Showing papers by "Environmental Molecular Sciences Laboratory published in 2000"
TL;DR: The design and some implementation details of the overall NWChem architecture facilitates rapid development and portability of fully distributed application modules and shows performance of a few of the modules within NWChem.
726 citations
TL;DR: In this article, a review of recent work on the growth of select, representative oxides that span the ranges of crystal structure, metal oxidation state, and stoichiometry is reviewed and used to illustrate the basic materials science.
551 citations
TL;DR: In this article, an accurate method for solving the electronic Schrodinger equation that is applicable to a broad range of moleculesthe CCSD(T) method and families of basis sets that systematically converge to the complete basis set limitthe correlation consistent basis sets is presented.
Abstract: During the past decade dramatic progress has been made in calculating the binding energies of molecules. This is the result of two advances reported in 1989: an accurate method for solving the electronic Schrodinger equation that is applicable to a broad range of moleculesthe CCSD(T) methodand families of basis sets that systematically converge to the complete basis set limitthe correlation consistent basis sets. The former provides unprecedented accuracy for the prediction of a broad range of molecular properties, including molecular binding energies. The latter provides a means to systematically approach the complete basis set limit, i.e., the exact solutions of approximations to the Schrodinger equation. These two advances combined with a thorough analysis of the errors involved in electronic structure calculations lead to clear guidelines for ab initio calculations of binding energies, ranging from the strong bonds derived from chemical interactions to the extremely weak binding due to dispersion int...
495 citations
413 citations
15 Aug 2000
TL;DR: In this paper, it has been shown that homodromic hydrogen bonding networks, i.e., those exhibiting donor-acceptor (da) arrangements between all water molecules, are associated with the largest nonadditivities among other networks present in low lying minima of small water clusters.
Abstract: Clusters of water molecules are held together by hydrogen bonding networks. These networks are differentiated by the participation of the individual water molecules in the hydrogen bonds either as proton donors (d), proton acceptors (a) or their combinations. It has long been assumed that the stability of clusters is determined by the dominant two-body interactions between the water molecules. We have found that homodromic hydrogen bonding networks, i.e. those exhibiting donor–acceptor (da) arrangements between all water molecules, are associated with the largest non-additivities among other networks present in low lying minima of small water clusters. This finding offers a novel explanation for the stability of homodromic rings that are the global minima for the clusters trimer through pentamer. Among the non-additive terms, three-body terms are mainly responsible for determining the relative stabilities between the various trimer through pentamer isomers. This suggests that purely two-body pairwise additive potentials will result in errors exceeding 20% for clusters larger than the pentamer. Among all higher order components, the three-body term was found to be the most important.
409 citations
TL;DR: In this article, a linear correlation between C−H···O bond energies and gas-phase anion proton affinities was reported and used to estimate values of De = −4.0 ± 0.5
Abstract: Although the existence of Cα−H···OC hydrogen bonds in protein structures recently has been established, little is known about their strength and, therefore, the relative importance of these interactions. We have discovered that similar interactions occur in N,N-dimethylformamide dimers. High level ab initio calculations (MP2/aug-cc-pTZV) yield electronic association energies (De) and association enthalpies (ΔH298) for four dimer geometries. These data provide a lower limit of De = −2.1 kcal mol-1 for the Cα−H···OC hydrogen bond. A linear correlation between C−H···O bond energies and gas-phase proton affinities is reported. The gas-phase anion proton affinity of a peptide Cα−H hydrogen was calculated (355 kcal mol-1) and used to estimate values of De = −4.0 ± 0.5 kcal mol-1 and ΔH298 = −3.0 ± 0.5 kcal mol-1 for the Cα−H···OC hydrogen bond. The magnitude of this interaction, roughly one-half the strength of the N−H···OC hydrogen bond, suggests that Cα−H···OC hydrogen bonding interactions represent a hithert...
382 citations
348 citations
TL;DR: Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods, demonstrating that structural proteomics is feasible and can play a central role in functional genomics.
Abstract: A set of 424 nonmembrane proteins from Methanobacterium thermoautotrophicum were cloned, expressed and purified for structural studies. Of these, ∼20% were found to be suitable candidates for X-ray crystallographic or NMR spectroscopic analysis without further optimization of conditions, providing an estimate of the number of the most accessible structural targets in the proteome. A retrospective analysis of the experimental behavior of these proteins suggested some simple relations between sequence and solubility, implying that data bases of protein properties will be useful in optimizing high throughput strategies. Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods. This demonstrates that structural proteomics is feasible and can play a central role in functional genomics.
