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PubMed2004

Evaluation of the impacts of dock structures and land use on tidal creek ecosystems in South Carolina estuarine environments.

Tidal creeks and their associated salt marshes are the primary link between uplands and estuaries in the southeastern region. They are also critical nursery and feeding grounds. In addition, the uplands surrounding creeks are preferred sites for homebuilding because of their natural beauty and the ability to access the estuary from a personal dock structure. The objective of this study was to evaluate the cumulative impacts of docks on tidal creek nursery habitats for both small and large tidal creeks. The number of docks was associated with the amount of impervious cover in both small and large creeks. The presence of docks had little measurable effect on sediment metal concentrations at the scale of small and large creeks. In small and large creeks, sediment polycyclic aromatic hydrocarbon (PAH) concentrations were related to the human activity in the upland that includes the presence of docks at the scale of small and large creeks. Some impacts on the benthic community were associated with docks and human activity in small creeks but not in large creeks. Suburban development may reduce fish and crustacean abundances, but the dock may potentially mediate the development effect. Individually, the harm to the marine environment resulting from dock shading, chrominated copper arsenate leachates, and PAH contamination was small at the scale of tidal creeks. However, impacts from dock structures could not be separated from anthropogenic watershed-scale effects. These results demonstrate that suburban development with its accompanying dock construction does represent a major source of environmental degradation to tidal creeks and associated salt marsh habitats.

Agriculture↗

PubMed1999

The Effects of Boat Docks on Eelgrass Beds in Coastal Waters of Massachusetts.

/ The effects of docks on eelgrass beds were measured using plant population characteristics (shoot density, canopy height, and growth rates), light levels, and an assessment of eelgrass bed quality in Massachusetts estuaries. Eelgrass populations were impacted under and directly adjacent to docks, as shown by depressed shoot density and canopy structure. Severe impacts can cause fragmentation of eelgrass beds, thus contributing to large-scale declines in estuaries such as Waquoit Bay. Impacts were fewer under docks supported by piers than under floating docks, and taller piers resulted in fewer impacts. Based on this investigation, we conclude that docks should be greater than 3 m in height above the bottom in areas with tidal ranges less than 1 m to allow enough light to sustain eelgrass beds under the docks. In addition to dock height, orientation and width were also found to be important factors affecting eelgrass. Narrow docks with a north-south orientation can best ensure the long-term survival of eelgrass under and near the dock. KEY WORDS: Docks; Shade; Eelgrass beds; Zostera marina; Seagrass

Journal Article↗

PubMed1991

"Soft docking": matching of molecular surface cubes.

Molecular recognition is achieved through the complementarity of molecular surface structures and energetics with, most commonly, associated minor conformational changes. This complementarity can take many forms: charge-charge interaction, hydrogen bonding, van der Waals' interaction, and the size and shape of surfaces. We describe a method that exploits these features to predict the sites of interactions between two cognate molecules given their three-dimensional structures. We have developed a "cube representation" of molecular surface and volume which enables us not only to design a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. The present molecular docking procedure may be divided into two stages. The first is the selection of a population of complexes by geometric "soft docking", in which surface structures of two interacting molecules are matched with each other, allowing minor conformational changes implicitly, on the basis of complementarity in size and shape, close packing, and the absence of steric hindrance. The second is a screening process to identify a subpopulation with many favorable energetic interactions between the buried surface areas. Once the size of the subpopulation is small, one may further screen to find the correct complex based on other criteria or constraints obtained from biochemical, genetic, and theoretical studies, including visual inspection. We have tested the present method in two ways. First is a control test in which we docked the components of a molecular complex of known crystal structure available in the Protein Data Bank (PDB). Two molecular complexes were used: (1) a ternary complex of dihydrofolate reductase, NADPH and methotrexate (3DFR in PDB) and (2) a binary complex of trypsin and trypsin inhibitor (2PTC in PDB). The components of each complex were taken apart at an arbitrary relative orientation and then docked together again. The results show that the geometric docking alone is sufficient to determine the correct docking solutions in these ideal cases, and that the cube representation of the molecules does not degrade the docking process in the search for the correct solution. The second is the more realistic experiment in which we docked the crystal structures of uncomplexed molecules and then compared the structures of docked complexes with the crystal structures of the corresponding complexes. This is to test the capability of our method in accommodating the effects of the conformational changes in the binding sites of the molecules in docking.(ABSTRACT TRUNCATED AT 400 WORDS)

Antigen-Antibody Complex↗

PubMed2005

Accounting for global protein deformability during protein-protein and protein-ligand docking.

