Dynamics and Conformations of a Full-Length CRESS-DNA Replicase.

Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses encode for a Replicase (Rep) that is essential for viral replication. Rep is a helicase with three domains: an endonuclease, an oligomeric, and an ATPase domain (ED, OD, and AD). Our recent cryo-EM structure of the porcine circovirus 2 (PCV2) Rep provided the first structure of a CRESS-DNA Rep. The structure visualized the ED to be highly mobile, Rep to form a homo-hexamer, bound ssDNA and nucleotides, and the AD to adopt a staircase arrangement around the ssDNA. We proposed a hand-over-hand mechanism by the ADs for ssDNA translocation. The hand-over-hand mechanism requires extensive movement of the AD. Here, we scrutinize this mechanism using all-atom Molecular Dynamics (MD) simulation of Rep in three states: (1) Rep bound to ssDNA and ADP, (2) Rep bound to ssDNA, and (3) Rep by itself. Each of the 700 nsec simulations converges within 200 nsec and provides important insight into the dynamics of Rep, the dynamics of Rep in the presence of these biomolecules, and the importance of ssDNA and ADP in driving the AD to adopt the staircase arrangement around the ssDNA. To the best of our knowledge, this is the first example of an all-atom MD simulation of a CRESS-DNA Rep. This study sets the basis of further MD studies aimed at obtaining a chemical understanding of how Rep uses nucleotide binding and hydrolysis to translocate ssDNA.

Preparation of Thermoplastic Cellulose Esters in [mTBNH][OAC] Ionic Liquid by Transesterification Reaction.

The transesterification of cellulose with vinyl esters in ionic liquid media is suggested as a prospective environmentally friendly alternative to conventional esterification. In this study, various long-chain cellulose esters (laurate, myristate, palmitate, and stearate) with a degree of substitution (DS) up to 1.8 have been synthesized in novel distillable ionic liquid, [mTBNH][OAC]. This IL has high dissolving power towards cellulose, which can improve homogeneous transesterification. Additionally, [mTBNH][OAC] has durability towards recycling and can be regenerated and re-used again for the next cycles of esterification. DMSO is used as a co-solvent because of its ability to speed up mass transport due to lower solvent viscosity. The optimization of the reaction parameters, such as co-solvent content, temperature (20-80 °C), reaction time (1-5 h), and a molar ratio of reactants (1-5 eq. AGU) is reported. It was found that within studied reaction conditions, DS increases with increasing reaction time, temperature, and added vinyl esters. Structure analysis using FTIR, 1H, and 13C NMR after acylation revealed the introduction of the alkyl chains into cellulose for all studied samples. The results also suggested that the substitution order of the OH group is C7-O6 > C7-O2 > C7-O3. Unique, complex thermal and rheological investigation of the cellulose esters shows the growth of an amorphous phase upon the degree of substitution. At the same time, the homogeneous substitution of cellulose with acyl chains increases the melt viscosity of a material. Internal plasticization in cellulose esters was found to be the mechanism for the melt processing of the material. Long-chain cellulose esters show the potential to replace commonly used externally plasticized cellulose derivatives.

Tensile and Surface Wettability Properties of the Solvent Cast Cellulose Fatty Acid Ester Films.

Thermoplastic cellulose esters are promising materials for bioplastic packaging. For that usage, it is important to understand their mechanical and surface wettability properties. In this study, a series of cellulose esters are prepared, such as laurate, myristate, palmitate, and stearate. The aim of the study is to investigate the tensile and surface wettability properties of the synthesized cellulose fatty acid esters to understand their suitability as a bioplastic packaging material. Cellulose fatty acid esters are first synthesized from microcrystalline cellulose (MCC), then dissolved in pyridine solution, and after the solvent cast into thin films. The cellulose fatty acid ester acylation process is characterized by the FTIR method. Cellulose esters hydrophobicity is evaluated with contact angle measurements. The mechanical properties of the films are tested with the tensile test. For all the synthesized films, FTIR provides clear evidence of acylation by showing the presence of characteristic peaks. Films' mechanical properties are comparable to those of generally used plastics such as LDPE and HDPE. Furthermore, it appears that with an increase in the side-chain length, the water barrier properties showed improvement. These results show that they could potentially be suitable materials for films and packaging materials.

Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly.

Spatiotemporal regulation of viral capsid assembly ensures the selection of the viral genome for encapsidation. The porcine circovirus 2 is the smallest autonomously replicating pathogenic virus, yet how PCV2 capsid assembly is regulated to occur within the nucleus remains unknown. We report that pure PCV2 capsid proteins, in the absence of nucleic acids, require acidic conditions to assemble into empty capsids in vitro. By employing constant pH replica exchange molecular dynamics, we unveil the atomistic mechanism of pH-dependency for capsid assembly. The results show that an appropriate protonation configuration for a cluster of acidic amino acids is necessary to appropriately position the GH-loop for driving the capsid assembly. We demonstrate that assembly is prohibited at neutral pH because deprotonation of these residues results in their electrostatic repulsion, shifting the GH-loop to a position incompatible with capsid assembly. We propose that encapsulation of nucleic acids overcomes this repulsion to suitably position the GH-loop. Our findings provide the first atomic resolution mechanism of capsid assembly regulation. These findings are useful for the development of therapeutics that inhibit PCV2 self-assembly.

Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus.

Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses infect members from all three domains of life (Archaea, Prokarya, and Eukarya). The replicase (Rep) from these viruses is responsible for initiating rolling circle replication (RCR) of their genomes. Rep is a multifunctional enzyme responsible for nicking and ligating ssDNA and unwinding double-stranded DNA (dsDNA). We report the structure of porcine circovirus 2 (PCV2) Rep bound to ADP and single-stranded DNA (ssDNA), and Rep bound to ADP and double-stranded DNA (dsDNA). The structures demonstrate Rep to be a member of the superfamily 3 (SF3) of ATPases Associated with diverse cellular Activities (AAA+) superfamily clade 4. At the Rep N terminus is an endonuclease domain (ED) that is responsible for ssDNA nicking and ligation, in the center of Rep is an oligomerization domain (OD) responsible for hexamerization, and at the C terminus is an ATPase domain (AD) responsible for ssDNA/dsDNA interaction and translocation. The Rep AD binds to DNA such that the ED faces the replication fork. The six AD spiral around the DNA to interact with the backbone phosphates from four consecutive nucleotides. Three of the six AD are able to sense the backbone phosphates from the second strand of dsDNA. Heterogeneous classification of the data demonstrates the ED and AD to be mobile. Furthermore, we demonstrate that Rep exhibits basal nucleoside triphosphatase (NTPase) activity. IMPORTANCE CRESS-DNA viruses encompass a significant portion of the biosphere's virome. However, little is known about the structure of Rep responsible for initiating the RCR of CRESS-DNA viruses. We use cryo-electron microscopy (cryo-EM) to determine the structure of PCV2 Rep in complex with ADP and ss/dsDNA. Our structures demonstrate CRESS-DNA Reps to be SF3 members (clade 4) of the AAA+ superfamily. The structures further provide the mechanism by which CRESS-DNA virus Reps recognize DNA and translocate DNA for genome replication. Our structures also demonstrate the ED and AD of PCV2 Rep to be highly mobile. We propose the mobile nature of these domains to be necessary for proper functioning of Reps. We further demonstrate that Reps exhibit basal NTPase activity. Our studies also provide initial insight into the mechanism of RCR.

A Structural Perspective of Reps from CRESS-DNA Viruses and Their Bacterial Plasmid Homologues.

Rolling circle replication (RCR) is ubiquitously used by cellular and viral systems for genome and plasmid replication. While the molecular mechanism of RCR has been described, the structural mechanism is desperately lacking. Circular-rep encoded single stranded DNA (CRESS-DNA) viruses employ a viral encoded replicase (Rep) to initiate RCR. The recently identified prokaryotic homologues of Reps may also be responsible for initiating RCR. Reps are composed of an endonuclease, oligomerization, and ATPase domain. Recent structural studies have provided structures for all these domains such that an overall mechanism of RCR initiation can begin to be synthesized. However, structures of Rep in complex with its various DNA substrates and/or ligands are lacking. Here we provide a 3D bioinformatic review of the current structural information available for Reps. We combine an excess of 1590 sequences with experimental and predicted structural data from 22 CRESS-DNA groups to identify similarities and differences between Reps that lead to potentially important functional sites. Experimental studies of these sites may shed light on how Reps execute their functions. Furthermore, we identify Rep-substrate or Rep-ligand structures that are urgently needed to better understand the structural mechanism of RCR.

All-Atom Molecular Dynamics Simulations of Whole Viruses.

Classical molecular dynamics modeling of whole viruses or their capsids in explicit water is discussed, and known examples from the literature are analyzed. Only works on all-atom modeling in explicit water are included. Physical chemistry of the whole system is the focus, which includes the structure and dynamics of the biomolecules as well as water and ion behavior in and around the virus particle. It was demonstrated that in most investigations molecular phenomena that currently can not be studied experimentally are successfully reproduced and explained by the simulations. These include, for example, transport and distribution of ions inside viruses that ultimately connected to their stability, the hydrodynamic pressure in the capsid related to viruses' elastic properties, the role of metal ions in virus swelling, and others. Current and future tendencies in the development of all-atom virus simulations are outlined.

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.

Permeability of water and oleic acid in composite films of phase separated polypropylene and cellulose stearate blends.

Cellulose esters with long carbon side chains (e.g. stearate) were produced via a homogenous reaction in ionic liquids. The degree of substitution was calculated to approximately 2. The melt rheology was studied for the pure cellulose esters but also combinations of the esters and polypropylene to study the processability of a blended composite material. It was shown that the compatibility between the two components was weak, which resulted in a phase-separated composite material. The morphology and permeability of water and oleic acid of the composite films were studied and it was shown that the water permeability decreased upon addition of the cellulose ester to the polymer. The permeability of oleic acid was however unchanged, which is most probable a result of high solubility in the cellulose ester rich domains of the composites. Also, the following hypothesis is stated: cellulose stearate influence the polypropylene crystallization process by decreasing the size of spherulites.