297 citations
TL;DR: In this paper, a brief historical introduction to the development of tandem mass spectrometry and its principal applications is presented, along with a discussion of the emerging dynamics principles governing energy transfer and dissociation of peptides.
Abstract: This review presents a brief historical introduction to the development of tandem mass spectrometry and its principal applications. It is placed in the context of the general principles underlying mass spectrometry, particularly the relationships between internal energy and fragmentation kinetics. The center-of-mass framework is presented as a convenient means of applying conservation of momentum to the energy transfer problem in tandem mass spectrometry as a means of deducing energy transfer in the collisional activation step and kinetic energy release as activated ions dissociate into fragment ions and neutrals. The principles of molecular beam methods are summarized and illustrative examples are given for which definitive information on reaction dynamics is available. The importance of scattering-very little appreciated in early discussions of tandem mass spectrometry-is shown to be the natural consequence of impulsive collisions, which appears to be a general mechanism for energy exchange in collisional activation. It is shown that the average energy transferred in single collisions is much less than the theoretical maximum given by the center-of-mass collision energy and the Massey criterion is presented as a simplistic rationale for understanding the essentially exponential decline in the energy transfer function above and below the relative velocity at which the probability for energy transfer is maximized. The issues of energy transfer in collisions of large molecular ions with low-mass neutrals are reviewed and a general description of energy transfer in multiple collisions is presented. It is shown that the center-of-mass and Massey criterion limitations are pragmatically overcome by multiple collision activation in ion traps. Surface-induced dissociation is presented as a viable alternative to multiple collision activation which is especially attractive for activation of large molecular ions. Finally, a few of the emerging dynamics principles governing energy transfer and dissociation of peptides are summarized. Copyright 2000 John Wiley & Sons, Ltd.
263 citations
TL;DR: In situ 13C NMR measurements on samples prepared using a pulse-quench catalytic reactor show that the 1,3-dimethylcyclopentenyl carbenium ion (1) is an intermediate in the synthesis of toluene from ethylene on zeolite catalyst HZSM-5.
Abstract: In situ 13C NMR measurements on samples prepared using a pulse-quench catalytic reactor show that the 1,3-dimethylcyclopentenyl carbenium ion (1) is an intermediate in the synthesis of toluene from ethylene on zeolite catalyst HZSM-5. Cation 1 forms in less than 0.5 s when ethylene is pulsed onto the catalyst bed at 623 K, and its presence obviates the kinetic induction period for conversion of a subsequent pulse of dimethyl ether, or methanol, into olefins (MTO chemistry). The kinetic induction period returns when the interval between pulses is many times the half-life of 1 in the catalyst bed. Density functional theory calculations (B3LYP/ 6-311G**) on a cluster model of the zeolite confirm that 1 is stable in the zeolite as a free cation and suggest why the alternative framework alkoxy is not observed. A π complex of the neutral cyclic diene is only 2.2 kcal/mol higher in energy than that of the ion pair. Theoretical (GIAO-MP2/tzp) 13C isotropic shifts of isolated 1 are in good agreement with the exper...
256 citations
TL;DR: In this article, photoemission methods were used to directly measure the valence and conduction band offsets at SrTiO3/Si(001) interfaces, as prepared by molecular-beam epitaxy within experimental error.
Abstract: We have used photoemission methods to directly measure the valence and conduction band offsets at SrTiO3/Si(001) interfaces, as prepared by molecular-beam epitaxy Within experimental error, the measured values are the same for growth on n- and p-Si, with the entire band discontinuity occurring at the valence band edge In addition, band bending is much larger at the p-Si heterojunction than at the n-type heterojunction Previously published threshold voltage behavior for these interfaces can now be understood in light of the present results
TL;DR: The new electrodynamic ion funnel displays a significant improvement in low-mass transmission (m/z >200) and sensitivity compared to previous designs and can be operated in two different modes, allowing fragile noncovalent complexes (as well as generally undesired adducts) to be transmitted.
