Conformational Fluctuations Research Articles

Weyl scaling invariant R2 gravity for inflation and dark matter

Inflation in the early universe can generate the nearly conformal invariant fluctuation that leads to the structures we observe at the present. The simple viable Starobinsky R2 inflation has an approximate global scale symmetry. We study the conformal symmetric Weyl Rˆ2 and general F(Rˆ) theories and demonstrate their equivalence to Einstein gravity coupled with a scalar and a Weyl gauge field. The scalar field in Weyl Rˆ2 gravity can be responsible for inflation with Starobinsky model as the attractor, potentially distinguishable from the latter by future experiments. The intrinsic Weyl gauge boson becomes massive once the Einstein frame is fixed, and constitutes as a dark matter candidate with mass up to ∼5×1016GeV.

Enzyme dynamics: Looking beyond a single structure.

Conventional understanding of how enzymes function strongly emphasizes the role of structure. However, increasing evidence clearly indicates that enzymes do not remain fixed or operate exclusively in or close to their native structure. Different parts of the enzyme (from individual residues to full domains) undergo concerted motions on a wide range of time-scales, including that of the catalyzed reaction. Information obtained on these internal motions and conformational fluctuations has so far uncovered and explained many aspects of enzyme mechanisms, which could not have been understood from a single structure alone. Although there is wide interest in understanding enzyme dynamics and its role in catalysis, several challenges remain. In addition to technical difficulties, the vast majority of investigations are performed in dilute aqueous solutions, where conditions are significantly different than the cellular milieu where a large number of enzymes operate. In this review, we discuss recent developments, several challenges as well as opportunities related to this topic. The benefits of considering dynamics as an integral part of the enzyme function can also enable new means of biocatalysis, engineering enzymes for industrial and medicinal applications.

Ordered Solid-State Microstructures of Conjugated Polymers Arising from Solution-State Aggregation.

Controlling the solution-state aggregation of conjugated polymers for producing specific microstructures remains challenging. Herein, a practical approach is developed to finely tune the solid-state microstructures through temperature-controlled solution-state aggregation and polymer crystallization. High temperature generates significant conformation fluctuation of conjugated backbones in solution, which facilitates the polymer crystallization from solvated aggregates to orderly packed structures. The polymer films deposited at high temperatures exhibit less structural disorders and higher electron mobilities (up to two orders of magnitude) in field-effect transistors, compared to those deposited at low temperatures. This work provides an effective strategy to tune the solution-state aggregation to reveal the relationship between solution-state aggregation and solid-state microstructures of conjugated polymers.

Ordered Solid‐State Microstructures of Conjugated Polymers Arising from Solution‐State Aggregation

AbstractControlling the solution‐state aggregation of conjugated polymers for producing specific microstructures remains challenging. Herein, a practical approach is developed to finely tune the solid‐state microstructures through temperature‐controlled solution‐state aggregation and polymer crystallization. High temperature generates significant conformation fluctuation of conjugated backbones in solution, which facilitates the polymer crystallization from solvated aggregates to orderly packed structures. The polymer films deposited at high temperatures exhibit less structural disorders and higher electron mobilities (up to two orders of magnitude) in field‐effect transistors, compared to those deposited at low temperatures. This work provides an effective strategy to tune the solution‐state aggregation to reveal the relationship between solution‐state aggregation and solid‐state microstructures of conjugated polymers.

Twisting mode of supercoil leucine-rich domain mediates peptide sensing in FLS2–flg22–BAK1 complex**Project supported by the National Natural Science Foundation of China (Grant No. 11704140), self-determined research funds of CCNU from the Colleges’ Basic Research and Operation of MOE (Grant No. CCNU20TS004) (Y. Z.), and the China Scholarship Council Fund (Grant No. 201708420039) (L. P.).

