Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

Effects of current speed and turbidity on stationary light-trap catches of larval and juvenile fishes

Light traps are one of a number of different gears used to sample pelagic larval and juvenile fishes. In contrast to conventional towed nets, light traps primarily collect larger size classes, including settlement-size larvae (Choat et al., 1993; Hickford and Schiel, 1999 ; Hernandez and Shaw, 2003), and, therefore, have become important tools for discerning recruitment dynamics (Sponaugle and Cowen, 1996; Wilson, 2001). The relative ease with which multiple synoptic light trap samples can be taken means that larval distribution patterns can be mapped with greater spatial resolution (Doherty, 1987). Light traps are also useful for sampling shallow or structurally complex habitats where towed nets are ineffective or prohibited (Gregory and Powles, 1985; Brogan, 1994; Hernandez and Shaw, 2003).

Effect of a Terrapin Excluder Device on Blue Crab, Callinectes sapidus, Trap Catches

Mortality of diamondback terrapins, Malaclemys terrapin, in blue crab, Callinectes sapidus, traps has become a controversial bycatch issue in some areas. Traps with turtle excluder devices (TED’s) had increased sublegal (14.5%), legal (32.9%), and total (25.7%) blue crab catch per trap day (CPUE). There were statistically significant differences between total (P=0.0202) and legal (0.0174) CPUE for standard traps and traps with TED’s. The increased catch rates of blue crabs in traps with TED’s may be due to decreased escapement through the entrance f

Blue Crab, Callinectes sapidus, Retention Rates in Different Trap Meshes

Percent escapements of blue crabs, Callinectes sapidus, by size and sex were determined for commercially available 38.1 mm square and hexagonal meshes and for five experimental squares. Commercial trap mesh sizes retained excessive numbers of sublegal blue crabs. Based on the criteria of maximizing sublegal crab escapement without an unacceptable loss of legal blue crabs, the 44.4 mm square (as measured from the inside of adjacent corners) was optimum and superior to either trap mesh used by fishermen.

Blue Crab, Callinectes sapidus, Trap Selectivity Studies: Mesh Size

Catch rates and sizes of blue crabs, Callinectes sapidus, were compared in traps with 2.54 cm (1.0 inch), 3.81 cm (1.5 inches), and 5.08 cm (2.0 inches) square mesh, 2.54 by 5.08 cm rectangular mesh, and 3.81 cm hexagonal mesh. Catch of legal blue crabs by number was significantly greater in the traditional hexagonal mesh trap than in all other trap types. Sublegal catch by number was highest (34.1-63.3% of total) in the 2.54 cm and 3.81 cm square mesh and rectangular mesh traps and lowest in the 5.08 cm square mesh trap. The hexagonal mesh trap had significantly lower catch rates of sublegal blue crabs than all other trap types except the 5.08 cm square mesh. Mean size of blue crabs by trap type exhibited an inverse pattern to that shown by catch of sublegal crabs. The most effective trap to maximize legal catch and minimize sublegal catch was the 3.81 cm hexagonal mesh trap followed by the 5.08 cm square mesh trap.