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PubMed2006

Volume and hydration changes of DNA-ligand interactions.

We report the volumetric and other thermodynamic properties of ethidium bromide (EB), propidium iodide (PI) and daunomycin (DAU) intercalating with poly(dA).poly(dT), poly[d(A-T)].poly[d(A-T)], and poly[d(G-C)].poly[d(G-C)], respectively, as well as minor groove binder Hoechst 33258 binding with poly[d(A-T)].poly[d(A-T)]. The data were obtained using fluorescence titration and hydrostatic pressure measurements. Our thermodynamic data are combined with enthalpies from literature reports to analyze the thermodynamic characteristics of the different interactions. The differences are interpreted based on three processes related to hydration: I. burial of non-polar hydrophobic solvent accessible surface, II. burial of polar surface and formation of solute-solute H-bonds, and III. disruption of "structural" hydration. Sequence dependent conformational changes may also be important when comparing ligand binding to different DNA sequences. We conclude that a combination of different thermodynamic parameters, especially volume change, is essential in order to understand the role of hydration in the energetics of DNA-ligand interactions.

Binding Sites↗
PubMed2005

An analysis of the breakdown of paper products (toilet paper, tissues and tampons) in natural environments, Tasmania, Australia.

An examination of the relative breakdown rates of unused toilet paper, facial tissues and tampons was undertaken in nine different environments typical of Tasmanian natural areas. Bags of the paper products (toilet paper, facial tissues, tampons) were buried for periods of 6, 12 and 24 months at depths of 5 and 15 cm. A nutrient solution simulating human body wastes was added to half of the samples, to test the hypothesis that the addition of nutrients would enhance the breakdown of paper products buried in the soil. Mean annual rainfall was the most important measured variable determining mean breakdown in the nutrient addition treatment between sites, with high rainfall sites (mean annual rainfall of greater than 650 mm) recording less decayed products than the drier sites (mean annual rainfall of 500-650 mm). Temperature and soil organic content were important influences on the breakdown of the unfertilised products. Toilet paper and tissues decayed more readily than tampons. Nutrient addition enhanced decay for all products across all sites. Depth of burial was not important in determining the degree to which products decayed. In alpine environments, burial under rocks at the surface did not increase the speed of decay of any product. The Western Alpine site, typical of alpine sites in the Tasmanian Wilderness World Heritage Area, showed very little decay over the two-year period, even for nutrient enhanced products. Management prescriptions should be amended to dissuade people from depositing human toilet waste in the extreme (montane to alpine) environments in western Tasmania. Tampons should continue to be carried out as currently prescribed.

Biodegradation, Environmental↗
PubMed2005

A new early Holocene human skeleton from Brazil: implications for the settlement of the New World.

Increasing skeletal evidence from the U.S.A., Mexico, Colombia, and Brazil strongly suggests that the first settlers in the Americas had a cranial morphology distinct from that displayed by most late and modern Native Americans. The Paleoamerican morphological pattern is more generalized and can be seen today among Africans, Australians, and Melanesians. Here, we present the results of a comparative morphological assessment of a late Paleoindian/early archaic specimen from Capelinha Burial II, southern Brazil. The Capelinha skull was compared with samples of four Paleoindian groups from South and Central America and worldwide modern groups from W.W. Howells' studies. In both analyses performed (classical morphometrics and geometric morphometrics), the results show a clear association between Capelinha Burial II and the Paleoindians, as well as Australians, Melanesians, and Africans, confirming its Paleoamerican status.

Anthropology, Physical↗
PubMed2005

ESR and U-series analyses of enamel and dentine fragments of the Banyoles mandible.