Plants and animals recognize microbial invaders by detecting pathogen-associated molecular patterns (PAMPs) through pattern-recognition receptors (PRRs). This recognition plays a crucial role in plant immunity. The newly discovered protein in plants that responds to bacterial flagellin, i.e., flagellin-sensitive 2 (FLS2), is ubiquitously expressed and present in many plants. The association of FLS2 and BAK1, facilitated by a highly conserved epitope flg22 of flagellin, triggers such downstream immune responses as activated MAPK pathway and elevated reactive oxygen species (ROS) for bacterial defense and plant immunity. Here we study the intrinsic dynamics and conformational change of FLS2 upon the formation of the FLS2–flg22–BAK1 complex. The top intrinsic normal modes and principal structural fluctuation components are very similar, showing two bending modes and one twisting mode. The twisting mode alone, however, accounts for most of the conformational change of FLS2 induced by binding with flg22 and BAK1. This study indicates that flg22 binding suppresses FLS2 conformational fluctuation, especially on the twisting motion, thus facilitating FLS2–BAK1 interaction. A detailed analysis of this sensing mechanism may aid better design on both PRR and peptide mimetics for plant immunity.

An Exactly Solvable Stochastic Kinetic Theory of Single-Molecule Force Experiments.

The unfolding of a protein in single-molecule pulling experiments subjected to a constant force (force-clamp) and constant velocity (force-ramp) is analyzed by introducing an exactly solvable two-state kinetic model framed based on the general stochastic approach of discrete state and continuous time formulation. The effect of perturbation is interpreted in the presence of dynamic disorder, resulting from intrinsic conformational fluctuations, by deriving an exact analytical expression for the unfolding time distribution, which in turn allowed us to calculate the expressions for the quantities of experimental interest explicitly. In particular, the novelty of our method lies in the fact that it reduced the need for a lengthy calculation, contrary to the previous dynamic disorder studies, and provides a fairly concise but sufficient mathematical analysis, which becomes much easier to implement quantitatively. We tested our results against the measured data from a number of force unfolding experiments on various proteins, ubiquitin, titin, and filamin, and the force unzipping of DNA and observed excellent agreement in each case. This asserts the reliability of the present technique, which suggests a plausible extension of the stochastic kinetic theory in single-molecule force experiments beyond its present-day widespread implications.

Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease.

Originating in the city of Wuhan in China in December 2019, COVID-19 has emerged now as a global health emergency with a high number of deaths worldwide. COVID-19 is caused by a novel coronavirus, referred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in pandemic conditions around the globe. We are in the battleground to fight against the virus by rapidly developing therapeutic strategies in tackling SARS-CoV-2 and saving human lives from COVID-19. Scientists are evaluating several known drugs either for the pathogen or the host; however, many of them are reported to be associated with side effects. In the present study, we report the molecular binding mechanisms of the natural alkaloid, noscapine, for repurposing against the main protease of SARS-CoV-2, a key enzyme involved in its reproduction. We performed the molecular dynamics (MD) simulation in an explicit solvent to investigate the molecular mechanisms of noscapine for stable binding and conformational changes to the main protease (Mpro) of SARS-CoV-2. The drug repurposing study revealed the high potential of noscapine and proximal binding to the Mpro enzyme in a comparative binding pattern analyzed with chloroquine, ribavirin, and favipiravir. Noscapine binds closely to binding pocket-3 of the Mpro enzyme and depicted stable binding with RMSD 0.1-1.9 Å and RMSF profile peak conformational fluctuations at 202-306 residues, and a Rg score ranging from 21.9 to 22.4 Å. The MM/PB (GB) SA calculation landscape revealed the most significant contribution in terms of binding energy with ΔPB -19.08 and ΔGB -27.17 kcal/mol. The electrostatic energy distribution in MM energy was obtained to be -71.16 kcal/mol and depicted high free energy decomposition (electrostatic energy) at 155-306 residues (binding pocket-3) of Mpro by a MM force field. Moreover, the dynamical residue cross-correlation map also stated that the high pairwise correlation occurred at binding residues 200-306 of the Mpro enzyme (binding pocket-3) with noscapine. Principal component analysis depicted the enhanced movement of protein atoms with a high number of static hydrogen bonds. The obtained binding results of noscapine were also well correlated with the pharmacokinetic parameters of antiviral drugs.