Computational docking methods are valuable tools aimed to simplify the costly process of drug development and improvement. Most current approaches assume a rigid receptor structure to allow virtual screening of large numbers of possible ligands and putative binding sites on a receptor molecule. However, inclusion of receptor flexibility can be of critical importance since binding of a ligand can lead to changes in the receptor protein conformation that are sterically necessary to accommodate a ligand. Recent approaches to efficiently account for receptor flexibility during docking simulations are reviewed. In particular, accounting efficiently for global conformational changes of the protein backbone during docking is a still challenging unsolved problem. An approximate method has recently been suggested that is based on relaxing the receptor conformation during docking in pre-calculated soft collective degrees of freedom (M. Zacharias, Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP, Proteins: Struct., Funct., Genet. 54 (2004) 759-767). Test applications on protein-protein docking and on docking the inhibitor staurosporine to the apo-form of cAMP-dependent protein kinase A catalytic domain indicate significant improvement of docking results compared to rigid docking at a very modest computational demand. Accounting for receptor conformational changes in pre-calculated global degrees of freedom might offer a promising route to improve systematic docking screening simulations.

Binding Sites↗

PubMed2004

GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm.

Based on an improved multi-population genetic algorithm, a new fast flexible docking program, GAsDock, was developed. The docking accuracy, screening efficiency, and docking speed of GAsDock were evaluated by the docking results of thymidine kinase (TK) and HIV-1 reverse transcriptase (RT) enzyme with 10 available inhibitors of each protein and 990 randomly selected ligands. Nine of the ten known inhibitors of TK were accurately docked into the protein active site, the root-mean-square deviation (RMSD) values between the docking and X-ray crystal structures are less than 1.7A; binding poses (conformation and orientation) of 9 of the 10 known inhibitors of RT were reproduced by GAsDock with RMSD values less than 2.0A. The docking time is approximately in proportion to the number of rotatable bonds of ligands; GAsDock can finish a docking simulation within 60s for a ligand with no more than 20 rotatable bonds. Results indicate that GAsDock is an accurate and remarkably faster docking program in comparison with other docking programs, which is applausive in the application of virtual screening.

Algorithms↗

PubMed1996

Cortisol responses of calves to two methods of tail docking used with or without local anaesthetic.

Tail docking of dairy cows to facilitate milking is carried out on calves or on heifers before calving. By monitoring changes in plasma cortisol concentrations, this study evaluated the distress in calves when docked by a rubber ring or docking iron (cautery) with or without local anaesthetic. The cortisol responses indicated that in most calves docking using a rubber ring or docking iron was no more distressing than control handling and simulated docking. A small proportion of calves in control and tail docked groups exhibited larger cortisol responses, the magnitudes of which suggested that they experienced some mild distress. There was no detectable benefit with either method of docking when local anaesthetic was used. The rubber ring is the preferable method, as there was some haemorrhage after docking with the docking iron.

Journal Article↗

PubMed1999

The Drosophila SH2-SH3 adapter protein Dock is expressed in embryonic axons and facilitates synapse formation by the RP3 motoneuron.

