Flexible ligand docking using conformational ensembles.

Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK, is modified to allow it to rapidly fit multiple conformations of ligands. Conformations of a given molecule are pre-calculated in the same frame of reference, so that each conformer shares a common rigid fragment with all other conformations. The ligand conformers are then docked together, as an ensemble, into a receptor binding site. This takes advantage of the redundancy present in differing conformers of the same molecule. The algorithm was tested using three organic ligand protein systems and two protein-protein systems. Both the bound and unbound conformations of the receptors were used. The ligand ensemble method found conformations that resembled those determined in X-ray crystal structures (RMS values typically less than 1.5 A). To test the method's usefulness for inhibitor discovery, multi-compound and multi-conformer databases were screened for compounds known to bind to dihydrofolate reductase and compounds known to bind to thymidylate synthase. In both cases, known inhibitors and substrates were identified in conformations resembling those observed experimentally. The ligand ensemble method was 100-fold faster than docking a single conformation at a time and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation.     

Flexible sigmoidoscopy in outpatients with suspected colonic disease.

One hundred and fifteen patients attending a gastroenterology clinic were investigated by flexible sigmoidoscopy as outpatients. There were asked to fast before the examination and give a high-volume enema and sedated before the examination. A standard long colonoscope was used rather than the 60-cm sigmoidoscope, which limits the distance that can be examined and forces the operator to work very close to the patient. Preparation was considered good in 95 patients and 49 were examined as far as the hepatic flexure or beyond. Sixty-one patients were found to have lesions of the colon, 25 of them ulcerative colitis, 16 a poly, and nine carcinoma. Despite the fact that these patients were selected (some of them had already had ulcerative colitis diagnosed), flexible sigmoidoscopy proved to be a valuable initial outpatient investigation. The proximal colon was well visualised in 46 patients and a subsequent barium enema was considered unnecessary. There were no complications and the procedure seemed to be well tolerated.     

Flexible Memory Networks

Networks of neurons in some brain areas are flexible enough to encode new memories quickly. Using a standard firing rate model of recurrent networks, we develop a theory of flexible memory networks. Our main results characterize networks having the maximal number of flexible memory patterns, given a constraint graph on the network’s connectivity matrix. Modulo a mild topological condition, we find a close connection between maximally flexible networks and rank 1 matrices. The topological condition is H ₁(X;ℤ)=0, where X is the clique complex associated to the network’s constraint graph; this condition is generically satisfied for large random networks that are not overly sparse. In order to prove our main results, we develop some matrix-theoretic tools and present them in a self-contained section independent of the neuroscience context.     

Flexible rhombic flap

A flexible rhombic flap which can be designed in accordance with the degree of tension of skin bordering a part of the defect has been described. This procedure provides sufficient coverage of a skin defect with very little dog-ear.     

Flexible protein-protein docking

Predicting the structure of protein-protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes. Flexibility can be addressed at several levels: implicitly, by smoothing the protein surfaces or allowing some degree of interpenetration (soft docking) or by performing multiple docking runs from various conformations (cross or ensemble docking); or explicitly, by allowing sidechain and/or backbone flexibility. Although significant improvements have been achieved in the modeling of sidechains, methods for the explicit inclusion of backbone flexibility in docking are still being developed. A few novel approaches have emerged involving collective degrees of motion, multicopy representations and multibody docking, which should allow larger conformational changes to be modeled.     

Flexible Kernel Memory

This paper introduces a new model of associative memory, capable of both binary and continuous-valued inputs. Based on kernel theory, the memory model is on one hand a generalization of Radial Basis Function networks and, on the other, is in feature space, analogous to a Hopfield network. Attractors can be added, deleted, and updated on-line simply, without harming existing memories, and the number of attractors is independent of input dimension. Input vectors do not have to adhere to a fixed or bounded dimensionality; they can increase and decrease it without relearning previous memories. A memory consolidation process enables the network to generalize concepts and form clusters of input data, which outperforms many unsupervised clustering techniques; this process is demonstrated on handwritten digits from MNIST. Another process, reminiscent of memory reconsolidation is introduced, in which existing memories are refreshed and tuned with new inputs; this process is demonstrated on series of morphed faces.     