The Banyoles mandible presents a puzzle. Its anatomy has been described as pre-Neandertal, but the travertine in which it was found has been dated to 45,000 +/- 4000 years. By this time, any pre-Neandertals had supposedly been absent from the European fossil record for more than 100,000 years. It was therefore proposed that the age of the travertine may represent a minimum age estimate, with the mandible possibly having been reworked from older deposits. We carried out a non-destructive ESR analysis of an enamel fragment removed from a molar and performed a series of in situ laser ablation U-series analyses on dentine fragments adjacent to the enamel piece. The analyses resulted in an apparent combined ESR-U-series age of 66,000 +/- 7000 years. The encasing travertine matrix was also analyzed for U-series isotopes and showed signs of U-mobilization. It cannot be excluded that the travertine matrix is older than the previously determined age. If the mandible was not reworked, then the combined ESR-U-series result on the tooth enamel would give its best age estimate. If, on the other hand, the mandible was reworked from another deposit, the actual ESR-U-series age will depend on the external dose rate from the previous matrix and the depth of its burial, which controls the degree of the attenuation of the cosmic dose rate over time. Considering a range of possible burial histories, the mean age of the mandible would lie somewhere between the combined ESR-U-series age and the previously determined age of the travertine matrix. Regarding the morphology of the mandible, a review of its features in the context of larger Neandertal samples indicates that the anatomy of the specimen is not incompatible with such a young age determination, although it further highlights morphological variation in the late Neandertal sample.

Age Determination by Teeth↗
PubMed2006

Modelling the long-term fate of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) in the Grenland Fjords, Norway.

The development and application of a predictive fate model (DIG--Dioxins in Grenland) for polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) in the marine environment of the Norwegian Grenland Fjords are described. The objective of the modelling study was to predict long-term future changes in PCDD/F concentrations in the fjord following the cessation of point source emissions. To assess the reliability of the model, the model performance was evaluated by comparing model results to field measurements collected between 1989 and 2001. Model bias (defined as the ratio of median predicted concentration and median observed concentration) for prediction of concentrations for three different PCDD/F congeners (2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 1,2,3,6,7,8-hexadibenzofuran (HxCDF) and octachlorodibenzofuran (OCDF)) in the fjord was between 0.53 and 24, which was deemed a satisfactory result for models of this type. The model was run to determine the dynamic change in concentrations between 1950 and 2050 and to examine the key fluxes of PCDD/Fs in the fjord. Between 1990 and 2050 sediment concentrations of TCDD, HxCDF and OCDF were predicted to fall at fairly constant but gradually slowing rates to concentrations 52, 98 and 88 times lower, respectively, of their 1990 values. Losses of PCDD/Fs from the bottom sediments in the Frierfjord were predicted to be a combination of sediment burial and net resuspension to the water column. Sediment burial was shown to be relatively more important in the fjord's deep-water sediments, whereas resuspension was relatively more important in the shallow sediments. For the shallower sediments, a net water-to-sediment flux was predicted for all three congeners up until the mid-1970s, when emission reductions were initiated, and thereafter a net sediment-to-water flux was predicted. The shallow sediments acted as net sources to the deeper sediments and to the fishing areas in the outer fjord.

Benzofurans↗
PubMed2006

Biogeochemical value of managed realignment, Humber estuary, UK.

We outline a plausible, albeit extreme, managed realignment scenario ('Extended Deep Green' scenario) for a large UK estuary to demonstrate the maximum possible biogeochemical effects and economic outcomes of estuarine management decisions. Our interdisciplinary approach aims to better inform the policy process, by combining biogeochemical and socioeconomic components of managed realignment schemes. Adding 7494 ha of new intertidal area to the UK Humber estuary through managed realignment leads to the annual accumulation of a 1.2 x 10(5) t of 'new' sediment and increases the current annual sink of organic C and N, and particle reactive P in the estuary by 150%, 83% and 50%, respectively. The increase in intertidal area should also increase denitrification. However, this positive outcome is offset by the negative effect of enhanced greenhouse gas emissions in new marshes in the low salinity region of the estuary. Short-term microbial reactions decrease the potential benefits of CO(2) sequestration through gross organic carbon burial by at least 50%. Net carbon storage is thus most effective where oxidation and denitrification reactions are reduced. In the Humber this translates to wet, saline marshes at the seaward end of estuaries. Cost-benefit analysis (CBA) was used to determine the economic efficiency of the Extended Deep Green managed realignment. When compared to a 'Hold-the-Line' future scenario, i.e. the present state/extent of sea defences in the estuary, the CBA shows that managed realignment is cost effective when viewed on >25 year timescales. This is because capital costs are incurred in the first years, whereas the benefits from habitat creation, carbon sequestration and reduced maintenance costs build up over time. Over 50- and 100-year timescales, the Extended Deep Green managed realignment scenario is superior in efficiency terms. The increased sediment accumulation is also likely to enhance storage of contaminant metals. In the case of Cu, a metal that currently causes significant water quality issues, Cu removal due to burial of suspended sediment in realigned areas translates to a value of approximately pounds sterling 1000 a(-1) (avoided clean up costs). Although this is not formally included in the CBA it illustrates another likely positive economic outcome of managed realignment. Although we focus on the Humber, the history of reclamation and its biogeochemistry is common to many estuaries in northern Europe.