The Dock SH2-SH3 domain adapter protein, a homolog of the mammalian Nck oncoprotein, is required for axon guidance and target recognition by photoreceptor axons in Drosophila larvae. Here we show that Dock is widely expressed in neurons and at muscle attachment sites in the embryo, and that this expression pattern has both maternal and zygotic components. In motoneurons, Dock is concentrated in growth cones. Loss of zygotic dock function causes a selective delay in synapse formation by the RP3 motoneuron at the cleft between muscles 7 and 6. These muscles often completely lack innervation in late stage 16 dock mutant embryos. RP3 does form a synapse later in development, however, because muscles 7 and 6 are normally innervated in third-instar mutant larvae. The absence of zygotically expressed Dock also results in subtle defects in a longitudinal axon pathway in the embryonic central nervous system. Concomitant loss of both maternally and zygotically derived Dock dramatically enhances these central nervous system defects, but does not increase the delay in RP3 synaptogenesis. These results indicate that Dock facilitates synapse formation by the RP3 motoneuron and is also required for guidance of some interneuronal axons The involvement of Dock in the conversion of the RP3 growth cone into a presynaptic terminal may reflect a role for Dock-mediated signaling in remodeling of the growth cone's cytoskeleton.

Adaptor Proteins, Signal Transducing↗

PubMed2004

Stimulation of insulin release by glucose is associated with an increase in the number of docked granules in the beta-cells of rat pancreatic islets.

Electron microscopy and quantitative stereological techniques were used to study the dynamics of the docked granule pool in the rat pancreatic beta-cell. The mean number of granules per beta-cell was 11,136. After equilibration in RPMI containing 5.6 mmol/l glucose, 6.4% of the granules (approximately 700) were docked at the plasma membrane (also measured as [means +/- SE] 4.3 +/- 0.6 docked granules per 10 microm of plasma membrane at the perimeter of the cell sections). After a 40-min exposure to 16.7 mmol/l glucose, 10.2% of the granules (approximately 1,060) were docked (6.4 +/- 0.8 granules per 10 microm of plasma membrane). Thus, the docked pool increased by 50% during stimulation with glucose. Islets were also exposed to 16.7 mmol/l glucose in the absence or presence of 10 micromol/l nitrendipine. In the absence and presence of nitrendipine, there were 6.1 +/- 0.7 and 6.3 +/- 0.6 granules per 10 microm of membrane, respectively. Thus, glucose increased granule docking independently of increased [Ca2+]i and exocytosis. The data suggest a limit to the number of docking sites. As the rate of docking exceeded the rate of exocytosis, docking is not rate limiting for insulin release. Only with extremely high release rates, glucose stimulation after a 4-h incubation with a high concentration of fatty acid-free BSA, was the docked granule pool reduced in size.

Animals↗

PubMed2002

Indicators of acute pain and fly avoidance behaviors in Holstein calves following tail-docking.

Previous work showed that the banding process of docking minimally affected mature cows' behavior and physiology, but cutting off the necrotic tail increased haptoglobin. Additionally the docked cows had more flies on the rear legs and exhibited more fly avoidance behaviors. Because many producers dock young calves while they are in hutches where fly problems are more pronounced, we investigated changes in behavior and physiology of young calves following docking by banding. Twenty calves (3 to 5 wk of age) were assigned to a docked or control group, at each of two locations (Indiana and Wisconsin). After applying a band to dock the tail, calves were tested every 15 min for sensitivity to heat below the band at the Indiana location. Calf behavior was recorded for 2 h postbanding and analyzed continuously for that period. After 3 wk, tails were removed and then 1 wk later, fly counts and fly avoidance behaviors were observed at both locations. Tails were sensitive to heat below the banding site, for 60 to 120 min postbanding (mean 87 min). Banded calves were more active than control calves during the 2 h following banding. Percentage of time spent lying was greater for control calves, and the percentage of time spent walking was greater for docked than control calves. More importantly, movements of the head to touch the tail were increased for banded calves (eight-fold more movements). Fly avoidance behaviors directed toward the rear of the calf were evident at noon or in the afternoon. Ear twitches were more frequent for the docked calves and less frequent in the morning for all calves. Licking was more frequent for the docked calves at 1200 and 1600 h. Tail swings were most frequent at 1200 and more frequent for control calves. Two acute phase proteins, haptoglobin and alpha1 acid-glycoprotein, were not different at any time. In this study, calves that were banded at 3-wk-of-age showed behaviors indicative of discomfort for 2 h, were attacked by more flies, and showed increased fly avoidance behaviors when docked.

