ordering of tasks in molecular dynamics problem

... communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements ... states Detection of global domain motions through DCCM Global domain motions in proteins involve the collective motion of backbone atoms and aid in the transitioning of the protein between different ... chain contacts, we calculate the inter-residue side chain distance time series using the minimum distance between all non-hydrogen side chain atoms of each of the amino acids Similarly, polar interactions

Ngày tải lên: 24/11/2022, 17:39

... to migrate inwards during substrate binding substrate binding They also indicated eqolisins show structural similarity with the carbohydrate-binding concanavalin A-like lectins/glucanases superfamily ... Mutual Information network is involved in substrate specificity a Cartoon of 2IFW with highlighted binding cleft Transition state inhibitor is indicated in purple licorice Sites are indicated in ... Ws, two instances of phenylalanine, one of tyrosine and one of glutamate The glutamate substitution in BCa0000005 would result in a buried but charged side-chain, which could be explained by

Ngày tải lên: 25/11/2020, 14:24

... domain.The intracellular region of ErbB proteins consists of approximately 540 amino acids, including a crucial tyrosine kinase domain (TKD) and a carboxyterminal tail (CTT) of about 230 amino ... of MD is to evaluate the stability of protein–ligand complexes after docking, providing insights into whether the binding pose is maintained under physiological conditions By monitoring key interactions ... targets like enzymes or proteins Its primary aim is to identify the best binding pose of a ligand within a protein's active site, enabling estimation of binding affinity and interaction specificity

Ngày tải lên: 23/07/2025, 00:30

... reduction in charge density on citrullinization of arginines (as occurs in multiple sclerosis) diminishes the interaction with negatively charged lipids in the myelin membrane, accounting for a certain ... illustrated in Table 3 Evidently, there is a preference for serine or threonine as an anchor point for position P9 of the MBP peptide-binding grooves Interestingly, truncation of the C-terminus of the ... importance of the nature of the amino acid at position 81 of the encephalitogenic sequence 74–85 of guinea MBP: replacement of Asp81 with an alanine seems to break a chain of electrostatic interactions,

Ngày tải lên: 07/03/2014, 16:20

... perturbation of the DNA-binding interface showed that, in the case of HPV-16, most of the binding energy comes from a ‘direct readout’ recognition mode [22] In fact, recognition of DNA by proteins, in ... alanine of the residues Lys325 and Lys327, located in the b2–b3 loop, produce a decrease in the DNA bind-ing [22] that is restored upon back mutation into arginine, indicating the importance of ... structural dynamics of the DNA-binding domains of two prototypic strains, human papillomavirus strain 16 and the bovine papillomavirus strain 1 The simulations underline different dynamic features in

Ngày tải lên: 16/03/2014, 10:20

... 10% off print titles Custom notification of new releases in your field of interest Special offers and discounts NATIONAL ACADEMY OF SCIENCES NATIONAL ACADEMY OF ENGINEERING INSTITUTE OF MEDICINE ... x 11 2011 of Supercomputing Time for the Study of Molecular Dynamics: Second Round Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics; ... represented in the 81 proposals that were considered by the committee They comprised a cross section of the biomolecular dynamics field in academia, industry and government including an array of both

Ngày tải lên: 16/03/2014, 15:20

... study of the lipocalins [15]. Retinol binding site Retinol binds to RBP in the core of the b-barrel. When bound, retinol is almost totally encapsulated by the protein, the b-ionone ring lying in ... 2005) doi:10.1111/j.1742-4658.2005.04898.x Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic con- ditions retinol-binding protein undergoes ... globule states of proteins are also postula- ted to be involved in a range of important physiologi- cal processes, including the insertion of proteins into membranes, the release of bound ligands

Ngày tải lên: 16/03/2014, 23:20

... Campinas, SP, Brazil §Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA –Department of Molecular Mechanisms of Mycobacterial Infections, Institut ... groups, by combining high affinity and low reactivity, opti-mized inhibitors of this kind should have minimal effects on other proteins in vivo Indeed, a prodrug version of an aldolase inhibitor kills ... site involving a His residue at position ‘0’ (i.e immediately preceding the natural initiator Met within the tail downstream of the thrombin cleavage site in the N-terminal extension containing

Ngày tải lên: 23/03/2014, 07:20

... Trang 4OEC proteins and also traces of D2 and the CP43 protein(Fig 1B) Interestingly, traces of PsbE protein (the a subunit of Cyt b559) could also be distinguished in young leaves of DpsbF (Fig ... PsbJ is critical in providingproper dockingsites, either directly or indirectly, by modifyingthe conformation of PSII on the lumenal side, makingefficient bindingof PsbQ and PsbP of the OEC possible ... PsbE protein was also present in tiny amounts in the thylakoid membranes of young, developing leaves of DpsbF Of the internal antenna proteins of PSII, the assembly of CP47 possibly also occurs

