arXiv subjects

G. Tiana

Publications and source records attributed to G. Tiana.

At least 37 records · Page 2Linked to original sources

arXiv2007

Exploring the Protein G Helix Free Energy Surface by Solute Tempering Metadynamics

The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling with an affordable computational effort. From the sampled free-energy surface we are able to reproduce a number of experimental observations, such as the fact that the lowest minimum corresponds to a globular conformation displaying some degree of beta-structure, that the helical state is metastable and involves only 65% of the chain. The calculations also show that the system populates consistently a pi-helix state and that the hydrophobic staple motif is present only in the free-energy minimum associated with the helices, and contributes to their stabilization. The use of metadynamics coupled with solute tempering results then particularly suitable to provide the thermodynamics of a short peptide, and its computational efficiency is promising to deal with larger proteins.

q-bio.BM↗

arXiv2007

Oscillations and temporal signalling in cells

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce oscillations in gene expression or protein concentration, using a framework of simple mathematical models. We focus on three eukaryotic genetic regulatory networks which show "ultradian" oscillations, with time period of the order of hours, and involve, respectively, proteins important for development (Hes1), apoptosis (p53) and immune response (NFkB). We argue that underlying all three is a common design consisting of a negative feedback loop with time delay which is responsible for the oscillatory behaviour.

q-bio.MN↗

arXiv2007

Use of the Metropolis algorithm to simulate the dynamics of protein chains

The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of 1 degree on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.

q-bio.OT↗

arXiv2005

What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical phases, namely a coil-like phase, an unfolded globule and a folded phase (plus other two phases, namely frozen and random coil, populated only at extremes temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed.

q-bio.BM↗

arXiv2005

A folding inhibitor of the HIV-1 Protease

Being the HIV-1 Protease (HIV-1-PR) an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved, as a rule hydrophobic, amino acids). These LES have evolved over myriad of generations to recognize and strongly attract each other, so as to make the protein fold fast and be stable in its native conformation. Consequently, peptides displaying a sequence identical to those segments of the monomers associated with LES are expected to act as competitive inhibitors and thus destabilize the native structure of the enzyme. These inhibitors are unlikely to lead to escape mutants as they bind to the protease monomers through highly conserved amino acids which play an essential role in the folding process. The properties of one of the most promising inhibitors of the folding of the HIV-1-PR monomers found among these peptides is demonstrated with the help of spectrophotometric assays and CD spectroscopy.

q-bio.BM↗

arXiv2005

Design of amino acid sequences to fold into C_alpha-model proteins

In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 20x20 quenched random matrix. The goal of the present work is to design and characterize amino acid sequences folding to the SH3 conformation, a 60-residues recognition domain common to many regulatory proteins. We show that a number of sequences can fold, starting from a random conformation, to within a distance root mean square deviation (dRMSD) of 2.6A from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence--independent threshold energy.

q-bio.BM↗

arXiv2005

Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers

One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a second problem arises, namely the eventual development of resistance. We wish to suggest a scheme for the design of non--conventional drugs which do not face any of these problems and apply it to the case of HIV--1 protease. It is based on the knowledge that the folding of single--domain proteins, like e.g. each of the monomers forming the HIV--1--PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting and highly conserved amino acids which play a central role in the folding process. Because LES have evolved over myriads of generations to recognize and strongly interact with each other so as to make the protein fold fast as well as to avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding--inhibitor drugs suggest themselves: short peptides (or eventually their mimetic molecules), displaying the same amino acid sequence of that of LES (p--LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance: in fact, mutations which successfully avoid their action imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations within the framework of a simple although not oversimplified model, which is able to reproduce the main thermodynamic as well as dynamic properties of monoglobular proteins, we first identify the LES of the HIV--1--PR and then show that the corresponding p--LES peptides act as effective inhibitors of the folding of the protease which do not create resistance.

q-bio.BM↗

arXiv2005

Early events in insulin fibrillization studied by time-lapse atomic force microscopy