Acute-Phase Proteins↗

PubMed1995

Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking.

Rigid-body docking of two molecules involves matching of their surfaces. A successful docking methodology considers two key issues: molecular surface representation, and matching. While approaches to the problem differ, they all employ certain surface geometric features. While surface normals are routinely created with molecular surfaces, their employment has surprisingly been almost completely overlooked. Here we show how the normals to the surface, at specific, well placed points, can play a critical role in molecular docking. If the points for which the normals are calculated represent faithfully and accurately the molecular surfaces, the normals can substantially ameliorate the efficiency of the docking in a number of ways. The normals can drastically reduce the combinatorial complexity of the receptor-ligand docking. Furthermore, they can serve as a powerful filter in screening for quality docked conformations. Below we show how deploying such a straight forward device, which is easy to calculate, large protein-protein molecules are docked with unparalleled short times and with a manageable number of potential solutions. Considering the facts that here we dock (1) two large protein molecules, including several large immunoglobulin-lysozyme complexes; (2) that we use the entire molecular surfaces, without a predefinition of the active sites, or of the epitopes, of neither the ligand nor the receptor; that (3) the docking is completely automated, without any labelling, or pre-specification, of the input structural database, and (4) with a single set of parameters, without any further tuning whatsoever, such results are highly desirable. This approach is specifically geared towards matching of the surfaces of large protein molecules and is not applicable to small molecule drugs.

Computer Graphics↗

PubMed1996

Wood preservative leachates from docks in an estuarine environment.

Environmental concentrations and biological effects of certain metals and organic compounds found in wood preservatives were examined. The study focused on leachates from private residential docks in South Carolina tidal creeks. Copper, chromium, arsenic, and polynuclear aromatic hydrocarbons (PAHs) were measured in composite samples of surficial sediments and naturally occurring oyster populations (Crassostrea virginica) from creeks with high densities of docks, and from nearby reference creeks with no docks. In some cases, metal concentrations in sediments and oysters were higher immediately adjacent to dock pilings than they were elsewhere in the same creek. Sediments from most sites had concentrations of metals and total PAHs which were below levels reported to cause biological effects, however. Solid-phase Microtox(R) bioassays using whole sediments and rotifer bioassays using sediment pore water showed no significant differences in acute toxicity between creeks with and without docks. Oysters growing directly on dock pilings had significantly higher concentrations of copper than oysters growing at least 10 m away; however, there was no significant difference in the physiological condition of these oysters. Four-day field bioassays measuring percent survival of mummichogs (Fundulus heteroclitus), mud snails (Ilyanassa obsoleta), juvenile red drum (Sciaenops ocellatus), and juvenile white shrimp (Penaeus setiferus) showed no significant differences between sites near to and distant from newly constructed docks. Hatchery-reared oysters showed no significant differences between dock and reference sites in percent survival, growth, or bioaccumulation of metals after six weeks of exposure. The results suggest that, in estuarine environments with a moderate tidal range (1.5-2.0 m), wood preservative leachates from dock pilings have no acutely toxic effects on four common estuarine species, nor do they affect the short-term survival or growth of juvenile oysters.

Animals↗

PubMed1987

Docking of chromaffin granules--a necessary step in exocytosis?

