Ice front blocking of ocean heat transport to an Antarctic ice shelf.

Mass loss from the Antarctic Ice Sheet to the ocean has increased in recent decades, largely because the thinning of its floating ice shelves has allowed the outflow of grounded ice to accelerate1,2. Enhanced basal melting of the ice shelves is thought to be the ultimate driver of change2,3, motivating a recent focus on the processes that control ocean heat transport onto and across the seabed of the Antarctic continental shelf towards the ice4-6. However, the shoreward heat flux typically far exceeds that required to match observed melt rates2,7,8, suggesting that other critical controls exist. Here we show that the depth-independent (barotropic) component of the heat flow towards an ice shelf is blocked by the marked step shape of the ice front, and that only the depth-varying (baroclinic) component, which is typically much smaller, can enter the sub-ice cavity. Our results arise from direct observations of the Getz Ice Shelf system and laboratory experiments on a rotating platform. A similar blocking of the barotropic component may occur in other areas with comparable ice-bathymetry configurations, which may explain why changes in the density structure of the water column have been found to be a better indicator of basal melt rate variability than the heat transported onto the continental shelf9. Representing the step topography of the ice front accurately in models is thus important for simulating ocean heat fluxes and induced melt rates.

Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution.

According to the "protein only" hypothesis, a conformational conversion of the non-pathogenic "cellular" prion isoform into a pathogenic "scrapie" isoform is the fundamental event in the onset of prion diseases. During this pathogenic conversion, helix H1 and two adjacent surface loops L2 and L3 of the normal prion protein are thought to undergo a conformational transition into an extended beta-like structure, which is prompted by interactions with the pre-existing beta-sheet. To get more insight into the interaction between the helix and one of the beta-strands in the partially unfolded prion protein, the solution structure of a synthetic linear peptide spanning helix H1 and beta-strand S2 (residues 142-166 in human numbering) was studied by circular dichroism and nuclear magnetic resonance spectroscopies. We found that, in contrast to many prion fragments studied earlier, this peptide (i) is highly soluble and does not aggregate up to a millimolar concentration range in aqueous medium and (ii) exhibits an intrinsic propensity to a beta-hairpin like conformation at neutral pH. This beta-propensity can be one of the internal driving forces of the molecular rearrangement responsible for the pathogenic conversion of the prion protein.

Molecular dynamics studies of sequence-directed curvature in bending locus of trypanosome kinetoplast DNA.

The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well documented example of sequence specific conformational modulations. Recently, a new hypothesis of its physical origin has been put forward. According to it, the intrinsic bends in B-DNA may represent one of the consequences of the compressed frustrated state of its backbone. The compressed backbone hypothesis agrees with many data and explains some controversial experimental observations. The original arguments of this theory came out from MD simulations of a DNA fragment with a strong bending propensity. Its sequence, however, was not experimental. It was constructed empirically so as to maximize the magnitude of bending in calculations. To make sure that our computations reproduce the experimental effect we carried out similar simulations with an A-tract repeat of a natural base pair sequence found in a bent locus of a minicircle DNA. We demonstrate spontaneous development of static curvature in the course of MD simulations excluding any initial bias except the base pair sequence. Its direction and magnitude agree with experimental estimates. The results confirm earlier qualitative conclusions and agree with the hypothesis of a compressed backbone as the origin of static bending in B-DNA.

Internal correlations in minor groove profiles of experimental and computed B-DNA conformations.

It has been noticed that converged conformations of B-DNA oligomers obtained in MD calculations often have very small atom position rmsd values from the canonical B-DNA and all helical parameters close to the standard values, but their minor grooves tend to be somewhat narrower. This apparent bias disappears, however, when C5' rather than phosphorus atoms are used for measuring the groove width. At the origin of this effect is the specific orientation of phosphate groups in the canonical B-DNA model which maximizes their separation across the minor groove. When measured by C5' traces, minor groove profiles of experimental structures available in the Nucleic Acids Database show much less tendency to narrow below the canonical width. Correlation analysis reveals a high degree of correspondence in shapes of minor grooves of calculated and experimental single-crystal structures of B-DNA oligomers.

Investigation of the conformational properties of a beta-(1-->3) branched beta-(1-->6) heptasaccharide elicitor and its analogues by internal coordinate stochastic dynamics.

