Exploring potential energy surfaces to reach saddle points above convex regions.

Saddle points on high-dimensional potential energy surfaces (PES) play a determining role in the activated dynamics of molecules and materials. Building on approaches dating back more than 50 years, many open-ended transition-state search methods have been developed to follow the direction of negative curvature from a local minimum to an adjacent first-order saddle point. Despite the mathematical justification, these methods can display a high failure rate: using small deformation steps, up to 80% of the explorations can end up in a convex region of the PES, where all directions of negative curvature vanish, while if the deformation is aggressive, a similar fraction of attempts lead to saddle points that are not directly connected to the initial minimum. In high-dimension PES, these reproducible failures were thought to only increase the overall computational cost, without having any effect on the methods' capacity to find all saddle points surrounding a minimum. Using activation-relaxation technique nouveau (ARTn), we characterize the nature of the PES around minima, considerably expanding on previous knowledge. We show that convex regions can lie on activation pathways and that not exploring beyond them can introduce significant bias in the saddle-point search. We introduce an efficient approach for traversing the convex regions, almost eliminating exploration failures, while multiplying by almost 10 the number of identified unique and connected saddle points as compared to the standard ARTn, thus underlining the importance of correctly handling convex regions for completeness of saddle point explorations.

Investigating the kinetics of the formation of a C Cottrell atmosphere around a screw dislocation in bcc iron: a mixed-lattice atomistic kinetic Monte-Carlo analysis.

We present a mixed-lattice atomistic kinetic Monte-Carlo algorithm (MLKMC) that integrates a rigid-lattice AKMC approach with the kinetic activation-relaxation technique (k-ART), an off-lattice/self-learning AKMC. This approach opens the door to study large and complex systems adapting the cost of identification and evaluation of transition states to the local environment. To demonstrate its capacity, MLKMC is applied to the problem of the formation of a C Cottrell atmosphere decorating a screw dislocation in α-Fe. For this system, transitions that occur near the dislocation core are searched by k-ART, while transitions occurring far from the dislocation are computed before the simulation starts using the rigid-lattice AKMC. This combination of the precision of k-ART and the speed of the rigid-lattice makes it possible to follow the onset of the C Cottrell atmosphere and to identify interesting mechanisms associated with its formation.

Interaction between interstitial carbon atoms and a ½ 〈1 1 1〉 self-interstitial atoms loop in an iron matrix: a combined DFT, off lattice KMC and MD study.

A static and kinetic study of the interaction between a 19 ½ 〈1 1 1〉 self-interstitial atoms loop and C atoms in body-centred cubic iron is presented in this work. An empirical potential matching the density functional theory calculations is used to study the static properties of the system. The usual kinetic Monte-Carlo (KMC) on-lattice restriction is not valid when the material is highly distorted, especially in the presence of a dislocation loop. Therefore, the dynamics of the system are investigated using both molecular dynamics simulations and k-ART, a self-learning/off-lattice atomic kinetic monte-carlo. The presented work is thus a full study of the C-loop and the C2-loop systems. A good agreement is observed between the statics and the kinetics (e.g. the discovery of a zone of stability of the C atom around the Fe cluster where the C can almost freely move), even though the kinetics show some unexpected behaviours of the studied systems. The pinning time of the loop induced by the C atoms is also estimated.

Structural and thermodynamical properties of early human amylin oligomers using replica exchange molecular dynamics: mutation effect of three key residues F15, H18 and F23.

Human islet amyloid polypeptide (hIAPP) is a 37-residue polypeptide, considered to be the main component of the pancreatic islet amyloid associated with type 2 diabetes and is one of the most amyloidogenic polypeptides known. Although the structure of hIAPP fibrils has already been obtained, structures of early oligomers and the mechanism of ß-sheet formation remain poorly understood. Herein, we characterize the atomic structure and the thermodynamics of the 14-37 residue fragment of hIAPP wild-type and mutated dimers and trimers. More precisely, three key residues, F15, H18 and F23, thought to affect the aggregation process, are the focus of this numerical study using replica exchange molecular dynamics coupled with the OPEP coarse-grained protein force field. Our simulations show that the oligomerization process takes place through the formation of anti-parallel ß-sheets most probably between C-terminal regions. Two main characteristics are associated with the onset of the fibrillation process. First, the sequence matching between the central (20-29) and C-terminal (30-37) regions, at intra and inter-molecular levels, helps in stabilizing the secondary structure and facilitates intermolecular interactions. Second, hydrophobic residues I26 and L27 are likely to promote the capture of further oligomeric structures and thus facilitate fibril elongation. Histidine mutation should have a more pronounced effect in the N-terminal region while phenylalanine mutations do not seem to prevent amyloid formation since central/C-terminal interactions are conserved through other contacts.