Putative docking of secretory vesicles comprising recognition of and attachment to future fusion sites in the plasma membrane has been investigated in chromaffin cells of the bovine adrenal medulla and in rat phaeochromocytoma (PC 12) cells. Upon permeabilization with digitonin, secretion can be stimulated in both cell types by increasing the free Ca2+-concentration to microM levels. Secretory activity can be elicited up to 1 hr after starting permeabilization and despite the loss of soluble cytoplasmic components indicating a stable attachment of granules to the plasma membrane awaiting the trigger for fusion. Docked granules can be observed in the electron microscope in permeabilized PC 12 cells which contain a large proportion of their granules aligned underneath the plasma membrane. The population of putatively docked granules in chromaffin cells cannot be as readily discerned due to the dispersal of granules throughout the cytoplasm. Further experiments comparing PC 12 and chromaffin cells suggest that active docking but not transport of granules can still be performed by permeabilized cells in the presence of Ca2+: a short (2 min) pulse of Ca2+ in PC 12 cells leads to the secretion of almost all releasable hormone over a 15 min observation period whereas, in chromaffin cells, with only a small proportion of granules docked, withdrawal of Ca2+ leads to an immediate halt in secretion. Transport of chromaffin granules from the Golgi to the plasma membrane docking sites seems to depend on a mechanism sensitive to permeabilization. This is shown by the difference in the amount of hormone released from the two permeabilized cell types, reflecting the contrast in the proportion of granules docked to the plasma membrane in PC 12 or chromaffin cells. Neither docking nor the docked state are influenced by cytochalasin B or colchicine. The permeabilized cell system is a valuable technique for the in vitro study of interaction between secretory vesicles and their target membrane.

Adrenal Gland Neoplasms↗

PubMed2004

Protein flexibility in ligand docking and virtual screening to protein kinases.

The main complicating factor in structure-based drug design is receptor rearrangement upon ligand binding (induced fit). It is the induced fit that complicates cross-docking of ligands from different ligand-receptor complexes. Previous studies have shown the necessity to include protein flexibility in ligand docking and virtual screening. Very few docking methods have been developed to predict the induced fit reliably and, at the same time, to improve on discriminating between binders and non-binders in the virtual screening process. We present an algorithm called the ICM-flexible receptor docking algorithm (IFREDA) to account for protein flexibility in virtual screening. By docking flexible ligands to a flexible receptor, IFREDA generates a discrete set of receptor conformations, which are then used to perform flexible ligand-rigid receptor docking and scoring. This is followed by a merging and shrinking step, where the results of the multiple virtual screenings are condensed to improve the enrichment factor. In the IFREDA approach, both side-chain rearrangements and essential backbone movements are taken into consideration, thus sampling adequately the conformational space of the receptor, even in cases of large loop movements. As a preliminary step, to show the importance of incorporating protein flexibility in ligand docking and virtual screening, and to validate the merging and shrinking procedure, we compiled an extensive small-scale virtual screening benchmark of 33 crystal structures of four different protein kinases sub-families (cAPK, CDK-2, P38 and LCK), where we obtained an enrichment factor fold-increase of 1.85+/-0.65 using two or three multiple experimental conformations. IFREDA was used in eight protein kinase complexes and was able to find the correct ligand conformation and discriminate the correct conformations from the "misdocked" conformations solely on the basis of energy calculation. Five of the generated structures were used in the small-scale virtual screening stage and, by merging and shrinking the results with those of the original structure, we show an enrichment factor fold increase of 1.89+/-0.60, comparable to that obtained using multiple experimental conformations. Our cross-docking tests on the protein kinase benchmark underscore the necessity of incorporating protein flexibility in both ligand docking and virtual screening. The methodology presented here will be extremely useful in cases where few or no experimental structures of complexes are available, while some binders are known.

Algorithms↗

PubMed2001

Effects of an oral dose of acetyl salicylate at tail docking on the behaviour of lambs aged three to six weeks.