Conservation of Natural Resources↗
PubMed2006

Removal of nutrients in various types of constructed wetlands.

The processes that affect removal and retention of nitrogen during wastewater treatment in constructed wetlands (CWs) are manifold and include NH(3) volatilization, nitrification, denitrification, nitrogen fixation, plant and microbial uptake, mineralization (ammonification), nitrate reduction to ammonium (nitrate-ammonification), anaerobic ammonia oxidation (ANAMMOX), fragmentation, sorption, desorption, burial, and leaching. However, only few processes ultimately remove total nitrogen from the wastewater while most processes just convert nitrogen to its various forms. Removal of total nitrogen in studied types of constructed wetlands varied between 40 and 55% with removed load ranging between 250 and 630 g N m(-2) yr(-1) depending on CWs type and inflow loading. However, the processes responsible for the removal differ in magnitude among systems. Single-stage constructed wetlands cannot achieve high removal of total nitrogen due to their inability to provide both aerobic and anaerobic conditions at the same time. Vertical flow constructed wetlands remove successfully ammonia-N but very limited denitrification takes place in these systems. On the other hand, horizontal-flow constructed wetlands provide good conditions for denitrification but the ability of these system to nitrify ammonia is very limited. Therefore, various types of constructed wetlands may be combined with each other in order to exploit the specific advantages of the individual systems. The soil phosphorus cycle is fundamentally different from the N cycle. There are no valency changes during biotic assimilation of inorganic P or during decomposition of organic P by microorganisms. Phosphorus transformations during wastewater treatment in CWs include adsorption, desorption, precipitation, dissolution, plant and microbial uptake, fragmentation, leaching, mineralization, sedimentation (peat accretion) and burial. The major phosphorus removal processes are sorption, precipitation, plant uptake (with subsequent harvest) and peat/soil accretion. However, the first three processes are saturable and soil accretion occurs only in FWS CWs. Removal of phosphorus in all types of constructed wetlands is low unless special substrates with high sorption capacity are used. Removal of total phosphorus varied between 40 and 60% in all types of constructed wetlands with removed load ranging between 45 and 75 g N m(-2) yr(-1) depending on CWs type and inflow loading. Removal of both nitrogen and phosphorus via harvesting of aboveground biomass of emergent vegetation is low but it could be substantial for lightly loaded systems (cca 100-200 g N m(-2) yr(-1) and 10-20 g P m(-2) yr(-1)). Systems with free-floating plants may achieve higher removal of nitrogen via harvesting due to multiple harvesting schedule.

Biodegradation, Environmental↗
PubMed2000

Calculations suggest a pathway for the transverse diffusion of a hydrophobic peptide across a lipid bilayer.

Alamethicin is a hydrophobic antibiotic peptide 20 amino acids in length. It is predominantly helical and partitions into lipid bilayers mostly in transmembrane orientations. The rate of the peptide transverse diffusion (flip-flop) in palmitoyl-oleyl-phosphatidylcholine vesicles has been measured recently and the results suggest that it involves an energy barrier, presumably due to the free energy of transfer of the peptide termini across the bilayer. We used continuum-solvent model calculations, the known x-ray crystal structure of alamethicin and a simplified representation of the lipid bilayer as a slab of low dielectric constant to calculate the flip-flop rate. We assumed that the lipids adjust rapidly to each configuration of alamethicin in the bilayer because their motions are significantly faster than the average peptide flip-flop time. Thus, we considered the process as a sequence of discrete peptide-membrane configurations, representing critical steps in the diffusion, and estimated the transmembrane flip-flop rate from the calculated free energy of the system in each configuration. Our calculations indicate that the simplest possible pathway, i.e., the rotation of the helix around the bilayer midplane, involving the simultaneous burial of the two termini in the membrane, is energetically unfavorable. The most plausible alternative is a two-step process, comprised of a rotation of alamethicin around its C-terminus residue from the initial transmembrane orientation to a surface orientation, followed by a rotation around the N-terminus residue from the surface to the final reversed transmembrane orientation. This process involves the burial of one terminus at a time and is much more likely than the rotation of the helix around the bilayer midplane. Our calculations give flip-flop rates of approximately 10(-7)/s for this pathway, in accord with the measured value of 1.7 x 10(-6)/s.

