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PubMed2006

Energy optimization for off-lattice protein folding.

Two three-dimensional AB off-lattice protein models consisting of hydrophobic and hydrophilic monomers are studied in this paper. By incorporating an extra energy contribution into the original energy function, the protein folding is converted from a constraint optimization problem into an unconstrained one which can be solved by the well-known gradient method. From the initial configurations randomly generated by the heuristic strategy proposed in this paper, our algorithm can find better results than those by nPERM for the four Fibonacci sequences. Based on the initial configurations obtained by energy landscape paving (ELP) routine, some of our results for the lowest energies are better than the best values reported in the literature.

Computer Simulation↗
PubMed2004

Directed polymers and interfaces in random media: free-energy optimization via confinement in a wandering tube.

We analyze, via Imry-Ma scaling arguments, the strong disorder phases that exist in low dimensions at all temperatures for directed polymers and interfaces in random media. For the uncorrelated Gaussian disorder, we obtain that the optimal strategy for the polymer in dimension 1+d with 0 1/2 for the wandering of the best favorable tube available. The corresponding free energy then scales as F approximately Lomega with omega=2nu-1 and the left tail of the probability distribution involves a stretched exponential of exponent eta=(4-d)/2. These results generalize the well known exact exponents nu=2/3, omega=1/3, and eta=3/2 in d=1, where the subleading transverse length R(S) approximately L(1/3) is known as the typical distance between two replicas in the Bethe ansatz wave function. We then extend our approach to correlated disorder in transverse directions with exponent alpha and/or to manifolds in dimension D+d= d(t) with 0 0 ). In particular, for an interface of dimension ( d(t) -1) in a space of total dimension 5/3< d(t) <3 with random-bond disorder, our approach yields the confinement exponent nu(S) =( d(t) -1)(3- d(t) )/(5 d(t) -7). Finally, we study the exponents in the presence of an algebraic tail 1/ V1+micro in the disorder distribution, and obtain various regimes in the (micro,d) plane.

Journal Article↗
PubMed2006

Pichia pastoris fermentation optimization: energy state and testing a growth-associated model.

A growth-associated model was applied to the production of recombinant ovine interferon-tau (rOvIFN-tau) with Pichia pastoris for the purpose of manufacturing preclinical and clinical active material. This model predicts that product yields will be the greatest when the specific growth of the culture is maintained at a steady and optimal rate. However, rOvIFN-tau yields did not meet the expected linear model but most closely corresponded to a polynomial relationship. After transitioning from glycerol to methanol, product accumulated for 31-45 h, and then the yield decreased. This production shift, which has been termed decoupling, was clearly related to time on methanol and not culture density. It was determined that a correlation exists between the decoupling point and a drop in energy state of the cell when expressing beta-galactosidase. By assigning decoupling as a constraint that limits productivity and by reformulating the growth medium, the time prior to decoupling increased to 46.8+/-2.4 h, product yield improved for rOvIFN-tau from 203 to 337 mg l(-1), and the coefficient of variation for yield decreased from 67.9 to 23.3%. A robust and stable fermentation process was realized, resulting in a 210% improvement in total yield from 557+/-357 to 1,172+/-388 mg.

Adenosine Diphosphate↗
PubMed1998

Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments.

We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by "homology distance constraints," while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good conformational energies and are physically reasonable. The effects of mis-alignment of the unknown and the template sequences were also explored in order to determine the feasibility of this homology modeling method for distinguishing possible sequence alignments based on considerations of the resulting conformational energies of modeled structures. Differences in the alignments of the unknown and the template sequences result in significant differences in the conformational energies of the calculated homology models. These results suggest that conformational energies and residual constraint violations in these homology-constrained simulated annealing calculations can be used as criteria to distinguish between correct and incorrect sequence alignments and chain folds.

Algorithms↗
PubMedDate not supplied

Human energy - optimal control of disturbance rejection during constrained standing.

An optimal control system that enables a subject to stand without hand support in the sagittal plane was designed. The subject was considered as a double inverted pendulum structure with a voluntarily controlled degree of freedom in the upper trunk and artificially controlled degree of freedom in the ankle joints. The control system design was based on a minimization of cost function that estimated the effort of the ankle joint muscles through observation of the ground reaction force position relative to the ankle joint axis. By maintaining the centre of pressure close to the ankle joint axis the objective of the upright stance is fulfilled with minimal ankle muscle energy cost. The performance of the developed controller was evaluated in a simulation-based study. The results were compared with the responses of an unimpaired subject to different disturbances in the sagittal plane. The proposed cost function was shown to produce a reasonable approximation of human natural behaviour.

Algorithms↗
PubMed2000

A statistical mechanical method to optimize energy functions for protein folding.

We present a method for deriving energy functions for protein folding by maximizing the thermodynamic average of the overlap with the native state. The method has been tested by using the pairwise contact approximation of the energy function and generating alternative structures by threading sequences over a database of 1, 169 structures. With the derived energy function, most native structures: (i) have minimal energy and (ii) are thermodynamically rather stable, and (iii) the corresponding energy landscapes are smooth. Precisely, 92% of the 1,013 x-ray structures are stabilized. Most failures can be attributed to the neglect of interactions between chains forming polychain proteins and of interactions with cofactors. When these are considered, only nine cases remain unexplained. In contrast, 38% of NMR structures are not assigned properly.

Protein Conformation↗
PubMed2005

The eccentric position of the heart in the mammalian body and optimal energy transfer in single tube models.

