Francisco Rodríguez-Ropero

Systematic coarse-graining methods for soft matter simulations - a review

Multiscale modelling of soft matter is an emerging field that has made rapid progress in the past decade. Several methods for systematic coarse-graining of molecular liquids and soft matter systems have been proposed in recent years. Herein, we review these methods and discuss a selected number of applications as well as limitations of the models and remaining challenges in developing representative and transferable pair potentials.

Directed evolution of a thermophilic endoglucanase (Cel5A) into highly active Cel5A variants with an expanded temperature profile.

Cel5A is a highly active endoglucanase from Thermoanaerobacter tengcongensis MB4, displaying an optimal temperature range between 75 and 80°C. After three rounds of error-prone PCR and screening of 4700 mutants, five variants of Cel5A with improved activities were identified by Congo Red based screening method. Compared with the wild type, the best variants 3F6 and C3-13 display 135±6% and 193±8% of the wild type specific activity for the substrate carboxymethyl cellulose (CMC), besides improvements in the relative expression level in Escherichia coli system. Remarkable are especially the improvements in activities at reduced temperatures (50% of maximum activity at 50°C and about 45°C respectively, while 65°C for the wild type). Molecular Dynamics simulations performed on the 3F6 and C3-13 variants show a decreased number of intra-Cel5A hydrogen bonds compared to the wild type, implying a more flexible protein skeleton which correlates well to the higher catalytic activity at lower temperatures. To investigate functions of each individual amino acid position site-directed (saturation) mutagenesis were generated and screened. Amino acid positions Val249 and Ile321 were found to be crucial for improving activity and residue Ile13 (encoded by rare codon AUA) yields an improved expression level in E. coli.

Direct Osmolyte-Macromolecule Interactions Confer Entropic Stability to Folded States

Protective osmolytes are chemical compounds that shift the protein folding/unfolding equilibrium toward the folded state under osmotic stresses. The most widely considered protection mechanism assumes that osmolytes are depleted from the proteins first solvation shell, leading to entropic stabilization of the folded state. However, recent theoretical and experimental studies suggest that protective osmolytes may directly interact with the macromolecule. As an exemplary and experimentally well-characterized system, we herein discuss poly(N-isopropylacrylamide) (PNiPAM) in water whose folding/unfolding equilibrium shifts toward the folded state in the presence of urea. On the basis of molecular dynamics simulations of this specific system, we propose a new microscopic mechanism that explains how direct osmolyte-macromolecule interactions confer stability to folded states. We show that urea molecules preferentially accumulate in the first solvation shell of PNiPAM driven by attractive van der Waals dispersion forces with the hydrophobic isopropyl groups, leading to the formation of low entropy urea clouds. These clouds provide an entropic driving force for folding, resulting in preferential urea binding to the folded state and a decrease of the lower folding temperature in agreement with experiment. The simulations further indicate that thermodynamic nonideality of the bulk solvent opposes this driving force and may lead to denaturation, as illustrated by simulations of PNiPAM in aqueous solutions with dimethylurea. The proposed mechanism provides a new angle on relations between the properties of protecting and denaturing osmolytes, salting-in or salting-out effects, and solvent nonidealities.

A rigid, chiral, dendronized polymer with a thermally stable, right-handed helical conformation

First- and second-generation dendronized polymethacrylates PG1 and PG2 carrying chiral 4-aminoproline-based dendrons were obtained on the half-gram scale in high molar masses (PG1: M(n)=5 x 10(6) g mol(-1), PG2: M(n)=1x10(6) g mol(-1)) by spontaneous (radical) polymerization of the corresponding vinyl macromonomers. NMR spectroscopic studies on PG2 together with its unprecedented high glass transition temperature (T(g)>200 degrees C, decomp) and structural parameters provided by atomistic MD simulations show this polymer to be rather rigid. Optical rotation and CD measurements revealed that PG2 adopts a helical conformation that remains unchanged over wide ranges of temperature and solvent polarity. It is also retained when the polymer is deprotected (and thus positively charged, de-PG2) at its terminal amino groups, by which the mass and steric demand of the dendrons is reduced by roughly 50 %. Molecular dynamics simulations on models of PG2 reveal its helical conformation to be right-handed, irrespective of backbone tacticity, and initial results also indicate that de-PG2 retains the right-handedness.