Alamethicin↗
PubMed1997

Thermodynamic and structural analysis of microtubule assembly: the role of GTP hydrolysis.

Different models have been proposed that link the tubulin heterodimer nucleotide content and the role of GTP hydrolysis with microtubule assembly and dynamics. Here we compare the thermodynamics of microtubule assembly as a function of nucleotide content by van't Hoff analysis. The thermodynamic parameters of tubulin assembly in 30-100 mM piperazine-N,N'-bis(2-ethanesulfonic acid), 1 mM MgSO4, 2 mM EGTA, pH 6.9, in the presence of a weakly hydrolyzable analog, GMPCPP, the dinucleotide analog GMPCP plus 2 M glycerol, and GTP plus 2 M glycerol were obtained together with data for taxol-GTP/GDP tubulin assembly (GMPCPP and GMPCP are the GTP and GDP nucleotide analogs where the alpha beta oxygen has been replaced by a methylene, -CH2-). All of the processes studied are characterized by a positive enthalpy, a positive entropy, and a large, negative heat capacity change. GMPCP-induced assembly has the largest negative heat capacity change and GMPCPP has the second largest, whereas GTP/2 M glycerol- and taxol-induced assembly have more positive values, respectively. A large, negative heat capacity is most consistent with the burial of water-accessible hydrophobic surface area, which gives rise to the release of bound water. The heat capacity changes observed with GTP/2 M glycerol-induced and with taxol-induced assembly are very similar, -790 +/- 190 cal/mol/k, and correspond to the burial of 3330 +/- 820 A2 of nonpolar surface area. This value is shown to be very similar to an estimate of the buried nonpolar surface in a reconstructed microtubule lattice. Polymerization data from GMPCP- and GMPCPP-induced assembly are consistent with buried nonpolar surface areas that are 3 and 6 times larger. A linear enthalpy-entropy and enthalpy-free energy plot for tubulin polymerization reactions verifies that enthalpy-entropy compensation for this system is based upon true biochemical correlation, most likely corresponding to a dominant hydrophobic effect. Entropy analysis suggests that assembly with GTP/2 M glycerol and with taxol is consistent with conformational rearrangements in 3-6% of the total amino acids in the heterodimer. In addition, taxol binding contributes to the thermodynamics of the overall process by reducing the delta H degree and delta S degree for microtubule assembly. In the presence of GMPCPP or GMPCP, tubulin subunits associate with extensive conformational rearrangement, corresponding to 10% and 26% of the total amino acids in the heterodimer, respectively, which gives rise to a large loss of configurational entropy. An alternative, and probably preferable, interpretation of these data is that, especially with GMPCP-tubulin, additional isomerization or protonation events are induced by the presence of the methylene moiety and linked to microtubule assembly. Structural analysis shows that GTP hydrolysis is not required for sheet closure into a microtubule cylinder, but only increases the probability of this event occurring. Sheet extensions and sheet polymers appear to have a similar average length under various conditions, suggesting that the minimum cooperative unit for closure of sheets into a microtubule cylinder is approximately 400 nm long. Because of their low level of occurrence, sheets are not expected to significantly affect the thermodynamics of assembly.

Animals↗
PubMed2003

Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?

A judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size (N<102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50,000 conformations along the longest all-atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide-carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide-carbonyl hydrogen-bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process.

Animals↗
PubMed2003

Early Holocene human skeletal remains from Santana do Riacho, Brazil: implications for the settlement of the New World.