Strain-driven diffusion process during silicon oxidation investigated by coupling density functional theory and activation relaxation technique.

The reaction of oxygen molecules on an oxidized silicon model-substrate is investigated using an efficient potential energy hypersurface exploration that provides a rich picture of the associated energy landscape, energy barriers, and insertion mechanisms. Oxygen molecules are brought in, one by one, onto an oxidized silicon substrate, and accurate pathways for sublayer oxidation are identified through the coupling of density functional theory to the activation relaxation technique nouveau, an open-ended unbiased reaction pathway searching method, allowing full exploration of potential energy surface. We show that strain energy increases with O coverage, driving the kinetics of diffusion at the Si/SiO2 interface in the interfacial layer and deeper into the bulk: at low coverage, interface reconstruction dominates while at high coverage, oxygen diffusion at the interface or even deeper into the bottom layers is favored. A changing trend in energetics is observed that favors atomic diffusions to occur at high coverage while they appear to be unlikely at low coverage. Upon increasing coverage, strain is accumulated at the interface, allowing the oxygen atom to diffuse as the strain becomes large enough. The observed atomic diffusion at the interface releases the accumulated strain, which is consistent with a layer-by-layer oxidation growth.

Sampling small-scale and large-scale conformational changes in proteins and molecular complexes.

Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.

ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes.

We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly.

Sampling activated mechanisms in proteins with the activation-relaxation technique.

The activated dynamics of proteins occur on time scales of milliseconds and longer. Standard all-atom molecular dynamics simulations are limited to much shorter times, of the order of tens of nanoseconds. Therefore, many activated mechanisms that are crucial for long-time dynamics will not be observed in such molecular dynamics simulation; different methods are required. Here, we describe in detail the activation-relaxation technique (ART) that generates directly activated mechanisms. The method is defined in the configurational energy landscape and defines moves in a two step fashion: (a) a configuration is first brought from a local minimum to a nearby first-order saddle point (the activation); and (b) the configuration is relaxed to a new metastable state (the relaxation). The method has already been applied to a wide range of problems in condensed matter, including metallic glasses, amorphous semiconductors and silica glass. We review the algorithm in detail, discuss some previously published results and present simulations of activated mechanisms for a two-helix bundle protein using an all-atom energy function.

Matrix proteinase inhibition by AE-941, a multifunctional antiangiogenic compound.

BACKGROUND: Matrix metalloproteinases (MMPs) play an important role in tissue remodeling under normal physiological and pathological conditions and are thus attractive targets for both diagnostic and therapeutic purposes. Here, we examined the effect of AE-941, an orally bioavailable standardized extract made of cartilage that shows significant antiangiogenic and antimetastatic properties in vivo, on the activity of various members of the MMP family. MATERIALS AND METHODS: The effect of AE-941 on the activity of MMPs was assessed by fluorimetric assays and by substrate gel zymography. RESULTS: AE-941 markedly inhibits the gelatinolytic activity of MMP-2 and to a lesser extent those of MMP-1, MMP-7, MMP-9 and MMP-13. AE-941 also inhibited the elastinolytic activities of MMP-2 and MMP-9 as well as MMP-12 (metalloelastase), porcine pancreatic elastase (PPE), and human leukocyte elastase (HLE). Western blot analysis revealed the presence within AE-941 of immunoreactive TIMP-like proteins, suggesting that these proteins may be at least partly responsible for the observed MMP inhibition. CONCLUSIONS: Taken together, these results demonstrate that AE-941 contains TIMP-like proteins that could be responsible for the specific inhibition of MMPs. Given the recent studies suggesting the presence within this compound of specific inhibitor(s) of endothelial cell proliferation, AE-941 appears as a pleotropic agent able to interfere with several biochemical steps leading to angiogenesis and to other physiopathological conditions. Since AE-941 is currently under Phase III clinical investigations, these findings are also of considerable importance for our understanding of its anticancer properties.

Shark cartilage extracts as antiangiogenic agents: smart drinks or bitter pills?

The use of crude cartilage for the treatment of human cancers remains a subject of controversy. In this brief commentary, we reviewed the current knowledge on the anticancer properties of cartilage. We then presented the properties of AE-941, a novel standardized water-soluble extract derived from shark cartilage that represents less than 5% of the crude cartilage. It is a multifunctional antiangiogenic product that contains several biologically active molecules. EA-941 is one of the few antiangiogenic drugs that is under phase III clinical investigation. It is currently evaluated in Europe and North America for the treatment of refractory renal cell carcinoma and in North America for metastatic non small cell lung cancer.

