Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases

Most proteins assume different conformations to perform their cellular functions. This conformational dynamics is physiologically regulated by binding events and post-translational modifications, but can also be affected by pathogenic mutations. Atomistic molecular dynamics simulations complemented by enhanced sampling approaches are increasingly used to probe the effect of mutations on the conformational dynamics and on the underlying conformational free energy landscape of proteins. In this short review we discuss recent successful examples of simulations used to understand the molecular mechanism underlying the deregulation of physiological conformational dynamics due to non-synonymous single point mutations. Our examples are mostly drawn from the protein kinase family

FREE ENERGIES IN BIOMOLECULAR SIMULATIONS: FROM PROTEIN-PROTEIN INTERACTIONS TO UNFOLDING INHIBITION

Part I - Microtubules are polymeric structures formed by the self association of tubulin dimers. They are extremely dynamical structures, that can undergo phases of growing and shrinking, playing a key role during cells proliferation process. Due to its importance for mitosis, tubulin is the target of many anticancer drugs currently in use or under clinical trial. The success of these molecules, however, is limited by the onset of resistant tumor cells during the treatment, so new resistance-proof compounds need to be developed. We analyze the protein-protein interactions allowing microtubules formation using molecular dynamics and free energy calculations. We were able to identify the most important amino acids for tubulin-tubulin binding and thus to design peptides, corresponding to tubulin subsequences. These peptides, able to interfere with microtubules formations, were proved to exhibit antitumoral activity. Part II - Understanding the molecular mechanisms that allow some organisms to survive in extremely harsh conditions is an important achievement that might disclose a wide range of applications and that is constantly drawing the attention of many research fields. The simple small organic molecules, called osmolytes, responsible for the high adaptability of these living creatures are well known and of common use; nevertheless a full disclosure of the machinery behind their activity is still to be obtained. We developed a computational approach that, taking advantage of advanced simulation techniques, allowed to fully describe the effects of osmo-protectants on a small hairpin peptide and on a full mini-protein. The computational study allowed to highlight interesting new features and to develop a theory on the \u201cosmoprotection driving force\u201d

Formamide as the main building block in the origin of nucleic acids

The simplest molecules grouping the four most common elements of the universe H,C,O and N (with the exception of the biologically inert He) are isocyanate HNCO and formamide H2NCOH. Reasons for the availability of formamide on prebiotic Earth are presented. We review evidence showing that formamide in the presence of largely available catalysts and by moderate heating yields the complete set of nucleic bases necessary for the formation of nucleic acids. Formamide also favours the formation of acyclonucleosides and the phosphorylation and trans-phosphorylation of nucleosides, thus providing a plausible chemical frame for the passage from a simple one-carbon compound to nucleic polymers. Physico-chemical conditions exist in which formamide favours the stability of the phosphoester bonds in nucleic polymers relative to that of the same bonds in monomers. Starting from a formamide-laden environment subject only to the laws of chemistry, a hypothesis is outlined sketching the passage towards an aqueous world in which Darwinian rules apply

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data

Properties and Structural Studies of Multi-Wall Carbon Nanotubes-Phosphate Ester Hybrids

Long chain phosphate esters bearing at least one or two aryl groups have been synthesized and used for the preparation of stable multi-walled carbon nanotube (MWCNT) hybrids. The non-covalent interaction ester/MWCNT has been in- vestigated by several techniques (SEM, UV-vis, 31P-NMR, RAMAN). The used phosphate ester derivatives demon- strated the ability to produce an excellent dispersion of MWCNT in CHCl3. The obtained dispersions showed a great stability from one to at least three weeks in the range of concentration considered. Thermal analysis showed an increase in the decomposition temperature for the hybrids with respect to pristine MWCNT

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function

The effect of silica nanoparticles on the morphology, mechanical properties and thermal degradation kinetics of polycarbonate

Polycarbonate/silica nanocomposites with different silica quantities were prepared by a melt compounding method. The effect of silica amount, in the range 1\u20135 wt.%, on the morphology, mechanical properties and thermal degradation kinetics of polycarbonate (PC) was investigated. Clusters of silica nanoparticles were well dispersed in the polycarbonate whose structure remained amorphous. NMR results showed intermolecular interactions involving the carbonyl groups of different polymeric chains which did not affect the intramolecular rotational motions. The presence of the lowest silica content showed a decrease in the storage and loss moduli below the glass transition temperature, probably due to a plasticization effect. However, an increase in the amount of silica increased the moduli. The presence of silica in PC slightly increased the thermal stability, except for the highest silica content which showed a decrease. The activation energies of thermal degradation for the nanocomposites depended on the amount of silica and on the degree of conversion

RNA-binding activity of the rat calmodulin-binding PEP-19 protein and of the long PEP-19 isoform

Synthesis of H1\u2da histone protein, in the developing rat brain, seems to be regulated mainly at the post-transcriptional level. Since regulation of RNA metabolism depends on a series of RNA-binding proteins, we have been searching for RNA-binding proteins involved in the post-transcriptional regulation of the H1\u2da gene. We recently reported isolation, from a cDNA expression library, of an insert encoding a novel protein, the C-terminal half of which is identical to that of PEP-19, a brain-specific protein involved in calcium metabolism. The novel protein was called long PEP-19 isoform (LPI). Herein we show that LPI, as well as PEP-19, can bind H1\u2da RNA. Moreover, in order to improve production of functional LPI/PEP-19, we modified the protocol normally adopted for preparing histidine tagged-proteins from bacteria, by adding an additional purification step. We also found that both LPI and PEP can compete for H1\u2da RNA binding with PIPPin (CSD-C2), another RNA-binding protein previously discovered in our laboratory. Since PEP19/LPI contain a calmodulin binding domain, we finally investigated whether their ability to bind RNA is affected by calmodulin. Our results show that calmodulin interferes with binding of H1\u2da RNA to both PEP-19 and LPI, while it is not able to bind RNA on its own. This finding suggests that calcium/calmodulin may have a role in controlling H1\u2da mRNA metabolism in the developing brain

Investigating allosteric effects on the functional dynamics of [small beta]2-adrenergic ternary complexes with enhanced-sampling simulations

Signalling by G-protein coupled receptors usually occurs via ternary complexes formed under cooperative binding between the receptor, a ligand and an intracellular binding partner (a G-protein or [small beta]-arrestin). While a global rational for allosteric effects in ternary complexes would be of great help in designing ligands with specific effects, the paucity of structural data for ternary complexes with [small beta]-arrestin, together with the intrinsic difficulty of characterizing the dynamics involved in the allosteric coupling, have hindered the efforts to devise such a model. Here we have used enhanced-sampling atomistic molecular-dynamics simulations to investigate the dynamics and complex formation mechanisms of both [small beta]-arrestin- and Gs-complexes with the [small beta]2-adrenergic receptor (ADRB2) in its apo-form and in the presence of four small ligands that exert different allosteric effects. Our results suggest that the structure and dynamics of arrestin-ADRB2 complexes depend strongly on the nature of the small ligands. The complexes exhibit a variety of different coupling orientations in terms of the depth of the finger loop in the receptor and activation states of ADRB2. The simulations also allow us to characterize the cooperativity between the ligand and intracellular binding partner (IBP). Based on the complete and consistent results, we propose an experimentally testable extended ternary complex model, where direction of the cooperative effect between ligand and IBP (positive or negative) and its magnitude are predicted to be a characteristic of the ligand signaling bias. This paves the avenue to the rational design of ligands with specific functional effects