Buried Atoms Research Articles

Fast, approximate algorithm for detection of solvent-inaccessible atoms

Up to about half of the atoms in biopolymers are inaccessible to solvents. If such atoms can be rapidly identified, time can be saved in the subsequent computation of atomic surface areas. A quick, approximate method, termed buried atom elimination (BAE), was developed for the detection of such atoms. Following the literature, the method makes use of a Gaussian function to calculate the neighbor density in four tetrahedral directions in 3-dimensional space, sometimes twice with different orientations. In macromolecules, our method detects between 63 and 81% of the buried atoms but also incorrectly classifies 2–8% of the exposed atoms as buried. These misidentified atoms all have small solvent-exposed (accessible) surface areas (SASAs): their surfaces sum to a maximum of 0.5% of the molecular SASA, and their maximum atomic SASA is 5.1 Å2. Using our recently reported LCPO method for computing atomic surfaces, which is one of the fastest available, the use of BAE increases the overall speed of computing the atomic SASAs by a factor of up to 1.6 for surfaces only and 1.9 when first and second derivatives are computed. BAE decreases the LCPO average absolute atomic error from about 2.3 Å2 to about 1.7 Å2 (average for larger compounds). BAE was introduced into the MacroModel molecular modeling package and tests show that it increases the efficiency of first- and second-derivative energy minimizations and molecular dynamics simulations without adversely affecting the stability or accuracy of the calculations. BAE parameters were developed for the most important atom types in biopolymers, based on a parameterization set of 18 compounds of different size (33–4346 atoms) and class (organics, proteins, DNA, and various complexes), consisting of a total of 23,186 atoms. ©1999 John Wiley & Sons, Inc. J Comput Chem 20, 586–596, 1999

Reliability of atomic displacement parameters in protein crystal structures.

Mean standard errors in atomic displacement parameters (ADPs) resulting from protein crystal structure determinations are estimated by comparing the ADPs of protein-chain pairs of identical sequence within the same crystal or within different crystals displaying the same or different space groups. The estimated ADP standard errors increase nearly linearly as the resolution decreases - an unexpected result given the nonlinear dependence of the resolution on the amount of diffraction data. The estimated ADP standard errors are larger for side-chain and solvent-exposed atoms than for main-chain and buried atoms and, surprisingly, are also larger for residues in the helical secondary structure relative to other local backbone conformations. The results allow an estimate of the influence of crystallographic refinement restraints on ADP standard errors. Such corrections should be applied when comparing different protein structures.

Solvent accessibility studies on glycosaminoglycans

Theoretical calculations on the solvent accessible surface area of the commonly occurring glycosaminoglycans (GAGs) have been carried out by employing the solvent accessibility technique of Lee and Richards. The results indicate that the average variation of solvent accessible surface area (ASA) for the different atoms is in the range of 2–28 Å 2. The average ASA for carbon (9.02 Å 2) and oxygen (19.3 Å 2) are relatively very high compared to that for nitrogen and sulfur. The total contribution of ASA by the buried atoms in all the molecules has been found to be small. Heparin complexed with the protein is less accessible to the solvent than the uncomplexed. The iduronic acid is also found to have a varied ASA due to its conformational flexibility. The sulfate groups in heparin have 50% of the total ASA of the molecule. Residue analysis indicates that in general d-configuration residues have higher ASA than l-configuration residues.

A solution of the doping problem for Ga delta-doping layers in Si

We have studied the incorporation of Ga in silicon during the fabrication of delta-doping layers. The delta-function doping profiles were grown by molecular beam deposition following a solid phase epitaxial growth method. Medium-energy ion scattering, secondary ion mass spectrometry, and Rutherford backscattering spectrometry were used to determine the structure and composition of the grown films. The interface velocity of the crystallization front and the diffusion coefficient of the impurity atoms in the Si matrix, both relevant parameters of the growth process, were measured. Optimum growth conditions were found that yield Ga doping profiles of less than 1.0 nm (full width at half maximum), with more than 95% of the buried dopant atoms on lattice sites. For these optimum growth conditions, a model is derived explaining the observed incorporation of the Ga atoms.

Hyperthermophiles: taking the heat and loving it.

Hyperthermophiles, a recently discovered group of microorganisms, are operationally defined as having an optimum growth temperature of at least 80°C and a maximum growth temperature of over 90°C. Most of the enzymes isolated so far from such organisms exhibit correspondingly enhanced thermostability. This property has been used both for investigation of fundamental biological questions of protein structure and stability, and for the development of technological applications that require protein stability at high temperatures. Examples of such applications of thermostable proteins include their use in biocatalysts, in various materials and in crystallization methods. The use of DNA polymerases from hyperthermophilic microorganisms in the polymerase chain reaction (PCR) is another of the more practical examples of the recent impact on biochemistry and molecular biology of enzymes isolated from hyperthermophilic organisms. To date, the maximum growth temperatures observed for a hyperthermophilic organism is about 110°C. Whether this is the upper limit for life is unknown; some workers estimate that the maximum growth temperature for, as yet, uncultured organisms may approach, or even exceed 150°C [1]. In any event, it is clear that the surface has barely been scratched in the study of extremely thermostable proteins from known hyperthermophiles. Two basic questions often come to mind when considering these enzymes: the practically motivated, how can I get some of these enzymes and the more fundamental question, how do these enzymes achieve extreme thermostability? Aspects of both of these issues are briefly discussed below. More detailed discussions of hyperthermophiles and their proteins may be found in review articles [2], [3], [4] and [5].