Dynamics of lennard-jones clusters: A characterization of the activation-relaxation technique

The potential energy surface of Lennard-Jones clusters is investigated using the activation-relaxation technique (ART). This method defines events in the configurational energy landscape as a two-step process: (a) a configuration is first activated from a local minimum to a nearby saddle-point and (b) is then relaxed to a new minimum. Although ART has been applied with success to a wide range of materials such as a-Si, a-SiO2 and binary Lennard-Jones glasses, questions remain regarding the biases of the technique. We address some of these questions in a detailed study of ART-generated events in Lennard-Jones clusters, a system for which much is already known. In particular, we study the distribution of saddle-points, the pathways between configurations, and the reversibility of paths. We find that ART can identify all trajectories with a first-order saddle point leaving a given minimum, is fully reversible, and samples events following the Boltzmann weight at the saddle point.

Matrix metalloproteinases and their inhibitors in human pituitary tumors.

OBJECTIVE: To determine the expression of matrix metalloproteinases (MMP)-1, -2, and -3 and the tissue inhibitors of metalloproteinases (TIMP)-1, -2, and -3 in 12 tissue samples from normal pituitary glands and in 28 human pituitary tumors ranging from Grade 0 to Grade IV, and to establish a correlation between the level of expression of MMPs and TIMPs and the tumor grade. METHODS: The expression of MMPs and TIMPs was determined by Western blotting. MMP activity was detected by gelatin zymography. RESULTS: MMPs were expressed in the majority of tumors, and their levels of expression were unrelated to tumor grade or to their invasive phenotype. Some correlation was observed between MMP activity detected by zymography and tumor grade. TIMP-2 and TIMP-3 were poorly expressed in high-grade tumors and strongly expressed in normal pituitary glands and in the majority of low-grade tumors. CONCLUSION: No correlation could be established between the invasive potential of tumors and MMP-1, -2, and -3 expression levels. Some correlation was observed between MMP activity detected by zymography and tumor grade. A good inverse correlation was observed between TIMP-2 and TIMP-3 expression levels and tumor grade. These data suggest that monitoring the expression of TIMP-2 and TIMP-3 or gelatinolytic activity could be of prognostic value.

Expression of matrix metalloproteinases and their inhibitors in human brain tumors.

Sixty human brain tumors, classified according to the New World Health Organization (WHO) classification including, grade I schwannomas, meningiomas and pilocytic astrocytomas, grade II astrocytomas, grade III anaplastic astrocytomas, grade IV glioblastomas, grade III anaplastic oligodendrogliomas and grade IV glioblastomas and lung and melanoma metastases were analyzed for the expression of three matrix metalloproteinases (MMPs), two tissue inhibitors of MMPs (TIMPs) and for MMP activity. Some correlation was found between MMP expression and the degree of malignancy. Western blotting analysis revealed a more uniform pattern of distribution of MMP-2 (gelatinase A) than of MMP-9 (gelatinase B) and MMP-12 (metalloelastase) among tumors. MMP-9 levels were found to be significantly higher in grade III anaplastic astrocytomas and anaplastic oligodendrogliomas than those in grade I schwannomas and meningiomas. Anaplastic astrocytomas and Grade IV glioblastomas expressed significantly higher levels MMP-12 than grade I meningiomas. All sixty tumors showed a similar pattern of activity in zymography, proMMP-9 being the major species detected. Interestingly, TIMP-1 and TIMP-2 expression levels were especially low in tumors of grade II and grade III but significantly higher in tumors of grade I, particularly in schwannomas. Taken together, these data suggest that: 1) a balance between MMPs and TIMPs has an important role to play in human brain tumors; 2) TIMP expression may be valuable markers for tumor malignancy.

Expression of matrix metalloproteinases and their inhibitors in human brain tumors.

Sixty human brain tumors, including grade I meningiomas, schwannomas, and pilocytic astrocytomas, grade II astrocytomas, grade III anaplastic astrocytomas and oligodendrogliomas, and grade IV glioblastomas and lung and melanoma metastases were analyzed for expression of four matrix metalloproteinases (MMPs), two tissue inhibitors of MMPs (TIMPs), and MMP activity. No marked correlation was found between MMP expression and the degree of malignancy. Western blotting analysis revealed a more uniform pattern of distribution of MMP-2 (gelatinase A) than of MMP-9 (gelatinase B) and MMP-12 (metalloelastase) among tumors. All 60 tumors showed a similar pattern of activity in zymography, MMP-2 being the major species detected. Interestingly, TIMP-1 and TIMP-2 expression levels were low in tumors of grade III but significantly higher in tumors of grade I, particularly schwannomas. Altogether, these data suggest that: (1) the balance between MMP-2 and TIMP-2 is important in human brain tumors; and (2) TIMP expression may be a valuable marker for tumor malignancy.

