand interaction areas. Here, we improve the baseline workflow of the FOD model by introducing symmetry to the hydrophobicity profile comparison and ellipsoid bounding procedures. In the first modification (FOD–JS), Kullback–Leibler divergence is enhanced with its Jensen–Shannon variant. In the second modification (FOD-PCA), the molecule is optimally aligned with the axes of the coordinate system via principal component analysis, and the size of its drop is determined by the standard deviation of all its effective atoms, making it less susceptible to structural outliers. Tests on several molecules with various shapes and functions confirm that the proposed modifications improve the accuracy, robustness, speed, and usability of Gauss function-based modeling of the density of hydrophobicity in protein structures. [ABSTRACT FROM AUTHOR]

A true native protein state is realized in a water solution where proteins exhibit their dynamic properties important for the functioning. This is way we have analyzed the dynamics of α-helices inside ribosomal protein L25 from Escherichia coli in a water solution. The dynamics of only main chain Cα-atoms have been simulated along the five independent trajectories at a total time 200ns. Superposed average dynamics picture of L25 structure coincides very well with the NMR protein structure in a water solution. Dynamic shifts of Cα-atoms of the α-helices are related with a restraint status of the residue side chain. In contrast, Cα-atoms of the β-sheet, which form a hydrophobic core, show very low dynamic motion and higher stability. Dynamic specificity of the main chain of protein L25 could explain its particular features in the complex with 5S rRNA and in the structure of the ribosome., Competing Interests: The authors declare no conflict of interest., (© 2024 The Authors.)

Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn's hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners. [ABSTRACT FROM AUTHOR]

According to actual literature data, hyaluronic acid (HA) that is presented in the extracellular matrix can interact with proteins and thereby affect several important functions of the cell membrane. The purpose of this work was to reveal the features of the interaction of HA with proteins using the PFG NMR method by sampling two systems: aqueous solutions of HA with bovine serum albumin (BSA) and aqueous solutions of HA with hen egg-white lysozyme (HEWL). It was found that the presence of BSA in the HA aqueous solution initiates a certain additional mechanism; as a result, the population of HA molecules in the gel structure increases to almost 100%. At the same time, for an aqueous solution of HA/HEWL, even in the range of low (0.01–0.2%) HEWL contents, strong signs of degradation (depolymerization) of some HA macromolecules were observed such that they lost the ability to form a gel. Moreover, lysozyme molecules form a strong complex with degraded HA molecules and lose their enzymatic function. Thus, the presence of HA molecules in the intercellular matrix, as well as in the state associated with the surface of the cell membrane, can, in addition to the known ones, perform one more important function: the function of protecting the cell membrane from the destructive action of lysozymes. The obtained results are important for understanding the mechanism and features of the interaction of extracellular matrix glycosaminoglycan with cell membrane proteins.

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.

Technological advances frequently interface biomolecules with nanomaterials at non-physiological conditions, necessitating response characterization of key processes. Similar encounters are expected in cellular contexts. We report in silico investigations of the response of diverse protein conformational states to lowering of temperature and imposition of spatial constraints. Conformational states are represented by folded form of the Albumin binding domain (ABD) protein, its compact denatured form, and structurally disordered nascent folding elements. Data from extensive simulations are evaluated to elicit structural, thermodynamic and dynamic responses of the states and their associated environment. Analyses reveal alterations to folding propensity with reduced thermal energy and confinement, with signatures of trend reversal in highly disordered states. Across temperatures, confinement has restrictive effects on volume and energetic fluctuations, leading to narrowing of differences in isothermal compressibility (κ) and heat capacities (C p ). While excess (over ideal gas) entropy of the hydration layer marks dependence on the conformational state at bulk, confinement triggers erasure of differences. These observations are largely consistent with timescales of protein-water hydrogen bonding dynamics. The results implicate multi-factorial associations within a simple bio-nano complex. We expect the current study to motivate investigations of more biologically relevant interfaces towards mechanistic understanding and potential applications., (© 2024 Wiley-VCH GmbH.)