Abstract: A new electrodynamic (rf) ion funnel has been developed and evaluated for use in the interface regions (at ∼1−10 Torr) of atmospheric pressure ion sources (e.g., electrospray ionization (ESI) for mass spectrometry). The ion funnel consists of a ring electrode ion guide with decreasing i.d. and with a superimposed dc potential gradient along the ring stack. The thicknesses of the ring electrodes and the spacings between them were reduced to 0.5 mm from 1.59 mm compared to those used for previous designs. The new ion funnel displays a significant improvement in low-mass transmission (m/z >200) and sensitivity compared to previous designs. The transmission efficiencies for electrosprayed peptides and proteins (ranging in mass from 200 to 17 000 Da) were typically 50−60% of total incoming currents from a heated capillary inlet. The transmitted ion currents were a factor of 30−56 greater than those of the standard interface for peptide samples and a factor of 18−22 greater than those for protein samples. The s...
TL;DR: The first neutral pentaatomic tetracoordinate planar carbon molecules, CAl 3Si and CAl3Ge, as well as their anions, were experimentally observed in the gas phase and characterized by ab initio calculations and anion photoelectron spectroscopy.
Abstract: The first neutral pentaatomic tetracoordinate planar carbon molecules, CAl 3Si and CAl3Ge, as well as their anions, CAl3Si - and CAl3Ge - , were experimentally observed in the gas-phase and characterized by ab initio calculations and anion photoelectron spectroscopy. A four-center bond involving ligand -ligand interactions was found to be critical in stabilizing the planar structures of the 17-valence-electron CAl 3Si and CAl3Ge and 18-valence-electron CAl3Si - and CAl3Ge - . These species violate the conventional expectation of tetrahedral structure for tetracoordinate carbon atoms and thus extend our concept of the range of chemical bonds that carbon can form.
TL;DR: The LEED results indicate a previously unobserved two-domain (1x4) reconstruction after sputtering and annealing the ( 1x1) surface.
Abstract: The reconstructed anatase TiO2(001) surface has been investigated by low-energy electron diffraction (LEED), x-ray photoelectron spectroscopy (XPS), and angle-resolved mass spectroscopy of recoiled ions (AR-MSRI). Prior investigations have observed or considered only a (1x1) unreconstructed termination for this surface with no detailed structural analysis. Our LEED results indicate a previously unobserved two-domain (1x4) reconstruction after sputtering and annealing the (1x1) surface. The XPS data for this reconstruction indicate the presence of only Ti4+. Simulations of the AR-MSRI experimental data indicate a best fit for a microfaceted surface, revealing both (103) and (1;03) surface planes.
TL;DR: In this article, a new experimental technique, using photodetachment photoelectron spectroscopy, electrospray, and ion-trap mass spectrometry, has been developed in the author's laboratory to probe multiply charged anions in the gas phase.
Abstract: Multiply charged anions are common in the condensed phase, and their existence has been generally taken for granted. But until very recently, these species have only rarely been observed in the gas phase. A new experimental technique, using photodetachment photoelectron spectroscopy, electrospray, and ion-trap mass spectrometry, has been developed in the author's laboratory to probe multiply charged anions in the gas phase. In this article, the principles of this technique and some of the initial results will be presented and discussed. The difference between photodetachment of singly and multiply charged anions is emphasized. Photodetachment photoelectron spectroscopy is ideal to probe the chemical and physical properties of free multiply charged anions. Among the initial findings, the repulsive Coulomb barriers existing in multiply charged anions have been directly observed. The relationship between the intramolecular electron−electron repulsion and the potential barrier is elucidated, culminating in th...
TL;DR: Methods are being developed for ultrasensitive protein characterization based upon electrospray ionization (ESI) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) that provide a detection limit of approximately 30 zmol for proteins with molecular weights ranging from 8 to 20 kDa.
Abstract: Methods are being developed for ultrasensitive protein characterization based upon electrospray ionization (ESI) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The sensitivity of a FTICR mass spectrometer equipped with an ESI source depends on the overall ion transmission, which combines the probability of ionization, transmission efficiency, and ion trapping in the FTICR cell. Our developments implemented in a 3.5 tesla FTICR mass spectrometer include introduction and optimization of a newly designed electrodynamic ion funnel in the ESI interface, improving the ion beam characteristics in a quadrupole-electrostatic ion guide interface, and modification of the electrostatic ion guide. These developments provide a detection limit of approximately 30 zmol (∼18 000 molecules) for proteins with molecular weights ranging from 8 to 20 kDa.
TL;DR: In this paper, standard and augmented correlation consistent sextuple zeta basis sets for the second-row atoms aluminum through argon have been determined for the ground states of HCl, PN, and P2.