Origins of the suppression of fibril formation in grafted methylcellulose solutions

We utilize coarse-grained molecular-dynamics simulations to probe the influence of grafting on the conformation and aggregation of methylcellulose chains in water, inspired by the recent experiments on solutions of methylcellulose (MC) chains grafted with polyethylene glycol (PEG) that showed inhibition of methylcellulose fibril formation at high PEG-grafting densities [S. Morozova et al., Macromolecules (Washington, DC, U. S.) 51, 9413 (2018)]. These simulations reveal three features of the grafted system that should frustrate fibril assembly. First, multichain simulations indicate that the distance between the centers of mass of the chains increases at high grafting densities, suggesting that the ability to form collapsed structures is disrupted. Second, single-chain simulations using grafted MC show that the formation of the precursor toroidal structure responsible for fibril formation is hampered at high grafting densities. Third, the frequency spectrum of conformational fluctuations indicates that low-frequency modes dominate at higher grafting densities, suggesting a larger decorrelation time in conformational fluctuations. Together, these results provide a macromolecular basis for the suppression in fibril formation in grafted methylcellulose solutions for grafting densities exceeding approximately 10%.

Protein-Nanoparticle Interaction: Corona Formation and Conformational Changes in Proteins on Nanoparticles.

Nanoparticles (NPs) are highly potent tools for the diagnosis of diseases and specific delivery of therapeutic agents. Their development and application are scientifically and industrially important. The engineering of NPs and the modulation of their in vivo behavior have been extensively studied, and significant achievements have been made in the past decades. However, in vivo applications of NPs are often limited by several difficulties, including inflammatory responses and cellular toxicity, unexpected distribution and clearance from the body, and insufficient delivery to a specific target. These unfavorable phenomena may largely be related to the in vivo protein–NP interaction, termed “protein corona.” The layer of adsorbed proteins on the surface of NPs affects the biological behavior of NPs and changes their functionality, occasionally resulting in loss-of-function or gain-of-function. The formation of a protein corona is an intricate process involving complex kinetics and dynamics between the two interacting entities. Structural changes in corona proteins have been reported in many cases after their adsorption on the surfaces of NPs that strongly influence the functions of NPs. Thus, understanding of the conformational changes and unfolding process of proteins is very important to accelerate the biomedical applications of NPs. Here, we describe several protein corona characteristics and specifically focus on the conformational fluctuations in corona proteins induced by NPs.

The energy transfer model of nonphotochemical quenching: Lessons from the minor CP29 antenna complex of plants

Antenna complexes in photosystems of plants and green algae are able to switch between a light-harvesting unquenched conformation and a quenched conformation so to avoid photodamage. When the switch is activated, nonphotochemical quenching (NPQ) mechanisms take place for an efficient deactivation of excess excitation energy. The molecular details of these mechanisms have not been fully clarified but different hypotheses have been proposed. Among them, a popular one involves excitation energy transfer (EET) from the singlet excited Chls to the lowest singlet state (S1) of carotenoids. In this work, we combine such model with μs-long molecular dynamics simulations of the CP29 minor antenna complex to investigate how conformational fluctuations affect the electronic couplings and the final EET quenching. The computational framework is applied to both CP29 embedding violaxanthin and zeaxantin in its L2 site. Our results demonstrate that the EET model is rather insensitive to physically reasonable variations in single chlorophyll-carotenoid couplings, and that very large conformational changes would be needed to see the large variation of the complex lifetime expected in the switch from light-harvesting to quenched state. We show, however, that a major role in regulating the EET quenching is played by the S1 energy of the carotenoid, in line with very recent spectroscopy experiments.

Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method.

Complexes formed among diverse proteins carry out versatile functions in nearly all physiological processes. Association rates which measure how fast proteins form various complexes are of fundamental importance to characterize their functions. The association rates are not only determined by the energetic features at binding interfaces of a protein complex but also influenced by the intrinsic conformational dynamics of each protein in the complex. Unfortunately, how this conformational effect regulates protein association has never been calibrated on a systematic level. To tackle this problem, we developed a multiscale strategy to incorporate the information on protein conformational variations from Langevin dynamic simulations into a kinetic Monte Carlo algorithm of protein-protein association. By systematically testing this approach against a large-scale benchmark set, we found the association of a protein complex with a relatively rigid structure tends to be reduced by its conformational fluctuations. With specific examples, we further show that higher degrees of structural flexibility in various protein complexes can facilitate the searching and formation of intermolecular interactions and thereby accelerate their associations. In general, the integration of conformational dynamics can improve the correlation between experimentally measured association rates and computationally derived association probabilities. Finally, we analyzed the statistical distributions of different secondary structural types on protein-protein binding interfaces and their preference to the change of association rates. Our study, to the best of our knowledge, is the first computational method that systematically estimates the impacts of protein conformational dynamics on protein-protein association. It throws lights on the molecular mechanisms of how protein-protein recognition is kinetically modulated.