In this paper, we show, discuss, and compare the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model, a coarse-grained model of density of hydrophobicity in proteins. In the FOD model, an input structure is enclosed in an axis-aligned ellipsoid called a drop. Two profiles of hydrophobicity are then calculated for its residues: theoretical (based on the 3D Gauss function) and observed (based on pairwise hydrophobic interactions). Condition of the hydrophobic core is revealed by comparing those profiles through relative entropy, while analysis of their local differences allows, in particular, determination of the starting location for the search for protein–protein and protein–ligand interaction areas. Here, we improve the baseline workflow of the FOD model by introducing symmetry to the hydrophobicity profile comparison and ellipsoid bounding procedures. In the first modification (FOD–JS), Kullback–Leibler divergence is enhanced with its Jensen–Shannon variant. In the second modification (FOD-PCA), the molecule is optimally aligned with the axes of the coordinate system via principal component analysis, and the size of its drop is determined by the standard deviation of all its effective atoms, making it less susceptible to structural outliers. Tests on several molecules with various shapes and functions confirm that the proposed modifications improve the accuracy, robustness, speed, and usability of Gauss function-based modeling of the density of hydrophobicity in protein structures.

Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn’s hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners.

A computer algorithm for assessment of globularity of protein structures is presented. By enclosing the input protein in a minimum volume ellipsoid (MVEE) and calculating a profile measuring how voxelized space within this shape (cubes on a uniform grid) is occupied by atoms, it is possible to estimate how well the molecule resembles a globule. For any protein to satisfy the proposed globularity criterion, its ellipsoid profile (EP) should first confirm that atoms adequately fill the ellipsoid’s center. This property should then propagate towards the surface of the ellipsoid, although with diminishing importance. It is not required to compute the molecular surface. Globular status (full or partial) is assigned to proteins with values of their ellipsoid profiles, called here the ellipsoid indexes (EI), above certain levels. Due to structural outliers which may considerably distort the measurements, a companion method for their detection and reduction of their influence is also introduced. It is based on kernel density estimation and is shown to work well as an optional input preparation step for MVEE. Finally, the complete workflow is applied to over two thousand representatives of SCOP 2.08 domain superfamilies, surveying the landscape of tertiary structure of proteins from the Protein Data Bank.

In this study, the effects of heating temperature (70 °C, 80 °C, 90 °C) and egg white dosage (5%, 7.5%, 10%) on the physicochemical properties of chicken egg white microgels (EWMGs) were investigated. The results showed that both temperature and EW dosage would affect the EWMG in terms of its particle size, surface hydrophobicity, contact angle and zeta potential. At a given temperature, the content of α-helix in the EWMG was positively correlated to the protein concentration; while at a fixed EW dosage, the content of α-helix in the EWMG was negatively correlated to the temperature. High inter-phase Pickering emulsions (HIPEs) with EWMGs prepared at high temperature-low protein as stabilizer were shown to have smaller droplet size and better thermal and centrifugal stability. Rheological analysis of these HIPEs showed slight upward trends for both storage modulus (G′) and loss modulus (G″) and relatively weak frequency dependency. The HIPEs showing both shear thinning and recovery rate can be used as good food ink for 3D printing, and the HIPEs stabilized by the EWMG obtained at 90°C-5% performed the best. [Display omitted] • The obtained egg white microgels (EWMGs) are globular and nanoscale particles. • EWGM prepared at high temperature-low dosage have better structural flexibility. • HIPEs stabilized by the EWGMs obtain at 90 °C-5% have better environmental stability. • HIPEs stability by the EWGMs can be used as the potential ink for 3D printing. [ABSTRACT FROM AUTHOR]