Ngày tải lên: 30/03/2014, 13:20

... functions determining interatomic interactions are known 2 NUMERICAL APPROACH In molecular dynamics (MD) simulations, interactions between molecules or atoms in a material are determined by a prescribed ... 10.1007/s10765-006-0137-zMolecular Dynamics Calculation of Critical Point of Nickel Changrui Cheng1 and Xianfan Xu1,2 Received: June 28, 2005 The critical point of nickel and the phase diagram near the critical point ... lines (binodes), as will be seen in the next section The peak of the two saturation lines is the critical point, and its parame-ters of temperature, pressure, and density can then be determined

Ngày tải lên: 06/05/2014, 08:54

... T δ initial temperature increase for calculating the specific heat T ∆ final temperature increase for calculating the specific heat v velocity x coordinate in x direction y coordinate in y ... the increase of the atomic kinetic energy in laser heating, atoms vibrate more in the crystal region, causing a lower peak of the number density of atoms and a wide distribution As laser heating ... capable of predicting the heating process induced by a picosecond laser pulse Laser Induced Phase Change In this section, various phenomena accompanying phase change in an argon target illuminated

Ngày tải lên: 06/05/2014, 08:55

... God is the principal originating source of being and goodness, including moral goodness Suarez is charging in effect that their theory has the unintended consequence of making God the ... might use our sins as instruments in bringing us to true humility and repentance, he cannot directly intend sin or be a causal source of sin or in any way induce us to sin Suarez summarizes ... genius is in bringing together in synthesis his own... evil and theodicy, equal in importance to the Rationalist dream of a perfect science, involves the labyrinthine problem of freedom

Ngày tải lên: 11/06/2014, 15:59

... resolu-tion of the analyzer operating in the linear mode or might result in overlapping of ions originating from protein/ peptides of very similar molecular masses In addition, because of technological ... included averaging of tech-nical repeats, interpolation of missing or non-aligned points, binning of neighboring points to reduce data com-plexity, removal of the spectral area below baseline and the ... destroyed the majority of protein interactions and allowed analysis of individual peptides dissociated from (not interacting with) other proteins (e.g., albumin) Characteristic features of MALDI ionization

Ngày tải lên: 18/06/2014, 15:20

... using molecular dynamics analysis The results show that the load, elastic and plastic energies, and relaxation force increased with increasing indentation depth and velocity Nanoindentation induced ... and 260.08 nN, respectively, indicating that the load increased with indentation depth This is due to the number of atoms in contact with the tip increasing with indentation depth Figure 4 shows ... and reproduction in any medium, Trang 2have the atoms in a stable state Figure 2a shows theinitial contact of indentation at 33 ps During indenta-tion, the potential energy of the tip affects

Ngày tải lên: 21/06/2014, 01:20

... couplings from protons whose nuclear spins are interacting only very weakly with the unpaired electron spin, e.g protons from the protein backbone within the cofactor binding pocket, protons of ... modification of the cofactorbinding site at the 8a-methyl group and at the linkage of the ribityl side chain Hence, as a first result, structural information regarding the distance and location of the ... (Fig 8), the positions of the two histidines were assigned surprisingly accurately by ENDOR His365 (the analog amino acid of His354 in X laevis) is indeed located in the binding pocket nearby the...

Ngày tải lên: 16/03/2014, 02:20

... are involved in recognition of the polyubiquitinated protein substrates, unfolding of the condemned protein [24], removing ubiquitin chains for recycling [25,26] and opening an axial gate into ... presence of proteasome, supporting the direct or indirect involvement of the flavin cofactor in protein complex formation [34] Mdm2 dependent polyubiquitination Fig Proposed mechanisms of ubiquitindependent ... state of the flavin cofactor present in the active site of Lot6p Recruitment of the transcription factor occurs when the flavin is in its fully reduced form This process is independent of the mode of...

Ngày tải lên: 16/03/2014, 02:20

... complaints of spinal and leg bone pain, was recognized as a type of chronic toxicity induced by excess Cd contamination of drinking water and cereals (mainly rice) Since then, the contamination of ... with lines depicting the kinetics of initial arrival of Cd in the respective ROI The X-intercepts of the fitting lines were adopted as the arrival times of the theoretical “leading edge” of the ... transporter protein involved in Cd storage in root vacuoles All high-Cd indica cultivars used in this study showed a loss of function of OsHMA3, resulting in failure to sequester Cd in their root...

Ngày tải lên: 11/08/2014, 11:21

... machining of brittle materials, the machining mechanism is not yet explained clearly In this research, a realistic molecular dynamics (MD) model taking into account the effect of tool cutting ... tool in grinding of ductile metals 12 Figure 1.5 Mechanism of material removal in grinding with machining with high negative rake tools .12 Figure 1.6 A projection of machining ... machining of brittle materials 1.2.4 Diamond Tool Wear in Ductile Mode Cutting Rapid wear of single point diamond tools is a limiting factor in ductile mode cutting of silicon wafers Because of...

Ngày tải lên: 12/09/2015, 08:16