A series of beta-(1-->3) branched beta-(1-->6) oligosaccharides that are known to take part in switching immune reactions in plants was studied by a molecular dynamics approach. A novel technique was applied which recently proved to be very efficient in polypeptide simulations. Molecular dynamics is simulated in internal rather than Cartesian coordinates with dramatically reduced numbers of degrees of freedom and a time step ten-fold larger than usual values. Comparison and classification of most populated conformational states revealed a few conformational motifs that are frequently adopted by highly active oligosaccharides and are not populated in an inactive analogue. As a result a putative biologically active conformation of the oligosaccharides is proposed.

The catalytic mechanism of alpha-amylases based upon enzyme crystal structures and model building calculations.

Based upon the known crystal structures of Taka-amylase A and the recently refined Porcine pancreatic alpha-amylase inhibitor complex a mechanism of catalysis in amylase active centers is proposed. The mechanism differs significantly from the well-known lysozyme model of catalysis. The hydrolysis is catalyzed by three carboxyl groups and its starts from a water nucleophilic attack and opening of the glucose ring in the catalytic center rather than from protonation of the glycosidic oxygen. The main supporting experimental observations are briefly discussed.

Multiple attack mechanism in the porcine pancreatic alpha-amylase hydrolysis of amylose and amylopectin.

The action pattern of the porcine pancreatic alpha-amylase (PPA) is studied with amylose and amylopectin used as substrates. For initial stages of enzyme hydrolysis, the shape of the product chain length distribution is estimated and compared with predictions of the theory of multiple attack. The theory assumes sliding of the enzyme along the substrate polysaccharide chain without dissociation between successive cleavages. Very different initial distributions of oligomers are observed for amylose and amylopectin. In both cases, however, the theory describes the chain length distributions well. The temperature dependence of the shape of the multiple attack product distribution indicates that with rising temperature the probability of sliding increases with respect to that of dissociation. This dependence can be expected if the sliding occurs in a loose complex where enzyme and substrate are bound mainly due to hydrophobic interactions between their two continuous hydrophobic surfaces. The possible physiological role of the multiple attack in the mechanism of pancreatic amylases of mammals is discussed. The correspondence between the average length of the sliding of PPA and characteristic chain lengths of alpha-1,4-bound glucose fragments in amylopectin suggests that the degree of multiple attack of PPA is close to the optimum level required for efficient digestion of starch in the small intestine.

Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin.

The equilibrium population of different conformational states of a polypeptide can in principle be obtained by a very long molecular dynamics simulation. The method of internal coordinate molecular dynamics earlier developed in this laboratory (A.K. Mazur and R.A. Abagyan J. Biomol. Struct. Dyn. 6,833 (1989)) allows one to use time steps much larger than usual for computing molecular trajectories. It is shown here that the sampling of the conformational space can be additionally enhanced by adding a random component to the set of forces applied to atoms. We describe the algorithms by which the random force is introduced and also a special method which excludes the fast rotation of polar hydrogens from equations of motion but keeps them movable. As a result the task stated in the title becomes realistic. Internal coordinate stochastic dynamics is applied for scanning the conformational space of the pentapeptide Met5-enkephalin which is a common test example widely used in theoretical studies. A large number of conformational transitions is observed during the 20 ns simulation starting from the global energy minimum thus allowing us to arrive at a nearly Boltzmann distribution of populations of conformational states. A few states are found which are distinguished by high apparent configurational entropy which turn out to correspond well to experimentally observed conformations of enkephalins.

[Multiple attack in the mechanism of endoglucanase action]. / Iavlenie mnogokratnoi ataki v mekhanizme deistviia éndogliukanaz.

The review deals with the phenomenon of repetitive catalytic acts occurring in one enzyme-substrate encounter of certain endo-glucanases with water soluble polysaccharides. Here are discussed experimental results and theoretical models applied in analysis of data.

Schematic methods for probabilistic enzyme kinetics.