Abstract: Standard and augmented correlation consistent sextuple zeta (cc-pV6Z and aug-cc-pV6Z) basis sets have been determined for the second-row atoms aluminum through argon. Using these sets, dissociation energies and spectroscopic constants for the ground states of HCl, PN, and P2 have been calculated using several theoretical methods, including Moller–Plesset perturbation theory, coupled cluster theory, and multireference configuration interaction theory (MRCI). The aug-cc-pV6Z and cc-pV6Z sets yield dissociation energies that are estimated to be within 0.1–0.2 kcal/mol of the complete basis set limit for HCl and within 1–1.5 kcal/mol for PN and P2. The MRCI and CCSD(T) methods are found to give the most consistently reliable results for the spectroscopic constants of all three species investigated. Use of the counterpoise correction improves the convergence behavior of the spectroscopic constants with increasing n for both the cc-pVnZ and aug-cc-pVnZ sets and should allow more accurate estimates of the complete basis set limit to be predicted. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 205–221, 2000
TL;DR: In this article, the heats of benzene and seven other small hydrocarbons (allyl, allene, cyclopropene, propene and propyne) have been calculated at high levels of ab initio molecular orbital theory.
Abstract: The heats of formation of benzene and seven other small hydrocarbons (allyl, allene, cyclopropene, propene, propyne, cyclopropane, and propane) have been calculated at high levels of ab initio molecular orbital theory. Geometries and frequencies were determined, in general, with coupled cluster theory, including a perturbative treatment of the connected triple excitations and with basis sets up through augmented quadruple-ζ in quality or, in some cases, augmented quintuple-ζ. Subsequent extrapolation of the total energies to the complete 1-particle basis set limit was performed, in an effort to further reduce the basis set truncation error. Additional improvements in the atomization energy were achieved by applying corrections for core/valence correlation, scalar relativistic, atomic spin−orbit, and higher-order correlation effects. Zero-point energies were based on an average of the vibrational energies obtained from the experimental fundamentals and theoretical harmonic frequencies. Using restricted ope...
TL;DR: In this article, the first scanning tunneling microscopy (STM) study of singlecrystalline anatase was performed and the results showed that the surface is stable with very few point defects and fourfoldcoordinated Ti atoms at step edges are preferred adsorption sites.
Abstract: We report the first scanning tunneling microscopy (STM) study of single-crystalline anatase. Atomically resolved images of the (101) surface are consistent with a bulk-truncated $(1\ifmmode\times\else\texttimes\fi{}1)$ termination. Step edges run predominantly in the [010], $[1\ifmmode\bar\else\textasciimacron\fi{}11],$ and $[1\ifmmode\bar\else\textasciimacron\fi{}1\ifmmode\bar\else\textasciimacron\fi{}1]$ directions. The surface is stable with very few point defects. Fourfold-coordinated Ti atoms at step edges are preferred adsorption sites and allow the identification of tunneling sites in STM.
TL;DR: In this paper, the second-order Moller−Plesset perturbation theory has been used to calculate the interaction energy between a water molecule and acenes as large as C96H24.
Abstract: Second-order Moller−Plesset perturbation theory has been used to calculate the interaction energy between a water molecule and acenes as large as C96H24. The results of these calculations lead to an estimated value of −5.8 ± 0.4 kcal/mol for the electronic binding energy of a water molecule with single-layer graphite. This value is comparable to the −5.0 ± 0.1 kcal/mol binding energy of the hydrogen bonded water dimer, suggesting that the water/graphite interactions will play an important role in determining the structure of water on graphite, as well as of water inside carbon nanotubes. The present estimate of the binding energy of a water molecule to a graphite sheet is appreciably larger than those previously reported in the literature.
TL;DR: Since only a few enzymatic fragments are necessary to unambiguously identify a protein from an appropriate database, it is anticipated that the multiplexed MS/MS method will allow the more rapid identification of complex protein mixtures with on-line separation of their enzymatically produced polypeptides.
Abstract: We report a new tandem mass spectrometric approach for the improved identification of polypeptides from mixtures (e.g., using genomic databases). The approach involves the dissociation of several species simultaneously in a single experiment and provides both increased speed and sensitivity. The data analysis makes use of the known fragmentation pathways for polypeptides and highly accurate mass measurements for both the set of parent polypeptides and their fragments. The accurate mass information makes it possible to attribute most fragments to a specific parent species. We provide an initial demonstration of this multiplexed tandem MS approach using an FTICR mass spectrometer with a mixture of seven polypeptides dissociated using infrared irradiation from a CO2 laser. The peptides were added to, and then successfully identified from, the largest genomic database yet available (C. elegans), which is equivalent in complexity to that for a specific differentiated mammalian cell type. Additionally, since on...