Structural studies of the engrailed homeodomain

The structure of the Drosophila engrailed homeodomain has been solved by molecular replacement and refined to an R-factor of 19.7% at a resolution of 2.1 A. This structure offers a high-resolution view of an important family of DNA-binding proteins and allows comparison to the structure of the same protein bound to DNA. The most significant difference between the current structure and that of the 2.8-A engrailed-DNA complex is the close packing of an extended strand against the rest of the protein in the unbound protein. Structural features of the protein not previously noted include a "herringbone" packing of 4 aromatic residues in the core of the protein and an extensive network of salt bridges that covers much of the helix 1-helix 2 surface. Other features that may play a role in stabilizing the native state include the interaction of buried carbonyl oxygen atoms with the edge of Phe 49 and a bias toward statistically preferred side-chain dihedral angles. There is substantial disorder at both ends of the 61 amino acid protein. A 51-amino acid variant of engrailed (residues 6-56) was synthesized and shown by CD and thermal denaturation studies to be structurally and thermodynamically similar to the full-length domain.

Satisfying Hydrogen Bonding Potential in Proteins

We have analysed the frequency with which potential hydrogen bond donors and acceptors are satisfied in protein molecules. There are a small percentage of nitrogen or oxygen atoms that do not form hydrogen bonds with either solvent or protein atoms, when standard criteria are used. For high resolution structures 9·5% and 5·1% of buried main-chain nitrogen and oxygen atoms, respectively, fail to hydrogen bond under our standard criteria, representing 5·8% and 2·1% of all main-chain nitrogen and oxygen atoms. We find that as the resolution of the data improves, the percentages fall. If the hydrogen bond criteria are relaxed many of these unsatisfied atoms form weak hydrogen bonds. However, there remain some buried atoms (1·3% NH and 1·8% CO) that fail to hydrogen bond without any immediately obvious compensating interactions.

Radiation Enhanced Diffusion in Mgo

AbstractMeasurements of marker spreading following 2.0 MeV Kr+irradiation at 25 to 1300°C have been performed on MgO samples containing O18, Ca and Zn buried tracer atoms. Ion beam mixing at room temperature on both sublattices was approximately 2.0 to 3.0 A5/eV. From 600 to 1000°C, the apparent activation enthalpy for diffusion on the anion sublattice (O18) was 0.35 eV and the diffusion coefficient was linear in the irradiation flux. From 1150 to 1300°C the measured activation enthalpy was 4.1 eV and the diffusion coefficient was proportional to the square root of flux. The measured activation enthalpy on the cation sublattice was roughly 0.30 eV up to 700°C for both Ca or Zn doped samples. Measurable extrinsic thermal diffusion from vacancies present for trivalent impurity charge compensation occurred above this temperature, complicating the analysis at higher temperatures. The observed kinetics in the lower temperature range are most likely controlled by interstitial loop formation. In the higher temperature range, vacancy traps with a binding energy of approximately 2 eV could account for the high activation enthalpy.

Ga delta-doping layers in silicon

Delta-doping layers in silicon have been made by deposition of 0.39 monolayer Ga on Si(001). The dopant atoms have been buried in the host crystal using a solid phase epitaxial growth method. The grown structures are characterized in situ by high-resolution Rutherford backscattering spectrometry. A fraction of 30% of the Ga atoms is located at subsitutional sites in a spike less than 1.0 nm wide; the other atoms are at the surface. The surface atoms desorb upon annealing at 985 K, whereas the buried atoms are redistributed only slightly. At temperatures higher than 1100 K the profile degrades completely.

Hydrogen exchange and the dynamic structure of proteins.

In native proteins, buried, labile protons undergo isotope exchange with solvent hydrogens, but the kinetics of exchange are markedly slower than in unfolded polypeptides. This indicates that, whereas buried protein atoms are shielded from solvent, the protein fluctuates around the time average structure and occasionally exposes buried sites to solvent. Generally, hydrogen exchange studies are designed to characterize the nature of the fluctuations between conformational substates, to monitor the shift in conformational equilibria among protein substates due to ligand binding or other factors, or to monitor the major cooperative denaturation transition. In this article, we review the recent reports of hydrogen exchange in proteins, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen exchange in folded proteins.