The theory of steady-state enzyme processes which avoids using the mass action law of chemical kinetics and consistently describes catalytic mechanisms by probabilistic concepts has recently been proposed (Mazur, 1991, J. theor. Biol. 148, 229-242). To facilitate the analysis of complex reaction graphs by this theory the possibility of constructing schematic rules similar to those used in classical kinetics is studied. It is found that due to the similarity of algebraic procedures the popular method of King & Altman can be applied in probabilistic kinetics in addition to the earlier proposed rule based on enumeration of cycles of the reaction graph. This similarity also allows one to adapt many other shortcut methods of classical kinetics for probabilistic reaction graphs. The paper considers separately the possibility of transforming reaction mechanisms so that the initial graph is replaced by a simpler but equivalent one. It is shown that there are few cases when a group of states can be replaced by one united state, with earlier known rules such as the rule of Cha for equilibrium stages being particular cases of a more general procedure. In addition a novel method is proposed which performs step-by-step reduction of any reaction graph. All the new methods can be adapted for traditional kinetics as well. The results obtained demonstrate that many schematic rules of classical kinetics are of probabilistic origin.

[Global optimization of the conformational energy of oligopeptides using a tunnel algorithm]. / Global'naia optimizatsiia konformatsionnoi énergii oligopeptidov s pomoshch'iu tunnel'nogo algoritma.

The tunneling algorithm has been suggested as a method for the searching of the low energy conformations of the oligopeptides. The efficiency of the method has been compared with other global energy minimization methods such as grid search and molecular dynamics. It has been shown that tunneling algorithm reached global minimum of potential energy of the molecule of 3-4 residues more effectively than other methods. Experiments with oligopeptides of more than 4 residues showed that although during reasonable time tunneling algorithm does not reach the global minimum it can very effectively find the low energy minimum.

A probabilistic view on steady-state enzyme reactions.

A new theoretical description of steady-state enzyme reactions is proposed. The description is based on the concepts of the probability theory instead of the conventional formalism of chemical kinetics. A general steady-state rate equation is obtained using a probabilistic model of the catalytic act. As a result, the classical problems of enzyme kinetics can be formulated and considered in a different aspect. It is shown that the new theory presents a clearer treatment of some commonly obscure questions, such as the steady-state establishment. The theory also gives additional possibilities in the interpretation of the experimental results of traditional methods and proposes certain new ways in experimental investigations of enzymes.

New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures.

A general methodology is proposed for the conformational modelling of biomolecular systems. The approach allows one: (i) to describe the system under investigation by an arbitrary set of internal variables, i.e., torsion angles, bond angles, and bond lengths; it offers a possibility to pass from the free structure to a completely fixed one with the number of variables from 3N to zero, respectively, where N is the number of atoms; (ii) to consider both, a single molecule and a complex of many molecules, (e.g., proteins, water, ligands, etc.) in terms of one universal model; (iii) to study the dynamics of the system using explicit analytical Lagrangian equations of motion, thus opening up possibilities for investigations of slow concerted motions such as domain oscillations in proteins etc.; (iv) to calculate the partial derivatives of various functions of conformation, e.g., the conformational energy or external constraints imposed, using a standard efficient procedure regardless of the variables and the structure of the system. The approach is meant to be used in various investigations concerning the conformations and dynamics of biomacromolecules.

New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles.

A new methodology for the conformational modelling of biomolecular systems (1) is extended to local deformations of chain molecules and to flexible molecular rings. It is shown that these two cases may be reduced to considering an equivalent molecular model with a regular tree-like topology. A simple procedure is developed to analyze any flexible rings (the five- and six-membered sugar rings of carbohydrates and nucleic acids, in particular) and local deformation regions by energy minimization. Dynamic equations are also derived for such molecular systems. As a result, a unified approach is proposed for the efficient energy minimization and simulation of dynamic behavior of multimolecular systems having any set of variable internal coordinates, local deformation regions and cycles. Advantages and domains of applicability of the approach are discussed.

[Computer modeling of enzymatic hydrolysis of a linear polysaccharide by endoglycanases]. / Matematicheskoe modelirovanie fermentativnogo gidroliza lineinogo polisakharida éndoglikanazami.

The kinetics of linear polysaccharide hydrolysis with endoglycanases was studied with the help of computer modelling. Simple hydrolysis of a substrate (polymerization degree 30) -- analogous to beta-1,3-glucan -- laminarin was considered. The theoretical action patterns of several enzymes having active centres with known subsite maps were compared with experimental data for endolaminarinase LIV from Spisula sachalinensis. Analysis of the data obtained revealed some characteristic features in the course of the reaction and showed how to achieve information on the active centres of endoglycanases on the basis of such an action pattern. The method of evaluating maximum distance from the catalytic site to the boundary of the active centre was proposed.