FTIR studies of collagen model peptides: complementary experimental and simulation approaches to conformation and unfolding

X-ray crystallography of collagen model peptides has provided high-resolution structures of the basic triple-helical conformation and its water-mediated hydration network. Vibrational spectroscopy provides a useful bridge for transferring the structural information from X-ray diffraction to collagen in its native environment. The vibrational mode most useful for this purpose is the amide I mode (mostly peptide bond C=O stretch) near 1650 cm-1. The current study refines and extends the range of utility of a novel simulation method that accurately predicts the infrared (IR) amide I spectral contour from the three-dimensional structure of a protein or peptide. The approach is demonstrated through accurate simulation of the experimental amide I contour in solution for both a standard triple helix, (Pro-Pro-Gly)10, and a second peptide with a Gly --> Ala substitution in the middle of the chain that models the effect of a mutation in the native collagen sequence. Monitoring the major amide I peak as a function of temperature gives sharp thermal transitions for both peptides, similar to those obtained by circular dichroism spectroscopy, and the Fourier transform infrared (FTIR) spectra of the unfolded states were compared with polyproline II. The simulation studies were extended to model early stages of thermal denaturation of (Pro-Pro-Gly)10. Dihedral angle changes suggested by molecular dynamics simulations were made in a stepwise fashion to generate peptide unwinding from each end, which emulates the effect of increasing temperature. Simulated bands from these new structures were then compared to the experimental bands obtained as temperature was increased. The similarity between the simulated and experimental IR spectra lends credence to the simulation method and paves the way for a variety of applications.     

Importance of proper renormalization scale-setting for QCD testing at colliders

A primary problem affecting perturbative quantum chromodynamic (pQCD) analyses is the lack of a method for setting the QCD running-coupling renormalization scale such that maximally precise fixed-order predictions for physical observables are obtained. The Principle of Maximum Conformality (PMC) eliminates the ambiguities associated with the conventional renormalization scale-setting procedure, yielding predictions that are independent of the choice of renormalization scheme. The QCD coupling scales and the effective number of quark flavors are set order-by-order in the pQCD series. The PMC has a solid theoretical foundation, satisfying the standard renormalization group invariance condition and all of the self-consistency conditions derived from the renormalization group. The PMC scales at each order are obtained by shifting the arguments of the strong force coupling constant α_s to eliminate all non-conformal {β_i} terms in the pQCD series. The {β_i} terms are determined from renormalization group equations without ambiguity. The correct behavior of the running coupling at each order and at each phase-space point can then be obtained. The PMC reduces in the N_C → 0 Abelian limit to the Gell-Mann-Low method. In this brief report, we summarize the results of our recent application of the PMC to a number of collider processes, emphasizing the generality and applicability of this approach. A discussion of hadronic Z decays shows that, by applying the PMC, one can achieve accurate predictions for the total and separate decay widths at each order without scale ambiguities. We also show that, if one employs the PMC to determine the top-quark pair forward-backward asymmetry at the next-to-next-to-leading order level, one obtains a comprehensive, self-consistent pQCD explanation for the Tevatron measurements of the asymmetry. This accounts for the “increasing-decreasing” behavior observed by the D0 collaboration for increasing tt¯ invariant mass. At lower energies, the angular distributions of heavy quarks can be used to obtain a direct determination of the heavy quark potential. A discussion of the angular distributions of massive quarks and leptons is also presented, including the fermionic component of the two-loop corrections to the electromagnetic form factors. These results demonstrate that the application of the PMC systematically eliminates a major theoretical uncertainty for pQCD predictions, thus increasing collider sensitivity to possible new physics beyond the Standard Model.     

