Iodine Oxidation of S-Trityl- and S-Acetamidomethyl-cysteine-peptides Containing Tryptophan: Conditions Leading to the Formation of Tryptophan-2-thioethers

Cystine peptides are conveniently prepared from S-acetamidomethyl- or S-trityl-protected cysteine derivatives by direct oxidation with iodine. Since the reaction proceeds through the formation of sulfenyl iodides, these highly reactive groups may substitute the indole ring of tryptophan residues, resulting in the formation of 2-thioethers. During the synthesis of the peptide hormone somatostatin, we investigated this possible side reaction. By-products of the tryptophan-2-thioether type can be produced under conditions which lead to a marked retardation of the disulfide bond formation. The largest amount of these compounds were formed when the oxidation was carried out in 90% aqueous trifluoroethanol. In model peptides in which tryptophan and cysteine residues were separated by 1 to 4 glycine residues, the ring size of the resulting thioether exerted a strong influence on the yield: in peptides with 1 and 2 glycines, only dimeric disulfides were formed. Incorporation of 3 and 4 glycine residues gave thioethers in yields of about 40% and 70% respectively. Conversely, under normal conditions of iodine oxidation, when disulfides are rapidly formed from the S-acetamidomethyl- or S-tritylcysteine residues, tryptophan-2-thioethers are produced only in insignificant amounts or not at all.     

Localized and Collective Motions in HET‐s(218‐289) Fibrils from Combined NMR Relaxation and MD Simulation

Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET‐s(218‐289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale‐specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross‐correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer‐range correlated motion. Similar trends on ns‐ and μs‐timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

On developing coarse-grained models for biomolecular simulation: a review

So-called coarse-grained models are a popular type of model for accessing long time scales in simulations of biomolecular processes. Such models are coarse-grained with respect to atomic models. But any modelling of processes or substances involves coarse-graining, i.e. the elimination of non-essential degrees of freedom and interactions from a more fine-grained level of modelling. The basic ingredients of developing coarse-grained models based on the properties of fine-grained models are reviewed, together with the conditions that must be satisfied in order to preserve the correct physical mechanisms in the coarse-graining process. This overview should help the reader to determine how realistic a coarse-grained model of a biomolecular system is, i.e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest.     

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution

The performance of enveloping distribution sampling (EDS) simulations to estimate free enthalpy differences associated with seven alchemical transformations of A-T into G-C base pairs at the netropsin binding site in the minor groove of a 13-base pair DNA duplex in aqueous solution is evaluated. It is demonstrated that sufficient sampling can be achieved with a two-state EDS Hamiltonian even for large perturbations such as the simultaneous transformation of up to three A-T into three G-C base pairs. The two parameters required to define the EDS reference state Hamiltonian are obtained automatically using a modified version of a scheme presented in earlier work. The sensitivity of the configurational sampling to a variation of these parameters is investigated in detail. Although for relatively small perturbations, that is, one base pair, the free enthalpy estimate depends only weakly on the EDS parameters, the sensitivity is stronger for the largest perturbation. Yet, EDS offers various convenient measures to evaluate the degree of sampling and thus the reliability of the free enthalpy estimate and appears to be an efficient alternative to the conventional thermodynamic integration methodology to obtain free energy differences for molecular systems.     

Thyrocalcitonin. II. Structure of alpha-thyrocalcitonin

The highly active peptide hormones isolated from pig thyroids – i.e. α-thyrocalcitonin and its sulfoxide, containing 32 amino acid residues – were subjected to sequence studies using chemical and enzymatic methods. On the basis of these studies the following structure was derived for α-thyrocalcitonin: In the α-thyrocalcitonin sulfoxide (designated formerly as β-thyrocalcitonin) the methionine residue is replaced by methionine sulfoxide.     

Total synthesis of human insulin under directed formation of the disulfide bonds

A preliminary account is given of a total synthesis of human insulin involving directed formation of the three disulfide bonds at different stages of the fragment-condensation approach. The synthesis was facilitated by the application of two new methods for the selective removal of protecting groups. In the first, two S-Trt-protected cysteine residues are converted to the disulfide without affecting S-Acm-protected cysteine residues. The second new method consists in a very mild, pH-controlled, acidolysis of N(α)-Trt, leaving intact N(α)-Bpoc and other acid-labile protecting groups. The last step of the synthesis was the formation of the disulfide bridge between the Acm-protected cysteine residues A7 and B7 by iodine. Extensive counter-current distribution yielded the synthetic hormone in pure form. It was compared and found to be identical with natural human insulin. Identification was achieved by means of thinlayer chromatography and electrophoretic procedures, as well as by comparing the pattern of break-down by enzymes (finger-printing). The natural and synthetic hormones were crystallized under identical conditions. The synthetic human insulin was found to possess full biological activity in an in vitro system.     

Human calcitonin. Structure of calcitonin M and D

Human calcitonin M and its dimer calcitonin D, two highly active peptides isolated from C cell tumours, were subjected to sequence studies using chemical and enzymatic methods. For calcitonin M, containing 32 amino acid residues, the following structure was derived: Though the disulphide bridge between position 1 and 7, and the C-terminal proline amide of human calcitonin M are the same as in porcine α-thyrocalcitonin, many amino acid residues - 18 in all - are different throughout the molecule. Arginine and tryptophan are absent; on the other hand, lysine and isoleucine are to be found at position 18 and 27 respectively. Methionine changes its place from position 25 to 8 adjacent to the disulphide bridge. Experimental evidence indicates that calcitonin D represents the antiparallel dimeer of calcitonin M.