The importance of understanding the mechanism of protein aggregation into insoluble amyloid fibrils relies not only on its medical consequences, but also on its more basic properties of self--organization. The discovery that a large number of uncorrelated proteins can form, under proper conditions, structurally similar fibrils has suggested that the underlying mechanism is a general feature of polypeptide chains. In the present work, we address the early events preceeding amyloid fibril formation in solutions of zinc--free human insulin incubated at low pH and high temperature. Aside from being a easy--to--handle model for protein fibrillation, subcutaneous aggregation of insulin after injection is a nuisance which affects patients with diabetes. Here, we show by time--lapse atomic force microscopy (AFM) that a steady-state distribution of protein oligomers with an exponential tail is reached within few minutes after heating. This metastable phase lasts for few hours until aggregation into fibrils suddenly occurs. A theoretical explanation of the oligomer pre--fibrillar distribution is given in terms of a simple coagulation--evaporation kinetic model, in which concentration plays the role of a critical parameter. Due to high resolution and sensitivity of AFM technique, the observation of a long-lasting latency time should be considered an actual feature of the aggregation process, and not simply ascribed to instrumental inefficency. These experimental facts, along with the kinetic model used, claim for a critical role of thermal concentration fluctuations in the process of fibril nucleation.

q-bio.BM↗

arXiv2004

Design of a folding inhibitor of the HIV-1 Protease

Being HIV-1-PR an essential enzyme in the viral life cycle, its inhibition can control AIDS. Because the folding of single domain proteins, like HIV-1-PR is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved amino acids) which have evolved over myriads of generations to recognize and strongly attract each other so as to make the protein fold fast, we suggest a novel type of HIV-1-PR inhibitors which interfere with the folding of the protein: short peptides displaying the same amino acid sequence of that of LES. Theoretical and experimental evidence for the specificity and efficiency of such inhibitors are presented.

q-bio.BM↗

arXiv2004

Thermodynamics of beta-amyloid fibril formation

Amyloid fibers are aggregates of proteins. They are built out of a peptide called $β$--amyloid (A$β$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the Amyloid Precursor Protein (APP). X-ray diffraction experiments have shown that these fibrils are rich in $β$--structures, whereas the shape of the peptide displays an $α$--helix structure within the APP in its biologically active conformation. A realistic model of fibril formation is developed based on the seventeen residues A$β$12--28 amyloid peptide, which has been shown to form fibrils structurally similar to those of the whole A$β$ peptide. With the help of physical arguments and in keeping with experimental findings, the A$β$12--28 monomer is assumed to be in four possible states (i.e., native helix conformation, $β$--hairpin, globular low--energy state and unfolded state). Making use of these monomeric states, oligomers (dimers, tertramers and octamers) were constructed. With the help of short, detailed Molecular Dynamics (MD) calculations of the three monomers and of a variety of oligomers, energies for these structures were obtained. Making use of these results within the framework of a simple yet realistic model to describe the entropic terms associated with the variety of amyloid conformations, a phase diagram can be calculated of the whole many--body system, leading to a thermodynamical picture in overall agreement with the experimental findings. In particular, the existence of micellar metastable states seem to be a key issue to determine the thermodynamical properties of the system.

q-bio.BM↗

arXiv2004

Deriving amino acid contact potentials from their frequencies of occurence in proteins: a lattice model study

The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such frequencies and, consequently, to develop a strategy to include in the calculations correlations due to the spatial proximity of the amino acids and to their overall tendency of being conserved in proteins. Making use of a lattice model to describe protein chains and defining a "true" potential, we test these strategies by selecting a database of folding model sequences, deriving the contact potentials from such sequences and comparing them with the "true" potential. Taking into account correlations allows for a markedly better prediction of the interaction potentials.

q-bio.BM↗

arXiv2004

Simple models of protein folding and of non--conventional drug design

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of a protein whose sequence is known. Using insight obtained from simple model simulations of the folding of proteins, in particular of the fact that this phenomenon is essentially controlled by conserved (native) contacts among (few) strongly interacting ("hot"), as a rule hydrophobic, amino acids, which also stabilize local elementary structures (LES, hidden, incipient secondary structures like $α$--helices and $β$--sheets) formed early in the folding process and leading to the postcritical folding nucleus (i.e., the minimum set of native contacts which bring the system pass beyond the highest free--energy barrier found in the whole folding process) it is possible to work out a succesful strategy for reading the native structure of designed proteins from the knowledge of only their amino acid sequence and of the contact energies among the amino acids. Because LES have undergone millions of years of evolution to selectively dock to their complementary structures, small peptides made out of the same amino acids as the LES are expected to selectively attach to the newly expressed (unfolded) protein and inhibit its folding, or to the native (fluctuating) native conformation and denaturate it. These peptides, or their mimetic molecules, can thus be used as effective non--conventional drugs to those already existing (and directed at neutralizing the active site of enzymes), displaying the advantage of not suffering from the uprise of resistance.