AdS/QCD and Applications of Light-Front Holography

Light-front holography leads to a rigorous connection between hadronic amplitudes in a higher dimensional anti-de Sitter(AdS) space and frame-independent light-front wavefunctions of hadrons in(3 + 1)-dimensional physical space-time,thus providing a compelling physical interpretation of the AdS/CFT correspondence principle and AdS/QCD,a useful framework which describes the correspondence between theories in a modified AdS 5 background and confining field theories in physical space-time.To a first semiclassical approximation,where quantum loops and quark masses are not included,this approach leads to a single-variable light-front Schro¨dinger equation which determines the eigenspectrum and the light-front wavefunctions of hadrons for general spin and orbital angular momentum.The coordinate z in AdS space is uniquely identified with a Lorentz-invariant coordinate ζ which measures the separation of the constituents within a hadron at equal light-front time.The internal structure of hadrons is explicitly introduced and the angular momentum of the constituents plays a key role.We give an overview of the light-front holographic approach to strongly coupled QCD.In particular,we study the photon-to-meson transition form factors(TFFs) FMγ(Q 2) for γ→ M using light-front holographic methods.The results for the TFFs for the η and η ' mesons are also presented.Some novel features of QCD are discussed,including the consequences of confinement for quark and gluon condensates.A method for computing the hadronization of quark and gluon jets at the amplitude level is outlined.     

Identification of partially disordered peptide intermediates through residue-specific NMR diffusion measurements

It is technically challenging to detect low-population partially disordered species that are in equilibrium with the folded and unfolded states. Residue-specific translational diffusion experiments measured by pulsed field gradient NMR have been used to detect the presence, and define the conformation, of such equilibrium intermediates. The experiment is demonstrated for equilibrium solutions of related triple helical peptides that model a small region of type I collagen with and without a mutation known to cause osteogenesis imperfecta. The data show that residue-specific diffusion coefficients of an interconverting trimer to monomer system can allow discrimination between a simple two-state model and more complex multistate models involving partially disordered intermediates.     

Global Analysis of Plasmodium falciparum Dihydropteroate Synthase Variants Associated with Sulfadoxine Resistance Reveals Variant Distribution and Mechanisms of Resistance: A Computational-Based Study

The continual rise in sulfadoxine (SDX) resistance affects the therapeutic efficacy of sulfadoxine-pyrimethamine; therefore, careful monitoring will help guide its prolonged usage. Mutations in Plasmodium falciparum dihydropteroate synthase (Pfdhps) are being surveilled, based on their link with SDX resistance. However, there is a lack of continuous analyses and data on the potential effect of molecular markers on the Pfdhps structure and function. This study explored single-nucleotide polymorphisms (SNPs) in Pfdhps that were isolated in Africa and other countries, highlighting the regional distribution and its link with structure. In total, 6336 genomic sequences from 13 countries were subjected to SNPs, haplotypes, and structure-based analyses. The SNP analysis revealed that the key SDX resistance marker, A437G, was nearing fixation in all countries, peaking in Malawi. The mutation A613S was rare except in isolates from the Democratic Republic of Congo and Malawi. Molecular docking revealed a general loss of interactions when comparing mutant proteins to the wild-type protein. During MD simulations, SDX was released from the active site in mutants A581G and A613S before the end of run-time, whereas an unstable binding of SDX to mutant A613S and haplotype A437A/A581G/A613S was observed. Conformational changes in mutant A581G and the haplotypes A581G/A613S, A437G/A581G, and A437G/A581G/A613S were seen. The radius of gyration revealed an unfolding behavior for the A613S, K540E/A581G, and A437G/A581G systems. Overall, tracking such mutations by the continuous analysis of Pfdhps SNPs is encouraged. SNPs on the Pfdhps structure may cause protein–drug function loss, which could affect the applicability of SDX in preventing malaria in pregnant women and children.     

Hunting for glueballs in electron-positron annihilation

We calculate the cross section for the exclusive production of J(PC)=0(++) glueballs G0 in association with the J/psi in e(+)e(-) annihilation using the perturbative QCD factorization formalism. The required long-distance matrix element for the glueball is bounded by CUSB data from a search for resonances in radiative Upsilon decay. The cross section for e(+)e(-)-->J/psi+G0 at sqrt[s]=10.6 GeV is similar to exclusive charmonium-pair production e(+)e(-)-->J/psi+h for h=eta(c) and chi(c0), and is larger by a factor of 2 than that for h=eta(c)(2S). As the subprocesses gamma(*)-->(cc)(cc) and gamma(*)-->(cc)(gg) are of the same nominal order in perturbative QCD, it is possible that some portion of the anomalously large signal observed by Belle in e(+)e(-)-->J/psiX may actually be due to the production of charmonium-glueball J/psiG(J) pairs.