Study of SOPC with embedded pristine and amide-functionalized single wall carbon nanotubes by DSC and FTIR spectroscopy

Using two typical experimental methods, differential scanning calorimetric (DSC) analysis and Fourier Transform Infrared (FTIR) spectroscopy, we have studied the effect of single wall carbon nanotubes (SWCNTs), both amide functionalized (f–SWCNTs) and non-functionalized pristine (p-SWCNTs), on the thermal and structural properties of the SOPC phospholipid. We proposed and discussed possible physical mechanisms driving the thermodynamic and structural states of the bionanocomposites – SOPC/pSWCNTs and SOPC/f-SWCNTs. By FTIR spectroscopy, we demonstrated that p-SWCNTs have less affinity to create and sustain hydrogen bonds polpulaion with the phospholipids carbonyl groups than of the f-SWCNTs. The asymmetric shape of the thermal peaks in the DSC curves suggests the presence of an intermediate state, between gel and liquid crystal, revealing the non-completeness of the transition characterized by the competition of van’t Hoff enthalpy and the calorimetric one. To gain insights into the SOPC molecule’s structure fluctuations with time, in the presence of functionalized and non-functionalized carbon nanotubes, we consider conformational fluctuations able to alter the thermal and spectral characteristics of the single molecule. The time between two non-correlated fluctuating conformational structures was used to assess the dynamic conformational evolution. We found that SOPC/f-SWCNTs is more stable than that of SOPC/p-SWCNTs due to the effective hydrogen-bonding role of the amide radical. Considering, the level of interdigitation of the hydrocarbon chains, we found that the liquid crystal-gel phase transition is more likely a transition between the non-interdigitated liquid crystals and an interdigitated gel phases.

Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors – an in silico docking and molecular dynamics simulation study

Coronavirus disease 2019 (COVID-19) is a viral respiratory disease which caused global health emergency and announced as pandemic disease by World Health Organization. Lack of specific drug molecules or treatment strategy against this disease makes it more devastating. Thus, there is an urgent need of effective drug molecules to fight against COVID-19. The main protease (Mpro) of SARS CoV-2, a key component of this viral replication, is considered as a prime target for anti-COVID-19 drug development. In order to find potent Mpro inhibitors, we have selected eight polyphenols from green tea, as these are already known to exert antiviral activity against many RNA viruses. We have elucidated the binding affinities and binding modes between these polyphenols including a well-known Mpro inhibitor N3 (having binding affinity −7.0 kcal/mol) and Mpro using molecular docking studies. All eight polyphenols exhibit good binding affinity toward Mpro (−7.1 to −9.0 kcal/mol). However, only three polyphenols (epigallocatechin gallate, epicatechingallate and gallocatechin-3-gallate) interact strongly with one or both catalytic residues (His41 and Cys145) of Mpro. Molecular dynamics simulations (100 ns) on these three Mpro–polyphenol systems further reveal that these complexes are highly stable, experience less conformational fluctuations and share similar degree of compactness. Estimation of total number of intermolecular H-bond and MM-GBSA analysis affirm the stability of these three Mpro–polyphenol complexes. Pharmacokinetic analysis additionally suggested that these polyphenols possess favorable drug-likeness characteristics. Altogether, our study shows that these three polyphenols can be used as potential inhibitors against SARS CoV-2 Mpro and are promising drug candidates for COVID-19 treatment.

Shape-Dependent Macromolecular Crowding on the Thermodynamics and Microsecond Conformational Dynamics of Protein Unfolding Revealed at the Single-Molecule Level

