Basic ingredients of free energy calculations: A review

Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and their utility when applied in practice to biomolecular systems. A free energy calculation is comprised of three basic components: (i) a suitable model or Hamiltonian, (ii) a sampling protocol with which one can generate a representative ensemble of molecular configurations, and (iii) an estimator of the free energy difference itself. Alternative sampling protocols can be distinguished according to whether one or more states are to be sampled. In cases where only a single state is considered, six alternative techniques could be distinguished: (i) changing the dynamics, (ii) deforming the energy surface, (iii) extending the dimensionality, (iv) perturbing the forces, (v) reducing the number of degrees of freedom, and (vi) multi‐copy approaches. In cases where multiple states are to be sampled, the three primary techniques are staging, importance sampling, and adiabatic decoupling. Estimators of the free energy can be classified as global methods that either count the number of times a given state is sampled or use energy differences. Or, they can be classified as local methods that either make use of the force or are based on transition probabilities. Finally, this overview of the available techniques and how they can be best used in a practical context is aimed at helping the reader choose the most appropriate combination of approaches for the biomolecular system, Hamiltonian and free energy difference of interest. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

On the role of the colloidal stability of mesoporous silica nanoparticles as gene delivery vectors

Mesoporous silica nanoparticles have been synthesized and functionalized with four different types of molecules containing amino groups, i.e., with primary amines only, with quaternary amines, with quaternized cyclic amines, or with polyethylenimine (PEI), which is formed by primary, secondary, and tertiary amines. These nanoparticles were then incubated with reporter plasmids and the ability of the resulting complexes to transfect human cells was studied. Only nanoparticles functionalized with PEI were efficient for transfection. The agglomeration behavior and the electrokinetic potential of the nanoparticle–plasmid complexes have been studied, as well as their cell internalization behavior using a fluorescent-labeled plasmid that allows its monitorization by confocal microscopy. The results indicate that the efficiency of PEI-functionalized nanoparticles for transfection resides to some extent in the different characteristics imparted to the nanoparticles regarding agglomeration and surface charge behavior.     

Characterization of three saponins from a fraction using 1D DOSY as a solvent signal suppression tool. Agabrittonosides E–F. Furostane Saponins from Agave brittoniana Trel. spp. Brachypus

A careful NMR analysis, especially by 1D TOCSY and 1D ROESY, of a refined saponin fraction allowed us to determine the structure of three saponins from a polar extract of Agave brittoniana Trel. spp. Brachypus leaves. The use of 1D DOSY for the suppression of the solvent signal was useful to obtain the chemical shifts of anomeric signals. A full assignment of the ¹H and ¹³C spectral data for the new saponins, agabrittonosides E–F (1–2) and the well‐known Karatavioside C (3) and their methoxyl derivatives, is reported. The structures were established using a combination of 1D and 2D (¹H, ¹H‐COSY, TOCSY, ROESY, g‐HSQC, g‐HMBC and g‐HSQC‐TOCSY) NMR techniques and ESI–MS. In addition, the methoxylation of these furostane saponins in the presence of MeOH was studied. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis of polymers containing regularly distributed tetrathia‐[7]‐elicene units along the backbone

A tetrathia‐[7]‐helicene bearing in the 2 and 13 positions cyanovinyl groups was used as comonomer in the Michael‐type polyaddition reaction with N,N′‐bis(β‐mercaptoethyl)piperazine. This led to a new polymer bearing tetrathia‐[7]‐helicene units regularly distributed along the polymer backbone, which may be regarded as the first example of a new family of potentially useful nonlinear optical materials. All products were structurally characterized by ¹H and ¹³C NMR spectroscopy. Differential scanning calorimetry characterizations revealed the presence, in both monomeric and polymeric helicenes, of glass‐transition like temperatures, associated to some conformational variation of the helicene units. The optical properties, the film formation and the morphology of the polymer‐containing tetratia‐[7]‐helicenes were also investigated. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Measure homology and singular homology are isometrically isomorphic

Measure homology is a variation of singular homology designed by Thurston in his discussion of simplicial volume. Zastrow and Hansen showed independently that singular homology (with real coefficients) and measure homology coincide algebraically on the category of CW-complexes. It is the aim of this paper to prove that this isomorphism is isometric with respect to the ℓ¹-seminorm on singular homology and the seminorm on measure homology induced by the total variation. This, in particular, implies that one can calculate the simplicial volume via measure homology – as already claimed by Thurston. For example, measure homology can be used to prove Gromov's proportionality principle of simplicial volume.     