To investigate a practical method of providing analgesia for docking of lambs' tails, the effectiveness of an oral dose of aspirin (acetyl salicylate) in reducing discomfort behaviour immediately following application of elastrator rings, was evaluated. The study involved a pilot trial and an experiment, both using Romney crossbred lambs aged 3-6 weeks accompanied by their mothers in a group pen, with behaviour recorded on videotape. In the pilot trial, lambs were manually restrained, an elastrator ring was applied, then lambs were given either an oral dose (26mg/kg) of aspirin dissolved in water (Treatment RA, n=5 lambs) or an oral dose of water (Treatment R, n=4 lambs), and released. RA lambs changed posture between sternal recumbency and standing less frequently than R lambs, significantly so from 10 to 20min post-treatment (11 times for RA, compared with 28% (S.E.D. 6.6%) for R lambs). In the experiment, 56 lambs were given one of two docking treatments (either RA: application of an elastrator ring plus the same aspirin treatment as in the pilot trial, or R: application of the ring plus water), or one of two control treatments (CA: restraint plus aspirin; or C: restraint plus water). During the hour after treatment, docking was associated with differences in over three quarters of 52 postures and activities used to describe behaviour (P<0.05), and marked changes over time in the postures/activities affected were observed. Differences were evident within 5min and some were still apparent at 60min post-treatment. When postures and activities were designated as 'normal' or 'abnormal' (typical of docked lambs), over the total hours of observation the mean frequency of abnormal postures was 3.5% for control lambs and 22.6% (S.E.D. 1.64%) for docked lambs, and the mean frequency of abnormal activities was 5.2% for control lambs and 19.3% (S.E.D. 1.40%) for docked lambs. Provision of aspirin to docked lambs was associated with similar levels to those seen in control lambs for two activities but was also associated with increased levels of some activities/postures (P<0.05). These effects were minor compared with the effects of docking and there was no indication of effective analgesia. Thus, when elastrator tail docking rings were applied, behavioural effects indicative of pain were observed immediately and did not subside fully within 1h. Despite indications in the pilot trial of an analgesic effect of aspirin, further experimentation did not substantiate this effect.

Journal Article↗

PubMed2003

C2 domain of protein kinase C alpha: elucidation of the membrane docking surface by site-directed fluorescence and spin labeling.

The C2 domain is a conserved signaling motif that triggers membrane docking in a Ca(2+)-dependent manner, but the membrane docking surfaces of many C2 domains have not yet been identified. Two extreme models can be proposed for the docking of the protein kinase C alpha (PKC alpha) C2 domain to membranes. In the parallel model, the membrane-docking surface includes the Ca(2+) binding loops and an anion binding site on beta-strands 3-4, such that the beta-strands are oriented parallel to the membrane. In the perpendicular model, the docking surface is localized to the Ca(2+) binding loops and the beta-strands are oriented perpendicular to the membrane surface. The present study utilizes site-directed fluorescence and spin-labeling to map out the membrane docking surface of the PKC alpha C2 domain. Single cysteine residues were engineered into 18 locations scattered over all regions of the protein surface, and were used as attachment sites for spectroscopic probes. The environmentally sensitive fluorescein probe identified positions where Ca(2+) activation or membrane docking trigger measurable fluorescence changes. Ca(2+) binding was found to initiate a global conformational change, while membrane docking triggered the largest fluorescein environmental changes at labeling positions on the three Ca(2+) binding loops (CBL), thereby localizing these loops to the membrane docking surface. Complementary EPR power saturation measurements were carried out using a nitroxide spin probe to determine a membrane depth parameter, Phi, for each spin-labeled mutant. Positive membrane depth parameters indicative of membrane insertion were found for three positions, all located on the Ca(2+) binding loops: N189 on CBL 1, and both R249 and R252 on CBL 3. In addition, EPR power saturation revealed that five positions near the anion binding site are partially protected from collisions with an aqueous paramagnetic probe, indicating that the anion binding site lies at or near the surface of the headgroup layer. Together, the fluorescence and EPR results indicate that the Ca(2+) first and third Ca(2+) binding loops insert directly into the lipid headgroup region of the membrane, and that the anion binding site on beta-strands 3-4 lies near the headgroups. The data support a model in which the beta-strands are tilted toward the parallel orientation relative to the membrane surface.

Amino Acid Substitution↗

PubMed1998

Location of the membrane-docking face on the Ca2+-activated C2 domain of cytosolic phospholipase A2.