• Effect of surface area (SA) fluctuation on the dilational modulus (E) was studied. • A SA fluctuation (ΔA/A) larger than ∼3 % had a notable influence on e. • Distinct peak and minimum in e were detected when ΔA/ A > ∼3 %. • A smaller SA fluctuation (ΔA/ A < 3 %) caused only slight variation in E. • E rose to a distinct high after rapid compression, then decreased to a minimum. Understanding how surface area (SA) fluctuation affects the dilational modulus (E) of globular protein films is crucial for evaluating their mechanical properties and practical utility. However, limited reports are available in the literature and the measurement error is unclear. The impact of SA fluctuation and large, forced perturbation on the E of bovine serum albumin (BSA) and human serum albumin (HSA) film was investigated. The E was evaluated by analyzing surface tension (ST) and SA relaxation data obtained using a pendant bubble tensiometer. The data revealed that a large fluctuation in SA exerted a notable influence on the E : a distinct peak and minima in E being detected at the onset and end, respectively (at magnitude ΔA/ A > ∼3 % and at oscillation frequency ƒ = 0.3 – 1.1 mHz for adsorbed BSA/HSA film). In contrast, a comparatively smaller SA fluctuation caused only a slight variation in E. Furthermore, a large, forced perturbation led to a rise in E , exhibiting a distinctly high value after a rapid bubble compression, followed by a subsequent decrease to a distinctly low E. [Display omitted] [ABSTRACT FROM AUTHOR]

A series of dye ligands are docked to three different proteins, E and 3a of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and E6 of human papilloma virus type 16 (HPV-16) using three different software. A four-level selection algorithm is used based on nonparametric statistics of numerical key values such as the "rank" derived from (i) averaged estimated binding energies (EBEs) and (ii) absolute EBE value of each of the software, (iii) frequency of ranking and (iv) rank of the area-under-curve values (AUCs) from decoy docking. A series of repurposing drugs and known antivirals used in experimental studies are docked for comparison. One dye ligand is ranked best for all proteins using the selection algorithm levels i - iii. Another three dye ligands are ranked top for the proteins individually when using all four levels. [Display omitted] • Repurposing dye ligands for E and 3a proteins of SARS-CoV-2 and E6 of HPV-16 • A four-level selection algorithm based on nonparametric statistics is proposed. • Application of three different docking software • Three dye ligands are ranked top. • Comparison with other repurposing ligands and antivirals [ABSTRACT FROM AUTHOR]

[Display omitted] • Surface properties dynamic/equilibrium surface tension (ST) and dilational modulus (E) of BSA and HSA were compared. • ST of HSA (aq) and BSA (aq) generally exhibited similar relaxation, but the ST of HSA relaxed faster at the post-induction regime. • The equilibrium ST of HSA (aq) and BSA (aq) remained constant at ∼ 52.5 mN/m from C = 0.01 to 90 (10−10 mol/cm3) • E of HSA and BSA films exhibited near-identical concentration dependency: E was reasonably constant at ∼ 21 mN/m from C = 0.05 to 0.2 (10−10 mol/cm3) • At further concentration elevations, E rose notably and levelled off at ∼ 52 and ∼ 45 mN/m for HSA and BSA. The biological functionalities of Human Serum Albumin (HSA) and Bovine Serum Albumin (BSA) have been extensively studied in the literature. However, limited information is available on their surface properties [dynamic/equilibrium surface tension (ST) and dilational modulus (E)]. This study compared the dynamic/equilibrium ST of HSA and BSA solutions and the E of the adsorbed films. A pendant bubble tensiometer was employed for measuring the relaxations of ST of HSA/BSA solutions at C = 0.01 – 90 (10−10 mol/cm3). The data revealed that while the dynamic ST of HSA (aq) and BSA (aq) exhibited a similar relaxation in general, the ST of HSA (aq) relaxed notably faster at the post-induction regime than BSA (aq). The equilibrium ST of both HSA and BSA was constant at 52.6 and 52.3 mN/m over a wide concentration range, C = 0.01 – 90 (10−10 mol/cm3). The E of HSA and BSA films exhibited a near-identical concentration dependency to each other: E was reasonably constant at ∼ 21 mN/m from C = 0.05 to 0.2 (10−10 mol/cm3), and at further concentration elevations, E rose notably, and eventually leveled off at ∼ 52 and ∼ 45 mN/m for HSA and BSA films, respectively. [ABSTRACT FROM AUTHOR]

