Bias in the journal impact factor

The ISI journal impact factor (JIF) is based on a sample that may represent half the whole-of-life citations to some journals, but a small fraction (<10%) of the citations accruing to other journals. This disproportionate sampling means that the JIF provides a misleading indication of the true impact of journals, biased in favour of journals that have a rapid rather than a prolonged impact. Many journals exhibit a consistent pattern of citation accrual from year to year, so it may be possible to adjust the JIF to provide a more reliable indication of a journal's impact.Comment: 9 pages, 8 figures; one reference correcte

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

Substrate transport activation is mediated through second periplasmic loop of transmembrane protein MalF in maltose transport complex of <em>Escherichia coli</em>.

In a recent study we described the second periplasmic loop P2 of the transmembrane protein MalF (MalF-P2) of the maltose ATP-binding cassette transporter (MalFGK(2)-E) as an important element in the recognition of substrate by the maltose-binding protein MalE. In this study, we focus on MalE and find that MalE undergoes a structural rearrangement after addition of MalF-P2. Analysis of residual dipolar couplings (RDCs) shows that binding of MalF-P2 induces a semiopen state of MalE in the presence and absence of maltose, whereas maltose is retained in the binding pocket. These data are in agreement with paramagnetic relaxation enhancement experiments. After addition of MalF-P2, an increased solvent accessibility for residues in the vicinity of the maltose-binding site of MalE is observed. MalF-P2 is thus not only responsible for substrate recognition, but also directly involved in activation of substrate transport. The observation that substrate-bound and substrate-free MalE in the presence of MalF-P2 adopts a similar semiopen state hints at the origin of the futile ATP hydrolysis of MalFGK(2)-E

Characterization of membrane proteins in isolated native cellular membranes by dynamic nuclear polarization solid-state NMR spectroscopy without purification and reconstitution.

Membrane proteins in their native cellular membranes are accessible by dynamic nuclear polarization magic angle spinning solid-state NMR spectroscopy without the need of purification and reconstitution (see picture). Dynamic nuclear polarization is essential to achieve the required gain in sensitivity to observe the membrane protein of interest

Dimer formation of a stabilized Gbeta1 variant. A structural and energetic analysis

In previous work, a strongly stabilized variant of the beta1 domain of protein G (Gbeta1) was obtained by an in-vitro selection method. This variant, termed Gbeta1-M2, contains the four substitutions E15V, T16L, T18I, and N37L. Here we elucidated the molecular basis of the observed strong stabilizations. The contributions of these four residues were analyzed individually and in various combinations, additional selections with focused Gbeta1 gene libraries were performed, and the crystal structure of Gbeta1-M2 was determined. All single substitutions (E15V, T16L, T18I, and N37L) stabilize wild-type Gbeta1 by contributions between 1.6 and 6.0 kJ mol(-1) (at 70 degrees C). Hydrophobic residues at the positions 16 and 37 provide the major contribution to stabilization by enlarging the hydrophobic core of Gbeta1. They also increase the tendency to form dimers, as shown by the dependence on concentration of the apparent molecular mass in analytical ultracentrifugation, by a concentration-dependent stability, and by a strongly increased van't Hoff enthalpy of unfolding. The 0.88 A crystal structure of Gbeta1-M2 and NMR measurements in solution provide the explanation for the observed dimer formation. It involves a head-to-head arrangement of two Gbeta1-M2 molecules via six intermolecular hydrogen bonds between the two beta strands 2 and 2' and an adjacent self-complementary hydrophobic surface area, which is created by the T16L and N37L substitutions and a large 120 degrees rotation of the Tyr33 side chain. This removal of hydrophilic groups and the malleability of the created hydrophobic surface provides the basis for dimer formation of the stabilized Gbeta1 variants