TL;DR: In this paper, collision-induced and surface-induced dissociation of protonated dialanine (Ala-AlaH+) was studied using a 7 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS).
Abstract: Collision-induced and surface-induced dissociation of protonated dialanine (Ala-AlaH+) was studied using a 7 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS). Energy-resolv...
TL;DR: In this paper, the electronic structure of magnetite (100) and (111) surfaces was examined after reaction with water vapor (p(H2O) ranging from 10−9 to 9ÕTorr) and liquid water at 298ÕK using chemical shifts in the O 1s core level photoelectron spectra obtained with a synchrotron radiation source.
TL;DR: In this paper, the surface termination, structure, morphology and composition of Fe 3 O 4 (001) using scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), low energy He + -ion scattering (LEIS) and X-ray photoelectron spectroscopy (XPS) were investigated.
TL;DR: In this paper, high-hydrophilic group-substituted celluloses were immobilized on the fused silica capillary inner wall for capillary isoelectric focusing (CIEF) of proteins.
Abstract: Highly hydrophilic group-substituted celluloses were immobilized on the fused silica capillary inner wall for capillary isoelectric focusing (CIEF) of proteins. The resultant capillaries were evaluated under typical CIEF conditions, and the results were compared with those obtained by using polyvinyl alcohol (PVA)- and linear polyacrylamide (LPA)-coated capillaries. A minimal resolved pI difference of 0.013 was obtained with a carrier ampholyte (pH 3-10) for hydroxyethyl cellulose- and hydroxypropyl cellulose-coated capillaries, while 0.019 was obtained on PVA- and LPA coated capillaries. Changing substituted groups from hydroxyl to hydroxylmethyl decreased the CIEF resolution from {approx}2.5 to {approx}1.0 for tested proteins at mobilization speed of {approx}0.9 cm min-1. Little loss in CIEF resolution was observed when increasing capillary length from 30 to 150 cm, however, flat peaks were observed when increasing column diameter up to >100 um. The present work indicates that mobilization speed ofl1 cm min-1 should be used to achieve high CIEF resolution.
TL;DR: Progress in the development of the combination of CIEF with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and its application to proteome characterization is described.
Abstract: Capillary isoelectric focusing (CIEF) can provide high-resolution separations of complex protein mixtures, but until recently it has primarily been used with conventional UV detection. This technique would be greatly enhanced by much more information-rich detection methods that can aid in protein characterization. We describe progress in the development of the combination of CIEF with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and its application to proteome characterization. Studies have revealed 400-1000 putative proteins in the mass range of 2-100 kDa from total injections of approximately 300 ng protein in single CIEF-FTICR analyses of cell lysates for both Escherichia coli (E. coli) and Deinococcus radiodurans (D. radiodurans). We also demonstrate the use of isotope labeling of the cell growth media to improve mass measurement accuracy and provide a means for quantitative proteome-wide measurements of protein expression. The ability to make such comprehensive and precise measurements of differences in protein expression in response to cellular perturbations should provide new insights into complex cellular processes.
TL;DR: In this article, the geometries and binding enthalpies of M+benzene complexes (M = Li, Na, K, Rb, and Cs) were obtained from large basis set secondorder perturbation theory and coupled cluster theory calculations.
Abstract: The geometries and binding enthalpies of M+(benzene) complexes (M = Li, Na, K, Rb, and Cs) were obtained from large basis set second-order perturbation theory and coupled cluster theory calculations. The best ΔH298 estimates (in kcal/mol) are Li+(benzene) = −36.8 ± 0.2 (theory) vs −37.9 and −39.3 ± 3.2 (expt), Na+(benzene) = −24.7 ± 0.3 (theory) vs −28.0 ± 1.5 and −22.5 ± 1.5 (expt), K+(benzene) = −20.1 ± 0.4 (theory) vs −19.2 and −17.1 ± 0.9 (expt), Rb+(benzene) = −16.4 ± 0.2 (theory) vs −16.4 ± 0.9 (expt), and Cs+(benzene) = −12.5 ± 0.2 (theory) vs −15.1 ± 1.1 (expt). The present findings include small corrections for core/valence correlation effects and lead to binding enthalpies uniformly larger than those of previous theoretical studies.