One of the main differences in the intercellular environment compared to the laboratory condition is the presence of macromolecular crowders of various compositions, sizes, and shapes. In this article, we have contemplated a systematic shape dependency of macromolecular crowders on the thermodynamics and microsecond conformational fluctuation dynamics of protein unfolding by taking human serum albumin (HSA) as the model protein and similar-sized crowders, namely, dextran-40, ficoll-70, and PEG-35 as macromolecular crowders of different shapes, to mimic the cell environment. We observed that dextran-40 and ficoll-70 counteract the thermal denaturation and PEG-35 assists it. A complete thermodynamic analysis suggests that the stabilization by dextran-40 and ficoll-70 occurs mainly through stabilizing entropic effect, which is somewhat counteracted by the destabilizing enthalpic effect, in line with what is expected from the traditional interpretation of excluded volume and soft interaction. Surprisingly, the destabilizing effect of PEG-35 is not through unfavorable interaction but through a destabilizing entropic effect, which is opposite to the excluded volume prediction. Our speculation is that the modulation of the associated water structure due to crowder-induced distortion plays a crucial role in modulating the entropic component. Moreover, while a two-state model can approximate the overall thermal denaturation of HSA in the absence and presence of various crowders, the thermal denaturation profile of domain III of HSA involves a distinct intermediate state. The active-site dynamics of HSA are altered significantly in the presence of all the three differently shaped crowders used in the study. Rod-shaped dextran-40 and spherical ficoll-70 hinder the microsecond conformational dynamics of domain III of HSA in all states except the intermediate state. Mesh-like PEG-35 in addition to hindering the microsecond conformational dynamics shifts the intermediate state from 40 to 30 °C. Overall, our results provide new insight into deciphering the mechanism of crowder-induced changes in protein. Through our interpretation, we not only explain the unfavorable entropic contribution but also provide a physical basis to explain the entropy-enthalpy compensation.

Structural Dynamics of a Protein Domain Relevant to the Water-Oxidizing Complex in Photosystem II as Visualized by High-Speed Atomic Force Microscopy.

Photosystem II (PSII) is a multiprotein complex that has a function of light-driven water oxidation. The catalytic site of water oxidation is the Mn4CaO5 cluster, which is bound to the lumenal side of PSII through amino acid residues from the D1 and CP43 proteins and is further surrounded by the extrinsic proteins. In this study, we have for the first time visualized the structural dynamics of the lumenal region of a PSII core complex using high-speed atomic force microscopy (HS-AFM). The HS-AFM images of a PSII membrane fragment showed stepwise dissociation of the PsbP and PsbO extrinsic proteins. Upon subsequent destruction of the Mn4CaO5 cluster, the lumenal domain of CP43 was found to undergo a conformational fluctuation. The observed structural flexibility and conformational fluctuation of the CP43 lumenal domain are suggested to play important roles in the biogenesis of PSII and the photoassembly of the Mn4CaO5 cluster.

The Glycosphingolipid GM3 Modulates Conformational Dynamics of the Glucagon Receptor

The extracellular domain (ECD) of class B1 G-protein-coupled receptors (GPCRs) plays a central role in signal transduction and is uniquely positioned to sense both the extracellular and membrane environments. Although recent studies suggest a role for membrane lipids in the modulation of class A and class F GPCR signaling properties, little is known about the effect of lipids on class B1 receptors. In this study, we employed multiscale molecular dynamics simulations to access the dynamics of the glucagon receptor (GCGR) ECD in the presence of native-like membrane bilayers. Simulations showed that the ECD could move about a hinge region formed by residues Q122–E126 to adopt both closed and open conformations relative to the transmembrane domain. ECD movements were modulated by binding of the glycosphingolipid GM3. These large-scale fluctuations in ECD conformation may affect the ligand binding and receptor activation properties. We also identify a unique phosphatidylinositol (4,5)-bisphosphate (PIP2) interaction profile near intracellular loop (ICL) 2/TM3 at the G-protein-coupling interface, suggesting a mechanism of engaging G-proteins that may have a distinct dependence on PIP2 compared with class A GPCRs. Given the structural conservation of class B1 GPCRs, the modulatory effects of GM3 and PIP2 on GCGR may be conserved across these receptors, offering new insights into potential therapeutic targeting.

Predicting optical spectra for optoelectronic polymers using coarse-grained models and recurrent neural networks

Coarse-grained modeling of conjugated polymers has become an increasingly popular route to investigate the physics of organic optoelectronic materials. While ultraviolet (UV)-vis spectroscopy remains one of the key experimental methods for the interrogation of these materials, a rigorous bridge between simulated coarse-grained structures and spectroscopy has not been established. Here, we address this challenge by developing a method that can predict spectra of conjugated polymers directly from coarse-grained representations while avoiding repetitive procedures such as ad hoc back-mapping from coarse-grained to atomistic representations followed by spectral computation using quantum chemistry. Our approach is based on a generative deep-learning model: the long-short-term memory recurrent neural network (LSTM-RNN). The latter is suggested by the apparent similarity between natural languages and the mathematical structure of perturbative expansions of, in our case, excited-state energies perturbed by conformational fluctuations. We also use this model to explore the level of sensitivity of spectra to the coarse-grained representation back-mapping protocol. Our approach presents a tool uniquely suited for improving postsimulation analysis protocols, as well as, potentially, for including spectral data as input in the refinement of coarse-grained potentials.