Systematic Mössbauer study of YBa2Cu3−x Fe x Oδ and PrBa2Cu3−x Fe x Oδ as a function of temperature

We study the similitudes and differences between YBa₂Cu_3?x Fe _x O_δ and PrBa₂Cu_3?x Fe _x O_δ systems, using Mössbauer spectroscopy. Both systems, withz=0.04, were studied at several temperatures. The spectra of PrBa₂Cu_3?x Fe _x O_δ showed four asymmetric quadrupole doublets with apparently different line widths, which were fitted with four symmetric superimposed quadrupole doublets with the same line width, but assuming a small (～4–6 kOe) residual magnetic field in the Fe sites, which are mainly the Cu(1) sites of the 1–2–3 structure. On the other hand, the PrBa₂Cu_3?x Fe _x O_δ spectra showed only three asymmetric quadrupole doublets which can be fitted with three superimposed symmetric doublets and a residual magnetic field. In this case, the Fe atoms also occupy the Cu(1) sites of the 1–2–3 structure. The temperature variations of the Mössbauer spectra and their parameters seem to indicate that, in the Pr-system, a structural change takes place between 12 K and 40 K.     

Literatur

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Contact between the β1 and β2 Segments of α‐Synuclein that Inhibits Amyloid Formation

Conversion of the intrinsically disordered protein α‐synuclein (α‐syn) into amyloid aggregates is a key process in Parkinson’s disease. The sequence region 35–59 contains β‐strand segments β1 and β2 of α‐syn amyloid fibril models and most disease‐related mutations. β1 and β2 frequently engage in transient interactions in monomeric α‐syn. The consequences of β1–β2 contacts are evaluated by disulfide engineering, biophysical techniques, and cell viability assays. The double‐cysteine mutant α‐synCC, with a disulfide linking β1 and β2, is aggregation‐incompetent and inhibits aggregation and toxicity of wild‐type α‐syn. We show that α‐syn delays the aggregation of amyloid‐β peptide and islet amyloid polypeptide involved in Alzheimer’s disease and type 2 diabetes, an effect enhanced in the α‐synCC mutant. Tertiary interactions in the β1–β2 region of α‐syn interfere with the nucleation of amyloid formation, suggesting promotion of such interactions as a potential therapeutic approach.     

Potential of prodendronic polyamines with modulated segmental charge density as novel coating for fast and efficient analysis of peptides and basic proteins by CE and CE‐MS

In this work, the suitability of a new polymer family has been investigated as capillary coatings for the analysis of peptides and basic proteins by CE. This polymer family has been designed to minimize or completely prevent protein–capillary wall interactions and to modify the EOF. These coating materials are linear polymeric chains bearing as side cationizable moiety a dentronic triamine derived from N,N,N’,N’‐tetraethyldiethylenetriamine (TEDETA), which is linked to the backbone through a spacer (unit labeled as TEDETAMA). Four different polymers have been prepared and evaluated: a homopolymer which comprised only of those cationizable repetitive units of TEDETAMA, and three copolymers that randomly incorporate TEDETAMA together with neutral hydrosoluble units of N‐(2‐hydroxypropyl) methacrylamide (HPMA) at different molar percentages (25:75, 50:50 and 75:25). It has been demonstrated that the composition of the copolymers influences the EOF and therefore the separation of the investigated biopolymers. Among the novel polymers studied, poly‐(TEDETAMA‐co‐HPMA) 50:50 copolymer was successfully applied as coating material of the inner capillary surface in CE‐UV and CE‐MS, providing EOF reversing together with fast and efficient baseline separation of peptides and basic proteins. Finally, the feasibility of the polymer‐coated capillary was shown through the analysis of lysozyme in a cheese sample.