In this study we compare the cranial morphology of several late Paleoindian skeletons uncovered at Santana do Riacho, Central Brazil, with worldwide human cranial variation. Mahalanobis Distance and Principal Component Analysis are used to explore the extra-continental morphological affinities of the Brazilian Paleoindian sample. Santana do Riacho is a late Paleoindian burial site where approximately 40 individuals were recovered in varying states of preservation. The site is located at Lagoa Santa/Serra do Cipó, State of Minas Gerais. The first human activities in this rockshelter date back to the terminal Pleistocene, but the burials are bracketed between circa 8200 and 9500BP. The collection contains only six skulls well-enough preserved to be measured. The Santana do Riacho late Paleoindians present a cranial morphology characterized by long and narrow neurocrania, low and narrow faces, with low nasal apertures and orbits. The multivariate analyses show that they exhibit strong morphological affinities with present day Australians and Africans, showing no resemblance to recent Northern Asians and Native Americans. These findings confirm our long held opinion that the settlement of the Americas was more complicated in terms of biological input than has been widely assumed. The working hypothesis is that two very distinct populations entered the New World by the end of the Pleistocene, and that the transition between the cranial morphology of the Paleoindians and the morphology of later Native Americans, which occurred around 8-9ka, was abrupt. This, in our opinion, is a more parsimonious explanation for the diversity detected than a long, local microevolutionary process mediated by selection and drift. The similarities of the first South Americans with sub-Saharan Africans may result from the fact that the non-Mongoloid Southeast Asian ancestral population came, ultimately, from Africa, with no major modification in the original cranial bau plan of the first modern humans.

Animals↗
PubMed2000

Sensitivity analysis of mercury human exposure.

We present a comprehensive analysis of the sensitivity of mercury (Hg) human exposure to environmental variables using a multimedia model of the fate and transport of Hg in the environment. The results of the analysis show that the Hg dose is most sensitive to the lake pH, the burial rate of Hg adsorbed to sediments, and the chemical speciation of Hg emissions to the atmosphere. The lake pH has a strong non-linear effect on the methylation rate and bioaccumulation of Hg in fish. The burial of sediments is a major pathway for removing Hg from the lake cycling. The speciation of Hg emissions is important because Hg(II) is deposited much more rapidly than Hg(0). These results highlight the importance of key variables that should be investigated through well-designed field programs, so that we can minimize the overall uncertainties associated with the modeling of mercury fate and transport.

Confounding Factors, Epidemiologic↗
PubMed1998

The distribution of lead within ancient and modern human teeth: implications for long-term and historical exposure monitoring.

The preservation of lead within human tissue makes it possible to monitor long-term exposure to the element and to model changing sources of lead pollution throughout the lifetime of an individual. Dental tissues have recently been shown to be particularly useful for this purpose. Enamel, for instance, forms at known stages of life and is chemically stable in vivo whereas dentine is remodelled in a predictable fashion. The relative stability of enamel is reflected in its excellent post-mortem preservation. This raises the possibility of using historical or archaeological material to reconstruct long-term trends and establish baseline data relating to exposure among pre-industrial or even prehistoric populations. The use of archaeological material is currently problematic, however, because of the site-specific nature of diagenesis and incomplete understanding of its chemistry, particularly in respect of lead uptake into dental tissue from the burial environment. A detailed study of lead distribution within both ancient and modern human teeth is presented. Conclusions are drawn on the pattern of lead distribution resulting from tissue formation and the manner of its alteration in the burial environment. In particular, attention is drawn to a consistent enrichment of lead within the outer 30 microns of the enamel of both ancient and modern teeth which appears to be unrelated to diagenesis. The implications for current approaches to long-term monitoring and for the reconstruction of historical and archaeological exposure patterns are discussed.

Archaeology↗
PubMed2001

Towards the MHC-peptide combinatorics.

The exponentially increased sequence information on major histocompatibility complex (MHC) alleles points to the existence of a high degree of polymorphism within them. To understand the functional consequences of MHC alleles, 36 nonredundant MHC-peptide complexes in the protein data bank (PDB) were examined. Induced fit molecular recognition patterns such as those in MHC-peptide complexes are governed by numerous rules. The 36 complexes were clustered into 19 subgroups based on allele specificity and peptide length. The subgroups were further analyzed for identifying common features in MHC-peptide binding pattern. The four major observations made during the investigation were: (1) the positional preference of peptide residues defined by percentage burial upon complex formation is shown for all the 19 subgroups and the burial profiles within entries in a given subgroup are found to be similar; (2) in class I specific 8- and 9-mer peptides, the fourth residue is consistently solvent exposed, however this observation is not consistent in class I specific 10-mer peptides; (3) an anchor-shift in positional preference is observed towards the C terminal as the peptide length increases in class II specific peptides; and (4) peptide backbone atoms are proportionately dominant at the MHC-peptide interface.