TL;DR: Using a combination of NMR experiments and theoretical methods, including chemical shift calculations at the GIAO-MP2 level, the authors showed that a previously observed 31P resonance at +27 ppm is due to P(CH3)4+, formed in a reaction that consumes a Bronsted site.
Abstract: The measurement of the type and number of acid sites on sulfated zirconia catalysts using the 31P NMR spectrum of adsorbed P(CH3)3 has been vexed by spectral assignment controversies. Using a combination of NMR experiments and theoretical methods, including chemical shift calculations at the GIAO-MP2 level, we show that a previously observed 31P resonance at +27 ppm is due to P(CH3)4+, formed in a reaction that consumes a Bronsted site. The coproduct of this reaction, PH(CH3)2, is protonated on the surface to yield a 31P resonance in the region expected for P(CH3)3 on a Lewis site. Further complications result from a signal due to OP(CH3)3, formed by oxidizing sites on the surface, complexed to unidentified acid sites. As an alternative, we show that carefully designed 15N experiments using the less reactive and less basic probe pyridine-15N provide more easily interpreted measurements of Bronsted and Lewis sites on sulfated zirconias of diverse composition, preparation, and treatment. Quantitative studie...
TL;DR: In this paper, the atomic structures and geometries, electronic structure, and temperature-dependent photoelectron spectra of aluminum clusters are studied both theoretically via ab initio local density-functional simulations, and experimentally with high-resolution measurements.
Abstract: Atomic structures and geometries, electronic structure, and temperature-dependent photoelectron spectra of ${\mathrm{Al}}_{N}^{\ensuremath{-}} (N=19\ensuremath{-}102)$ clusters are studied both theoretically via ab initio local-density-functional simulations, and experimentally with high-resolution measurements. The use of a theoretically well-defined energy shift in conjunction with a generalized Koopmans' theorem enables direct comparisons between the calculated density of states and the experimental photoelectron spectrum. Such comparisons, using photoelectron spectra calculated for various relaxed cluster geometries, enables a determination of the optimal structures of the clusters. The atomic arrangements in the ground-state structures of ${\mathrm{Al}}_{19}^{\ensuremath{-}},$ ${\mathrm{Al}}_{20}^{\ensuremath{-}},$ and ${\mathrm{Al}}_{23}^{\ensuremath{-}}$ are found and they exhibit oblate, prolate, and octupole deformed shapes, respectively. In addition to the low-temperature spectra, high-temperature calculated spectra of these clusters obtained via ab initio molecular-dynamics simulations reproduce the experimentally observed trends measured for hot clusters. For larger cluster anions $(Ng~36),$ the level of agreement between the theoretically calculated spectra and the measured ones is less satisfactory, indicating that while certain structural motifs are identified, the optimal ground-state structures may not have been fully determined. fcc-like low-energy structures are found in the larger cluster-size range, with decreasing distortions of the internal structures when the cluster size is increased. Indications are found pertaining to an octahedral growth pattern of larger aluminum clusters.
TL;DR: The global fold of the fragment corresponding to this domain (RPA70Δ169) is solved and it is found residues 8–108 of the N-terminal domain are structured and the remaining C-Terminal residues are unstructured and may form a flexible linker to the DNA-binding domain of RPA70.
Abstract: Human Replication Protein A (hsRPA) is required for multiple cellular processes in DNA metabolism including DNA repair, replication and recombination. It binds single-stranded DNA with high affinity and interacts specifically with multiple proteins. hsRPA forms a heterotrimeric complex composed of 70-, 32- and 14-kDa subunits (henceforth RPA70, RPA32, and RPA14). The N-terminal 168 residues of RPA70 form a structurally distinct domain that stimulates DNA polymerase α activity, interacts with several transcriptional activators including tumor suppressor p53, and during the cell cycle it signals escape from the DNA damage induced G2/M checkpoint. We have solved the global fold of the fragment corresponding to this domain (RPA70Δ169) and we find residues 8–108 of the N-terminal domain are structured. The remaining C-terminal residues are unstructured and may form a flexible linker to the DNA-binding domain of RPA70. The globular region forms a five-stranded anti-parallel β-barrel. The ends of the barrel are capped by short helices. Two loops on one side of the barrel form a large basic cleft which is a likely site for binding the acidic motifs of transcriptional activators. Many lethal or conditional lethal yeast point mutants map to this cleft, whereas no mutations with severe phenotype have been found in the linker region.