q-bio.BM↗

arXiv2003

Understanding the determinants of stability and folding of small globular proteins from their energetics

The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native conformation, which simulate the protein and the surrounding solvent at full--atom level, we generate an energetic map of the equilibrium state of the protein and simplify it with an Eigenvalue decomposition. The components of the Eigenvector associated with the lowest Eigenvalue indicate which are the "hot" sites responsible for the stability and for the fast folding of the protein. Comparison of these predictions with the results of mutatgenesis experiments, performed for five small proteins, provide an excellent agreement.

cond-mat.soft↗

arXiv2002

Role of bulk and of interface contacts in the behaviour of model dimeric proteins

Some dimeric proteins first fold and then dimerize (three--state dimers) while others first dimerize and then fold (two--state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences obeying to one or to the other mechanism on the basis of the partition of the ground state energy between bulk than for interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both in the the folding and in the evolutionary history of the protein. Three--state dimers, where a large fraction of the energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchycal pathway controlled by local elementary structures, as also happens in the folding of single--domain monomeric proteins. On the other hand, two--state dimers display a relative contact energy of interface contacts which is larger than the corresponding quantity associated with the bulk. In this case, the assembly of the interface stabilizes the system and lead the two chains to fold. The specific properties of three--state dimers acquired through evolution are expected to be more robust than those of two--state dimers, a fact which has consequences on proteins connected with viral diseases.

cond-mat↗

arXiv2002

Resistance proof, folding-inhibitor drugs

Conventional drugs work, as a rule, by inhibiting the enzymatic activity of specific proteins, capping their active site. In this paper we present a model of non- conventional drug design based on the inhibiting effects small peptides obtained from segments of the protein itself have on the folding ability of the system. Such peptides attach to the newly expressed (unfolded) protein and inhibit its folding, inhibition which cannot be avoided but through mutations which in any case denaturate the enzyme. These peptides, or their mimetic molecules, can be used as effective alternative drugs to those already available, displaying the advantage of not suffering from the upraise of resistence.

cond-mat.soft↗

arXiv2002

Time delay as a key to Apoptosis Induction in the p53 Network

A feedback mechanism that involves the proteins p53 and mdm2, induces cell death as a controled response to severe DNA damage. A minimal model for this mechanism demonstrates that the respone may be dynamic and connected with the time needed to translate the mdm2 protein. The response takes place if the dissociation constant k between p53 and mdm2 varies from its normal value. Although it is widely believed that it is an increase in k that triggers the response, we show that the experimental behaviour is better described by a decrease in the dissociation constant. The response is quite robust upon changes in the parameters of the system, as required by any control mechanism, except for few weak points, which could be connected with the onset of cancer.

cond-mat.dis-nn↗

arXiv2002

Design and Folding of Dimeric Proteins

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of biological recognition. Dimerization is studied by following the evolution of two identical 20--letter amino acid chains within the framework of a lattice model and using Monte Carlo simulations. It is found that when design (evolution pressure) selects few, strongly interacting (conserved) amino acids to control the process, a three--state folding scenario follows, where the monomers first fold forming the halves of the eventual dimeric interface independently of each other, and then dimerize ("lock and key" kind of association). On the other hand, if design distributes the control of the folding process on a large number of (conserved) amino acids, a two--state folding scenario ensues, where dimerization takes place at the beginning of the proces, resulting in an "induced type" of association. Making use of conservation patterns of families of analogous dimers, it is possible to compare the model predictions with the behaviour of real proteins. It is found that theory provides an overall account of the experimental findings.

cond-mat.soft↗

arXiv2001

Designability of lattice model heteropolymers

Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20 letter lattice model of proteins which, relying only on the Central Limit Theorem, has a generality which goes beyond the simple model used in its derivation. This expression displays an exponential dependence on the energy of the optimal sequence folding on the given conformation measured with respect to the lowest energy of the conformational dissimilar structures, energy difference which constitutes the only parameter controlling designability. Accordingly, the designability of a native conformation is intimately connected to the stability of the sequences folding to them.

cond-mat↗