Animals↗
PubMed1998

Comparison of lipid composition in two types of human putrefactive liquid.

The decomposition of a human cadaver was stopped after solidification of putrefactive liquid during a GIS Burial experiment. Knowledge of this phenomenon is necessary to optimize burial conditions and to decrease cemetery congestion. In this preliminary study, we devised a method using thin-layer chromatography and gas chromatography to compare different putrefactive liquids. A comparison of lipid composition among two cadavers revealed a decrease in the decomposition rate of the cadaver that had the gelled putrefactive liquid. Essentially, fatty acids were observed in two types of extracts. The difference was quantitative: there was a higher amount of fatty acids in the gelled sample than in the standard liquid, suggesting a decrease of decomposition rate in the gelled extract. A large quantity of oleate salts may be favourable for solidification. In addition, an isomer of oleic acid (elaidic acid) could be present which may have a determining factor in the phenomenon of gelled putrefaction. A large amount of stearic acid was present in the gelled extract and may be involved in solidification. This method was efficient for comparing the lipid composition of different putrefactive liquids and may be used for a large-scale study. This is the first report concerning methods to determine the lipid composition of human decomposition liquids after 4 years postmortem.

Aged↗
PubMed1998

In- and out-flows of elements in bones embedded in reference soils.

Possible exchanges of elements between bone and the surrounding soil after being embedded underground for 2 years were estimated. Bone pieces were samples from human vertebrae without any treatments after resection. Sixteen elements were determined by atomic emission mass spectrometry. These were divided into three types; Type I, an in-flow in which elements increased, as in Fe, Al and Ba; type II, a balanced decrease in which changes were found in S, Mg and Zn; and type III, an out-flow in which elements, such as Ca and P, entered into bones from embedded soils. These exchanges depended on the varying nature of soils and also on the time underground. The exchanges were progressed in duration of the time after burial. Data obtained are possible references to judge the time-lapse after burial of bones in relating to characters of soils embedded, and to identify proper bone elements from containment elements.

Adult↗
PubMed1997

Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies.

BACKGROUND: There are many pairs and groups of proteins with similar folds and interaction patterns, but whose sequence similarity is below the threshold of easily recognizable sequence homology. The existence of multiple sequence solutions for a given fold has inspired fold prediction methods in which structural information from one protein is used to estimate the energy of another, putatively similar, structure. RESULTS: A set of 68 pairs of proteins with similar folds and sequence identity in the 8-30% range is identified from the literature. for each pair, the energy of one protein, calculated using knowledge-based statistical potentials, is compared to the estimated energy, calculated with the same potentials but using the structural information (burial status and interaction pattern) of another protein with the same fold. Different energy estimates, corresponding to approximations used in various fold recognition algorithms, are calculated and compared to each other, as well as to the correct energy. It is shown that the local energy terms, based on burial and secondary structure preferences, can be reliably estimated with an accuracy close to 70%. At the same time, the two-body nonlocal energy loses over 60% of its value due to the repacking of the structure. Further approximations, such as the 'frozen approximation', can bring it to an essentially random value. CONCLUSIONS: Local energy terms could be used safely to improve fold recognition algorithms. To utilize pair interaction information, specially designed pair potentials and/or a self-consistent description of pair interactions is necessary.

Algorithms↗
PubMed1998

Pairwise calculation of protein solvent-accessible surface areas.

BACKGROUND: The tractability of many algorithms for determining the energy state of a system depends on the pairwise nature of an energy expression. Some energy terms, such as the standard implementation of the van der Waals potential, satisfy this criterion whereas others do not. One class of important potentials that are not pairwise involves benefits and penalties for burying hydrophobic and/or polar surface areas. It has been found previously that, in some cases, a pairwise approximation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation. RESULTS: We develop a pairwise expression with one scalable parameter that closely reproduces both the true buried and the true exposed solvent-accessible surface areas. We then refit our previously published coiled-coil stability data to give solvation parameters of 26 cal/mol A2 favoring hydrophobic burial and 100 cal/mol A2 opposing polar burial. CONCLUSIONS: An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.

Algorithms↗