Use of capillary electrophoresis for the characterization of human serum albumin heterogeneity.

Human serum albumin (HSA) is used in large amounts as an excipient in many biopharmaceutical formulation to prevent loss of the active ingredient through adsorption and/or degradation. Traditionally, iso-electric focusing has been used to demonstrate charge heterogeneity in HSA preparations. In an effort to develop new methods for the analysis of formulation components, a capillary zone electrophoresis method was developed for the analysis of HSA. Under initial separation conditions using untreated silica capillaries and 20 mM sodium phosphate, pH 6.0 as electrophoretic buffer, HSA migrated as a single peak. Addition of 1,4-diaminobutane allowed separation of several components which could be further resolved by varying the buffer pH. Optimal separation conditions were attained at 5 mM 1,4-diaminobutane and pH 8.5. The reproducibility of the separation conditions was verified by using capillaries from a different manufacturer. A comparative analysis of HSA preparations from different manufacturers provided evidence that the method may be used to qualitatively differentiate individual preparations. The analysis of rhEPO formulations, composed largely of HSA, showed levels of heterogeneity comparable to that of HSA preparations. Electrospray ionisation mass spectrometry (ESA-MS) was used as an independent method to confirm the heterogeneous nature of HSA.

Increased basal expression of hepatic Cyp1a1 and Cyp1a2 genes in inbred mice selected for susceptibility to acetaminophen-induced hepatotoxicity.

Susceptibility to acetaminophen-induced hepatotoxicity was found to vary widely in an outbred colony of Swiss Webster mice. Some acetaminophen-treated male mice showed a significant elevation in serum levels of the hepatic enzyme alanine aminotransferase at a normally non-hepatotoxic oral dose. A selective breeding program over 17 generations produced inbred mice which were either susceptible or nonsusceptible to the hepatotoxic effects of acetaminophen. Liver microsomes from the susceptible group showed a statistically significant increase in the ability to metabolize acetaminophen to a reactive intermediate which covalently binds N-acetylcysteine. Microsomal cytochrome P450 activities associated with CYP1A2 (acetanilide 4-hydroxylation and methoxyresorufin O-demethylase) were significantly increased in the susceptible group. Ethoxyresorufin O-deethylase activity, associated with both CYP1A1 and CYP1A2, was also significantly elevated in this group. Further examination of both CYP1A isoforms revealed that hepatic CYP1A1 and CYP1A2 mRNA and protein levels were significantly elevated in animals from the susceptible group. In vivo caffeine 3-demethylation, which is associated with CYP1A2 activity, co-segregated with acetaminophen susceptibility and showed a significant positive correlation (r = 0.626, p < 0.005) with CYP1A2 mRNA expression in animals from both the susceptible and nonsusceptible groups. The co-segregation of elevated basal Cyp1a1 and CYP1a2 gene expression levels in animals selected for susceptibility to acetaminophen-induced hepatotoxicity suggested a common heritable basis for regulation of basal expression of both of these CYP1A isoforms. This was supported by the correlated expression of both CYP1A mRNAs within individual mice (r = 0.644, p < 0.02).

Differences in caffeine 3-demethylation activity among inbred mouse strains: a comparison of hepatic Cyp1a2 gene expression between two inbred strains.

The 3-demethylation of caffeine can be used as an index of cytochrome P450 CYP1A2 activity in vivo. We compared the plasma levels of caffeine and the 3-demethylated metabolite. 1,7-dimethylxanthine, in six common inbred strains (A/J, P/J, BALB/cJ, C3H/HeJ, AKR/J, and SWR/J) and one inbred strain (APN) derived in our laboratory from outbred Swiss-Webster mice on the basis of its relative susceptibility to acetaminophen-induced hepatotoxicity. We found significant variations between a number of the common strains, all of which produced significantly higher caffeine 3-demethylation indices than our APN strain. In three of the six common strains, there was a significant difference between males and females, with the females having consistently lower 1,7-xanthine/caffeine ratios. Hepatic Cyp1a2 expression was compared between APN and C3H/HeJ males. Microsomal methoxyresorufin O-demethylation, acetanilide 4-hydroxylation, and CYP1A2 immunoreactive protein levels were significantly higher in C3H/HeJ relative to APN mice, as were hepatic CYP1A2 mRNA levels. These results indicate the importance of strain and gender to the outcome of pharmacological or toxicological studies involving CYP1A2-mediated metabolism, as well as the suitability of the plasma 1,7-dimethylxanthine/caffeine ratio as a marker of CYP1A2 activity in the mouse. The striking differences observed between the APN and C3H/HeJ mice suggest that these strains may be suitable for a genetic analysis of the regulation of the basal expression of CYP1A2, a key enzyme in procarcinogen activation.