The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor.

Nucleoside monophosphate kinases play crucial roles in biosynthesis and regeneration of nucleotides. These are bi-substrate enzymes that catalyze reversible transfers of a phosphoryl group between ATP and nucleoside monophosphate. These enzymes are comprised of the CORE domain, the NMP-binding domain, and the LID domain. Large conformational rearrangement of the three domains occurs during the catalytic cycle. Although many structures of CMP kinase have been determined, only limited structural information has been available on the conformational changes along the reaction pathway. We determined five crystal structures of CMP kinase of Thermus thermophilus HB8 in ligand-free form and the CMP "open", CMP "closed", ADP-CDP-Gd3+-, and CDP-bound forms at resolutions of 1.7, 2.2, 1.5, 1.6, and 1.7 Å, respectively. The ligand-free form was in an open conformation, whereas the structures of the CMP "closed", ADP-CDP-Gd3+-, and CDP-bound forms were in a closed conformation, in which the shift of the NMP-binding domain and LID domain caused closure of the substrate-binding cleft. Interestingly, the CMP "open" form was in an open conformation even with CMP bound, implying intrinsic conformational fluctuation. The structure of the ADP-CDP complex is the first structure of CMP kinase with a phosphoryl group donor and an acceptor. Upon simultaneous binding of ADP and CDP, the side chains of several residues in the LID domain moved toward the nucleotides without global open−closed conformational changes compared to those in the CMP "closed" and CDP complexes. These global and local conformational changes may be crucial for the substrate recognition and catalysis. The terminal phosphate groups of ADP and CDP had similar geometry to those of two ADP in AMP kinase, suggesting common catalytic mechanisms to other nucleoside monophosphate kinases. Our findings are expected to contribute to detailed understanding of the reaction mechanism of CMP kinase.

Insight into the Mechanism of Reduced IgG/IgE Binding Capacity in Ovalbumin as Induced by Glycation with Monose Epimers through Liquid Chromatography and High-Resolution Mass Spectrometry.

Ovalbumin (OVA) is one of the major food allergens in hen eggs. In this work, it was demonstrated that glycation with d-glucose and its epimers, including d-mannose, d-allose, d-galactose, and l-idose, could effectively attenuate the IgG/IgE binding of OVA, which was attributed to the covalent masking by sugars and to its structural changes. The glycation sites were determined, and their average degree of substitution was found using liquid chromatography coupled with high-resolution mass spectrometry. Fluctuations in OVA conformation were monitored by conventional spectrometry. Compared to those of OVA-Man and OVA-Glu, OVA-All, OVA-Gal, and OVA-Ido showed a higher glycation extent, and the alterations on their steric layouts were more drastic, suggesting that the configuration of hydroxyl groups at positions C-3, C-4, and C-5 in sugars might be important for the glycation reactivity; as such, their capabilities in binding with IgG/IgE decreased more significantly. Attempts were made to provide valuable information for in-depth understanding of the differences in biochemical functionality among epimeric sugars. These insights would be helpful for designing sweetened food products with a desirable level of safety.

Conformation, flexibility and hydration of hyaluronic acid by molecular dynamics simulations

Hyaluronic acid (HA) is a biopolymer of disaccharide with two alternate glycosidic bonds, β(1,3) and β(1,4). A molecular dynamics study presented here unveiled conformational variability in association with the flexibility of the glycosidic linkers, which depends on the number of disaccharide units. HA chain maintains a rigid rod-like conformation with short chain lengths. Crossover from a rod-like to a random−coil conformation is observed with increasing the chain length. The conformation with the β(1,4) linkage is more flexible than that with the β(1,3) linkage. Variation of the radius of gyration and conformational fluctuation showed that the β(1,4) linkers along with the HA chain length enhance the overall conformational flexibility and therefore elastic response of the polymer chain. Besides the inter-saccharide hydrogen bonding, Na+ binds preferably at the β(1,4) site. The hydration number of HA increases as an increase in the chain length. The hydration per disaccharide unit remains constant with the chain length.