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Sandro Mecozzi

Publications and source records attributed to Sandro Mecozzi.

7 recordsLinked to original sources
PubMed2006

Binding properties of aromatic carbon-bound fluorine.

A systematic computational analysis of the ability of aromatic carbon-bound fluorine to participate in hydrogen bonding and electrostatic interactions has been completed. The interaction energies between the most common fluoroaromatics used in medicinal chemistry and both water, the prototypical hydrogen bond donor, and several cations have been calculated at different levels of theory (HF, MP2, DFT). Our results show that aromatic fluorine can participate in significant hydrogen bonds and can also interact with charged molecules.

Carbon↗
PubMed2006

Stabilizing and destabilizing effects of phenylalanine --> F5-phenylalanine mutations on the folding of a small protein.

We report a systematic evaluation of phenylalanine-to-pentafluorophenylalanine (Phe --> F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F5-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than aryl-aryl interactions and because perfluoroaryl units are more hydrophobic than are analogous aryl units. One mutant, Phe-10 --> F5-Phe, provides enhanced tertiary structural stability relative to the native sequence. The other six mutants analyzed caused a decrease in stability.

Amino Acid Sequence↗
PubMed2006

Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques.

In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology.

Algorithms↗
PubMed2005

Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity.

Aptamers are nucleic acids developed by in vitro evolution techniques that bind to specific ligands with high affinity and selectivity. Despite such high affinity and selectivity, however, in vitro evolution does not necessarily reveal the minimum structure of the nucleic acid required for selective ligand binding. Here, we show that a 35mer RNA aptamer for the cofactor flavin mononucleotide (FMN) identified by in vitro evolution can be computationally evolved to a mere 14mer structure containing the original binding pocket and eight scaffolding nucleotides while maintaining its ability to bind in vitro selectively to FMN. Using experimental and computational methodologies, we found that the 14mer binds with higher affinity to FMN (K(D) approximately 4 microM) than to flavin adenine dinucleotide (K(D) approximately 12 microM) or to riboflavin (K(D) approximately 13 microM),despite the negative charge of FMN. Different hydrogen-bond strengths resulting from differing ring-system electron densities associated with the aliphatic-chain charges appear to contribute to the selectivity observed for the binding of the 14mer to FMN and riboflavin. Our results suggest that high affinity and selectivity in ligand binding is not restricted to large RNAs, but can also be a property of extraordinarily short RNAs.

Aptamers, Nucleotide↗
PubMed2005

Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline.

RNA plays critical roles in numerous biological processes and constitutes valuable therapeutic targets. RNA is significant not only for its roles in transmitting the genetic code but also for its enzymatic functions in ribozymes and in peptide bond formation in ribosomes. Recent studies have shown that RNAs containing as few as 22 nucleotides can be key elements in cellular functions. This suggests the possibility of using short RNAs as regulatory elements. Here, we show that ligand recognition and selectivity by RNA molecules can occur with only the presence of a binding pocket and as few as six additional scaffolding nucleotides holding the binding pocket in place. A 13-mer RNA truncation of a 33-mer aptamer for theophylline preserves the ability to bind to theophylline and to discriminate against the structurally similar compound caffeine. The truncated aptamer retains nearly all of the same structural elements in its binding site as those present in the original aptamer. This is the first demonstration of selective ligand binding by a 13-mer RNA.

Base Sequence↗
PubMed2004

Aqueous solubilization of highly fluorinated molecules by semifluorinated surfactants.

The physical and chemical properties of organic compounds are deeply affected by the introduction of fluorinated substituents. Perfluorinated and highly fluorinated organic molecules are both hydrophobic and lipophobic. This makes the recognition and the binding of fluorinated molecules extremely difficult to achieve through classical elements of molecular recognition. Here we show that semifluorinated water-soluble block copolymers can generate micellar structures having a fluorous phase-based inner core in aqueous solution. Furthermore, we show that these micelles can be used to encapsulate and bind highly fluorinated molecules through association in the internal fluorous phase (fluorophobic effect). We report that semifluorinated block copolymers can be used for the aqueous solubilization of the widely diffused gaseous anesthetic sevoflurane, thereby suggesting the possibility of the intravenous delivery of this commonly used anesthetic.

Anesthesia, Inhalation↗