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1.  An Electron Paramagnetic Resonance Spectroscopic Study of Copper Hopping in Doped Bis(L-histidinato)cadmium Dihydrate 
The journal of physical chemistry. A  2013;117(16):3414-3427.
Electron Paramagnetic Resonance (EPR) spectroscopy was used to study Cu(II) dynamic behavior in a doped biological model crystal; bis(L-histidinato)cadmium dihydrate, in order to gain better insight into copper site stability in metalloproteins. Temperature dependent changes in the low temperature X-band EPR spectra became visible around 100 K and continued up to room temperature. The measured 298 K g-tensor (principal values: 2.17, 2.16, 2.07) and copper hyperfine coupling tensor (principal values: −260, − 190, −37 MHz) were similar to the average of the 77 K tensor values pertaining to two neighboring histidine binding sites. The observed temperature dependence was interpreted using Anderson’s theory of motional narrowing, where the magnetic parameters for the different states are averaged as the copper rapidly hops between sites. The EPR pattern was also found to undergo a sharp sigmoidal-shaped, temperature dependent conversion between two species with a critical temperature Tc ≈ 160 K. The species below Tc hops between the two low temperature site patterns, and the one above Tc represents an average of the molecular spin Hamiltonian coupling tensors of the two 77 K sites. In addition, the low and high temperature species hop between one another, contributing to the dynamic averaging. Spectral simulations using this 4-state model determined a hop rate between the two low temperature sites νh4 = 4.5 × 108 s−1 and between the low and high temperature states νh2 = 1.7 × 108 s−1 at 160 K. An Arrhenius relationship of hop rate and temperature gave energy barriers of ΔE4 = 389 cm−1 and ΔE2 = 656 cm−1 between the two low temperature sites, and between the low and high temperature states, respectively.
doi:10.1021/jp401477m
PMCID: PMC3740127  PMID: 23530765
Anderson; Arrhenius; dynamics; temperature; histidine; crystal; structure; rate; energy
2.  Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme 
The structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase has been determined in a hexagonal crystal form and gives insight into the possible paths that the substrate carbamoyl phosphate may follow to reach the active site during catalysis.
Crystals of the catalytic chain of Methanococcus jannaschii aspartate trans­carbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6322, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K+ ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. janna­schii will provide further insight into these points.
doi:10.1107/S1744309112011037
PMCID: PMC3374506  PMID: 22691781
aspartate transcarbamoylase; Methanococcus jannaschii; catalytic chain; enzyme mechanisms; protein structure-function
3.  Aspects of Structure and Bonding in Copper-Amino Acid Complexes Revealed by Single Crystal EPR/ENDOR Spectroscopy and Density Functional Calculations 
The journal of physical chemistry. A  2009;113(19):5700-5709.
This work deduces from a series of well defined copper-doped amino acid crystals, relationships between structural features of the copper complexes and ligand-bound proton hyperfine parameters. These were established by combining results from electron paramagnetic resonance (EPR)/electron-nuclear double resonance (ENDOR) studies, crystallography and were further assessed by quantum mechanical (QM) calculations. A detailed evaluation of previous studies on Cu2+-doped into α-glycine, triglycine sulfate, α-glycylglycine and l-alanine crystals reveal correlations between geometric features of the copper sites and proton hyperfine couplings from amino bound and carbon bound hydrogens. Experimental variations in proton isotropic hyperfine coupling values (aiso) could be fit to cosine-square dependences on dihedral angles, namely, for Cα-bound hydrogens, aiso = −1.09 + 8.21cos2θ MHz, and for amino hydrogens, aiso = −6.16 + 4.15cos2φ MHz. For the Cα hydrogens, this dependency suggests a hyperconjugative-like mechanism for transfer of spin density into the hydrogen 1s-orbital. In the course of this work, it was also necessary to reanalyze the ENDOR measurements from Cu2+-doped α-glycine since the initial study determined the 14N coupling parameters without holding its nuclear quadrupole tensor traceless. This new treatment of the data was needed to correctly align the 14N hyperfine tensor principal directions in the molecular complex. In order to provide a theoretical basis for the coupling variations, QM calculations performed at the Density Functional Theory (DFT) level were used to compute the proton hyperfine tensors in the four crystal complexes as well as in a geometry-optimized Cu2+(glycine)2 model. These theoretical calculations confirmed systematic changes in couplings with dihedral angles, but greatly overestimated the experimental geometric sensitivity to the amino hydrogen isotropic coupling.
doi:10.1021/jp811249s
PMCID: PMC2896622  PMID: 19378965
proton hyperfine couplings; hyperconjugation; spin density; glycine; triglycine sulfate; alanine; glycylglycine
4.  Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form 
The structure of the catalytic subunit of M. jannaschii aspartate transcarbamoylase has been determined in space group P212121 using synchrotron data to a resolution of 3.0 Å and was refined to a final R work and R free of 0.215 and 0.269, respectively.
Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallo­graphically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4° between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4° between crystal forms.
doi:10.1107/S1744309108025359
PMCID: PMC2531265  PMID: 18765902
aspartate transcarbamoylase; catalytic subunit; Methanococcus jannaschii
5.  Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1 
Nucleic Acids Research  2002;30(7):1531-1538.
The RNA-recognition motif (RRM) is a common and evolutionarily conserved RNA-binding module. Crystallographic and solution structural studies have shown that RRMs adopt a compact α/β structure, in which four antiparallel β-strands form the major RNA-binding surface. Conserved aromatic residues in the RRM are located on the surface of the β-sheet and are important for RNA binding. To further our understanding of the structural basis of RRM-nucleic acid interaction, we carried out a high resolution analysis of UP1, the N-terminal, two-RRM domain of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), whose structure was previously solved at 1.75–1.9 Å resolution. The two RRMs of hnRNP A1 are closely related but have distinct functions in regulating alternative pre-mRNA splice site selection. Our present 1.1 Å resolution crystal structure reveals that two conserved solvent-exposed phenylalanines in the first RRM have alternative side chain conformations. These conformations are spatially correlated, as the individual amino acids cannot adopt each of the observed conformations independently. These phenylalanines are critical for nucleic acid binding and the observed alternative side chain conformations may serve as a mechanism for regulating nucleic acid binding by RRM-containing proteins.
PMCID: PMC101846  PMID: 11917013

Results 1-5 (5)