Conformational effects of interaction between bovine and human serum albumin (SA) molecules and nanoparticles of shungite carbon (ShC) in aqueous dispersion have been studied in the temperature range 17 – 72 °С K using electron spin resonance (EPR) spin probing (P). The temperature and kinetic dependences of the parameters of the EPR spectrum for solutions and dispersions of SA and ShC as well as for their mixtures have been obtained. The interaction of SA molecules with ShC nanoparticles has been shown to affect significantly the thermally induced protein conformational changes that determine the ability of the SH group of Cys-35 of SA to convert the NO group of the doxyl stearic fatty acid (FA) used as the probe to diamagnetic state. The temperature transitions reflecting the SA conformational changes in the localization region of P become less pronounced and shift toward higher temperatures in the presence of ShC. This may be due to a change in the oxidation-reduction balance of the set of SA molecules in solution or dispersion, since ShC acts as an oxidant with respect to SA. Therefore, ShC can also be considered an agent affecting the degree of oxidation of Cys-34 of SA with free radicals, such as P. ShC nanoparticles and P compete with each other during the oxidation of Cys-34. Furthermore, the transfer of P from SA to nanoparticles is facilitated due to the conformational transitions, and the reduction of the probe NO group by the protein SH groups is impeded. This allows considering ShC nanoparticles a factor of regulation of the redox balance in systems involving SA, including physiological media.

An analysis of standard thermodynamic functions of protein structure in solution allows revealing important features of protein solution phase behavior, particularly the presence of higher and lower critical solution temperatures on phase diagram (PD). Linking the phase and the corresponding conformational transitions of protein molecules to phase transitions of the protein solution as a whole will provide consideration of the relationship between protein conformation and the structural organization of protein systems in predenaturational interval. A phase diagram (PD) for the globular protein solution is presented in the temperature-entropy coordinate plane. Solution phase states have been analyzed and a probable interrelation of topological structures arising in the supercritical region with the phase processes in low- and high-temperature range has been defined when considering PD. This shows the possibility to superpose two types of PD: for normal and retrograde protein solubility. PD in the temperature-packing density plane has been presented for a protein solution with low and high critical solution temperatures and a supercritical zone between them typical of native protein solution, and a closed zone typical of denatured protein solution in the near physiological temperature interval. Supramolecular organization of protein solution has been described on this basis including metastable phases of protein molecules in conformations altered with respect to native (N) and denatured (D) states as well as dynamical protein clusters and oligomers in the supercritical zone. The contribution of the solvent in the low- and high-temperature ranges has also been taken into account. Various PD regions have been interpreted under the assumption that molecules in conformations, corresponding to N and D states are capable of forming different nanocrystal lattices which define the topological features of the corresponding solutions in a wide temperature range. Probable significance of supercritical phase states of protein solutions for the self-regulation of the components chemical potentials at the expense of the solution supramolecular organization at changing temperature and/or salt concentration and thereby at changing environmental factors has been discussed.

Experimental force spectroscopy has been effectively utilized for measuring structural characterization of biomolecules and mechanical properties of biomaterials. Specifically, atomic force microscopy (AFM) has been widely used to portray biomolecular characterization in single-molecule experiment by observing the unfolding behavior of the proteins. Not only the experimental techniques enable us to characterize globular protein, but computational methods like molecular dynamics (MD) also gives insight into understanding biomolecular structures. To better comprehend the behavior of biomolecules, conditions such as pulling velocities and loading rates are put to the test, yet there are still limitations in understanding the unfolding behavior of biomolecules with the effect of different loading devices. In this study, we performed an all-atom MD and steered molecular dynamics (SMD) simulations considering different loading device effects such as “soft” and “stiff” to characterize the anisotropic unfolding behavior of ubiquitin protein. We found out the anisotropic unfolding pathways of the protein through the broken number of hydrogen bonds and geometric secondary structures of the biomolecule. Our study provides the importance for usage of various loading-devices on biomolecules when analyzing the structural compositions and the characteristics of globular biomolecules. [ABSTRACT FROM AUTHOR]