Docking of C2 domains to target membranes is initiated by the binding of multiple Ca2+ ions to a conserved array of residues imbedded within three otherwise variable Ca2+-binding loops. We have located the membrane-docking surface on the Ca2+-activated C2 domain of cPLA2 by engineering a single cysteine substitution at 16 different locations widely distributed across the domain surface, in each case generating a unique attachment site for a fluorescein probe. The environmental sensitivity of the fluorescein-labeled cysteines enabled identification of a localized region that is perturbed by Ca2+ binding and membrane docking. Ca2+ binding to the domain altered the emission intensity of six fluoresceins in the region containing the Ca2+-binding loops, indicating that Ca2+-triggered environmental changes are localized to this region. Similarly, membrane docking increased the protonation of six fluoresceins within the Ca2+-binding loop region, indicating that these three loops also are directly involved in membrane docking. Furthermore, iodide quenching measurements revealed that membrane docking sequesters three fluorescein labeling positions, Phe35, Asn64, and Tyr96, from collisions with aqueous iodide ion. These sequestered residues are located within the identified membrane-docking region, one in each of the three Ca2+-binding loops. Finally, cysteine substitution alone was sufficient to dramatically reduce membrane affinity only at positions Phe35 and Tyr96, highlighting the importance of these two loop residues in membrane docking. Together, the results indicate that the membrane-docking surface of the C2 domain is localized to the same surface that cooperatively binds a pair of Ca2+ ions, and that the three Ca2+-binding loops themselves provide most or all of the membrane contacts. These and other results further support a general model for the membrane specificity of the C2 domain in which the variable Ca2+-binding loops provide headgroup recognition at a protein-membrane interface stabilized by multiple Ca2+ ions.

Amino Acid Substitution↗

PubMedDate not supplied

Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring.

Docking and scoring are critical issues in virtual drug screening methods. Fast and reliable methods are required for the prediction of binding affinity especially when applied to a large library of compounds. The implementation of receptor flexibility and refinement of scoring functions for this purpose are extremely challenging in terms of computational speed. Here we propose a knowledge-based multiple-conformation docking method that efficiently accommodates receptor flexibility thus permitting reliable virtual screening of large compound libraries. Starting with a small number of active compounds, a preliminary docking operation is conducted on a large ensemble of receptor conformations to select the minimal subset of receptor conformations that provides a strong correlation between the experimental binding affinity (e.g., Ki, IC50) and the docking score. Only this subset is used for subsequent multiple-conformation docking of the entire data set of library (test) compounds. In conjunction with the multiple-conformation docking procedure, a two-step scoring scheme is employed by which the optimal scoring geometries obtained from the multiple-conformation docking are re-scored by a molecular mechanics energy function including desolvation terms. To demonstrate the feasibility of this approach, we applied this integrated approach to the estrogen receptor alpha (ERalpha) system for which published binding affinity data were available for a series of structurally diverse chemicals. The statistical correlation between docking scores and experimental values was significantly improved from those of single-conformation dockings. This approach led to substantial enrichment of the virtual screening conducted on mixtures of active and inactive ERalpha compounds.

Protein Binding↗

PubMed2003

Protein-protein docking with a reduced protein model accounting for side-chain flexibility.

A protein-protein docking approach has been developed based on a reduced protein representation with up to three pseudo atoms per amino acid residue. Docking is performed by energy minimization in rotational and translational degrees of freedom. The reduced protein representation allows an efficient search for docking minima on the protein surfaces within. During docking, an effective energy function between pseudo atoms has been used based on amino acid size and physico-chemical character. Energy minimization of protein test complexes in the reduced representation results in geometries close to experiment with backbone root mean square deviations (RMSDs) of approximately 1 to 3 A for the mobile protein partner from the experimental geometry. For most test cases, the energy-minimized experimental structure scores among the top five energy minima in systematic docking studies when using both partners in their bound conformations. To account for side-chain conformational changes in case of using unbound protein conformations, a multicopy approach has been used to select the most favorable side-chain conformation during the docking process. The multicopy approach significantly improves the docking performance, using unbound (apo) binding partners without a significant increase in computer time. For most docking test systems using unbound partners, and without accounting for any information about the known binding geometry, a solution within approximately 2 to 3.5 A RMSD of the full mobile partner from the experimental geometry was found among the 40 top-scoring complexes. The approach could be extended to include protein loop flexibility, and might also be useful for docking of modeled protein structures.

Algorithms↗