Flexible exportation mechanisms of arthrofactin in Pseudomonas sp. MIS38

Aims: To obtain further insights into transportation mechanisms of a most effective biosurfactant, arthrofactin in Pseudomonas sp. MIS38. Methods and Results: A cluster genes arfA/B/C encodes an arthrofactin synthetase complex (ArfA/B/C). Downstream of the arfA/B/C lie genes encoding a putative periplasmic protein (ArfD, 362 aa) and a putative ATP‐binding cassette transporter (ArfE, 651 aa), namely arfD and arfE, respectively. The arfA/B/C, arfD, and arfE form an operon suggesting their functional connection. Gene knockout mutants ArfD:Km, ArfE:Km, ArfD:Tc/ArfE:Km, and gene overexpression strains MIS38(pME6032_arfD/E) and ArfE:Km(pME6032_arfD/E) were prepared and analysed for arthrofactin production profiles. It was found that the production levels of arthrofactin were temporally reduced in the mutants or increased in the gene overexpression strains, but they eventually became similar level to that of MIS38. Addition of ABC transporter inhibitors, glibenclamide and sodium ortho‐vanadate dramatically reduced the production levels of arthrofactin. This excludes a possibility that arthrofactin is exported by diffusion with the aid of its own high surfactant activity. Conclusions: ArfD/E is not an exclusive but a primary exporter of arthrofactin during early growth stage. Reduction in the arthrofactin productivity of arfD and arfE knockout mutants was eventually rescued by another ABC transporter system. Effects of arfD and arfE overexpression were evident only for 1‐day cultivation. Multiple ATP dependent active transporter systems are responsible for the production of arthrofactin. Significance and Impact of the Study: Pseudomonas bacteria are characterized to be endued with multiple exporter and efflux systems for secondary metabolites including antibiotics, plant toxins, and biosurfactants. The present work demonstrates exceptionally flexible and highly controlled transportation mechanisms of a most effective lipopeptide biosurfactant, arthrofactin in Pseudomonas sp. MIS38. Because lipopeptide biosurfactants are known to enhance efficacy of bioactive compounds and arfA/B/C/D/E orthologous genes are also found in plant pathogenic P. fluorescens and P. syringae strains, the knowledge would also contribute to develop a technology controlling plant diseases.     

Simulations of Flexible Manifolds

Monte Carlo simulations of flexible two-dimensional model membranes embedded in three space dimensions are reported. We explain in detail the techniques how to simulate fluid open membranes and fluid closed membranes (vesicles). It is shown that polymerized open membranes are rough and flat. Accordingly, the two larger components of the inertia tensor are proportional to the number of monomers of the surface, λ₃ ≈ λ₂ ～ N, whereas the smallest λ₁ ～ N ^0.65. Polymerized vesicles are isotropic and their mean square radius of gyration is R ² ～ λ _k ～ N. In contrast, fluid membranes and vesicles exhibit crumpled shapes with λ _k ～ N ^0.8 for k = 1,2,3. A monomer on a fluid surface exhibits a time-dependent mean squared displacement of r ² (t) ～ t ^0.8.     

Flexible and robust networks

We consider networks with two types of nodes. The v-nodes, called centers, are hyperconnected and interact with one another via many u-nodes, called satellites. This centralized architecture, widespread in gene networks, possesses two fundamental properties. Namely, this organization creates feedback loops that are capable of generating practically any prescribed patterning dynamics, chaotic or periodic, or having a number of equilibrium states. Moreover, this organization is robust with respect to random perturbations of the system.     

Three-dimensional structure of apotransketolase. Flexible loops at the active site enable cofactor binding.

The structure determination of apotransketolase and the comparison of its three-dimensional structure with that of the holoenzyme has revealed that no large conformational changes are associated with cofactor binding. Two loops at the active site are flexible in the apoenzyme which enables ThDP to reach its binding site. Binding of the cofactor induces defined conformations for these two loops at the active site. One of these loops is directly involving in binding of the cofactors, Ca2+ and ThDP. This loop acts like a flap which closes off the diphosphate binding site. After binding of the cofactor, residues of this loop form interactions to residues of loop 383-398 from the second subunit. These interactions stabilize the conformation of the two loops from a flexible to a 'closed' conformation.