Many phenomena cannot be explained by traditional haemodynamics models. For example, the hearts of all mammals are neither at one end of the circulatory system nor at the geometric centre. Based on a new circulation model, we report that if the heart is located at either of these two positions, the energy saving rule will be violated. We assume that the main arterial system is under a steady, distributed transverse vibration with the heart as the input power source. The equation of motion of the artery is governed by a new pressure wave equation with total energy. We analyse the effects of the heart position on the pressure pulse shape and the spectrum. By a simplifying T-tube model, we find that there are many harmonic oscillating modes for the overall arterial system. The position of the heart affects the weights of different modes. If the heart is at the midpoint or at one end of the body, none of the even harmonic modes can be excited. If the heart is at a third along the whole system, the third oscillation mode in the system is missing. Thus, from an efficiency point of view, this model gives a strong reason for all mammals' hearts being at an eccentric position. Tube simulations were carried out to confirm the theoretical prediction. A new standing wave model to analyse the variation of the pressure pulse shape along the artery is discussed. The interesting result indicates that our new pressure wave equation possesses a high problem solving potential. It provides a new tool for studying arterial dynamics.

Animals↗
PubMed2001

The concept of energy homeostasis for optimal health during training.

From all nutritional variables optimal energy supply is considered as most vital for human performance. It is postulated that lack of energy homeostasis is the basic problem in the development of overtraining. Most if not all clinical symptoms are directly or indirectly related to the physiological mechanisms of energy homeostasis. The rapidly increasing knowledge in the field of body weight control with several new regulatory neuro-peptides such as leptin, will give new opportunities to tackle this unbalance between training load and energy availability. The central role of leptin and insulin as adiposity signals has focussed attention on the anti-obesity aspects of leptin. However as member of the cytokine family, leptin is also closely linked to the immune and reproductive system. New data indicates clearly the dual function of leptin at both ends at the energy balance; starvation vs. overfeeding. It links also nutrition to the reproductive system. Lack of available energy has a much greater impact on leptin levels than exercise stress. It is suggested that application of the rapidly increasing knowledge in the obesity field will benefit the research on the mechanisms involved in the derailment of the delicate balance between training load and energy homeostasis in athletes.

Energy Metabolism↗
PubMed2004

Optimizing physical energy functions for protein folding.

We optimize a physical energy function for proteins with the use of the available structural database and perform three benchmark tests of the performance: (1) recognition of native structures in the background of predefined decoy sets of Levitt, (2) de novo structure prediction using fragment assembly sampling, and (3) molecular dynamics simulations. The energy parameter optimization is based on the energy landscape theory and uses a Monte Carlo search to find a set of parameters that seeks the largest ratio deltaE(s)/DeltaE for all proteins in a training set simultaneously. Here, deltaE(s) is the stability gap between the native and the average in the denatured states and DeltaE is the energy fluctuation among these states. Some of the energy parameters optimized are found to show significant correlation with experimentally observed quantities: (1) In the recognition test, the optimized function assigns the lowest energy to either the native or a near-native structure among many decoy structures for all the proteins studied. (2) Structure prediction with the fragment assembly sampling gives structure models with root mean square deviation less than 6 A in one of the top five cluster centers for five of six proteins studied. (3) Structure prediction using molecular dynamics simulation gives poorer performance, implying the importance of having a more precise description of local structures. The physical energy function solely inferred from a structural database neither utilizes sequence information from the family of the target nor the outcome of the secondary structure prediction but can produce the correct native fold for many small proteins.

Algorithms↗
PubMed2001

Optimizing cardiac energy metabolism: how can fatty acid and carbohydrate metabolism be manipulated?

Optimizing energy metabolism in the heart is a novel approach for the management of ischaemic heart disease, especially in conjunction with optimizing or restoring coronary flow. In particular, promoting myocardial glucose metabolism can enhance heart function, lessen injury to tissue, or both. Several pharmacological agents that directly stimulate myocardial glucose oxidation or indirectly stimulate glucose oxidation secondary to inhibition of oxidation of fatty acids are now available. Trimetazidine is the first compound in the class of 3-ketoacyl-coenzyme A thiolase inhibitors to see wide-spread clinical use. This agent increases glucose metabolism in the heart secondary to a direct inhibition of fatty acid metabolism. Considering results of experimental and clinical studies on other agents, it is clear that metabolic agents may provide a new approach to treating cardiovascular disease that should complement and improve existing therapies.

Animals↗
PubMedDate not supplied

[Means of optimizing light energy conversion in the primary stages of photosynthesis. II. Optimization of the structure of an uniform photosynthetic unit lattice].

The possibility of optimization of the structure of a model photosynthetic unit lattice is analysed. The efficiency of the photosynthetic unit operation is evaluated from the time of excitation energy trapping by reaction centers. The calculations assume a Förster inductive resonance mechanism for energy transfer within light--harvesting antenna and pairwise dipolar interactions. We use the probability matrix method which is adapted to excitation trapping time (but not to excitation jumps number) calculation. It is shown that the specific anisotropy of the distances between antenna molecules (which is in principle possible due to the diskshaped form of chlorophyll molecules) in combination with the optimal spatial arrangement of reaction centers as "well regulated clusters" allows to decrease the time of excitation energy trapping by over an order of magnitude. The requirements for optimization of the structure of a macroscopic photosynthetic unit lattice and the consequences following from them for the in vivo systems are formulated.

Chlorophyll↗