Mechanism of Polymer Collapse in Miscible Good Solvents

We propose a physical mechanism for co-nonsolvency of a stimulus-responsive polymer in water/methanol mixed solution based on results obtained with molecular simulations. Even though the phenomenon is well known, the mechanism behind co-nonsolvency is still under debate. Herein, we study co-nonsolvency of poly(N-isopropylacrylamide) (PNiPAM) in methanol aqueous solutions, the most widely studied and experimentally well-characterized system. Our results show that at low alcohol content of the solution methanol preferentially binds to the PNiPAM globule and drives polymer collapse. The energetics of electrostatic, hydrogen bonding, or bridging-type interactions with the globule is found to play no role. Instead, preferential methanol binding results in a significant increase in the globules configurational entropy, stabilizing methanol-enriched globular structures over wet globular structures in neat water. This mechanism drives the reduction of the lower critical solution temperature with increasing methanol content in the co-nonsolvency regime and eventually leads to polymer collapse. The globule-to-coil re-entrance at high methanol concentrations is instead driven by changes in solvent-excluded volume of the coil and globular states imparted by a decrease in solvent density with increasing methanol content of the solution: with increasing proportion of larger solvent particles (methanol), the entropic (cavity formation) cost of redistributing solvent molecules upon polymer re-entrance becomes smaller. This effect provides a natural explanation for the experimentally observed dependence of the re-entrance transition on chain molecular weight.

Ab initio calculations on π‐stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters

π‐Stacked complexes formed by two, three, and four thiophene rings have been investigated using abinitio quantum mechanical calculations. The relative orientation between the rings was investigated for each complex by exploring the corresponding potential energy surface at the MP2/6‐31+G(d,p) level, the inter‐ring distance, and the degree of tilting being examined in each case. Interaction energies were calculated at the MP2, MP3, MP4, and CCSD, levels of theory. Negligible or even slightly positive n‐body effects have been predicted for the stacked thiophene arrangements studied in this work. This is consequence of the cancellation of favorable induction contribution by the destabilizing dispersion component. On the other hand analysis of the optimized geometries obtained for the trimer and tetramer revealed that the orientation of the rings presents a preferred degree of periodicity. Finally, we found that the lowest transition energy decreases when the size of the complex increases, this feature being attributed to desestabilization of the HOMO and stabilization of the LUMO that occur simultaneously.

Hexaazatriphenylene (HAT) versus tri-HAT: The Bigger the Better?

A new hexaazatriphenylene (HAT) derivative formed by the fusion of three HAT units has been prepared and its electronic and molecular structures have been fully characterized by optical and vibrational Raman spectroscopy, electrochemistry, solid-state UV and inverse photoemission spectroscopy (UPS and IPES), and by quantum-chemical calculations. A comparative HAT versus tri-HAT study was performed. The fusion of three HAT molecules causes modifications in the optical and electrochemical properties consistent with enhanced π-electron delocalization attained in a bigger planar core. Such combined experimental and theoretical studies are useful to balance chemical design with supramolecular engineering directed to find enhanced characteristics for new organic semiconductor applications.

Nanocompartments with a pH release system based on an engineered OmpF channel protein

Synthosomes are a subclass of Polymersomes with a block copolymer membrane (PMOXA–PDMS–PMOXA) and a modified embedded transmembrane channel protein which acts as a selective gate. A synthosome based pH release system functioning increasing the pH from 5 to 7 was developed by introducing six histidine mutations to the OmpF constriction site (OmpF 6His). The pH-dependent compound release (acridine orange, positively charged between 5 ≤ pH ≤ 7) has been found to be tuned by the constriction site electrostatics and size by local structural modifications.

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular beta-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acids (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of beta-helical motifs indicates that the stability of such excised building blocks as well as the nanoassemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the beta-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e., when the rigidity introduced by the strain of the ring decreases.

Comparison of Different TMAO Force Fields and Their Impact on the Folding Equilibrium of a Hydrophobic Polymer

Trimethylamine N-oxide (TMAO) is a protective osmolyte able to preserve protein folded states in the presence of denaturants like urea and under extreme thermodynamic conditions of high pressure and temperature. The current understanding posits that TMAO exerts its stabilizing effect on proteins by preferential exclusion from the macromolecular hydration shell. Additionally, TMAO is also known to favor the folding of hydrophobic polymers. In this latter case, theoretical and experimental studies support a scenario in which TMAO directly interacts with the macromolecule. While atomistic simulations may potentially elucidate the precise TMAO-induced stabilization mechanism, the comparative accuracy of the different TMAO force field models available in the literature remains elusive. Herein, we compare four different TMAO models, study their structural hydration properties, and validate the models against experimental osmotic coefficients and air-water surface tension data over a broad range of TMAO concentrations. The models were furthermore applied to study the effect of TMAO on the folding equilibrium of a generic hydrophobic polymer in aqueous solution. Interestingly, we find that TMAO increasingly stabilizes the compact globular state of the polymer up to approximately 1 M TMAO, while in turn destabilizing it with further increase in TMAO concentration. Hence, TMAO acts as a stabilizing osmolyte or as a denaturant depending on the TMAO concentration of the solution. TMAO-induced stabilization up to 1 M is accompanied by positive preferential TMAO binding and with an increase in the chain configurational entropy, which is reduced at concentrations higher than 1 M. These results are qualitatively independent of the TMAO force field.