Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.     

Toward efficient photomodulation of conjugated polymer emission: optimizing differential energy transfer in azobenzene-substituted PPV derivatives

We present fluorescence studies of quenching behavior in photoaddressable azobenzene-substituted derivatives of the fluorescent conjugated polymer poly(p-phenylenevinylene) (PPV). The azobenzene side chains partially quench the PPV fluorescence, and we have shown previously that the quenching efficiency is greater when the azobenzene side chains are cis than when they are trans. This effect provides a photoaddressable means of modulating the fluorescence intensity of PPV derivatives. To optimize the efficiency of photoinduced intensity modulation, it is important to understand the molecular nature of quenching by both trans- and cis-azobenzene side chains. Here we investigate the photophysical origins of quenching by the two isomers using steady-state and time-resolved fluorescence spectroscopy. We present results from the azobenzene-modified PPV derivative poly(2-methoxy-5-((10-(4-(phenylazo)phenoxy)decyl)oxy)-1,4-phenylenevinylene) (MPA-10-PPV) and two new related polymers, a copolymer lacking half of the azobenzene side chains and an analogue of MPA-10-PPV with a tert-butyl-substituted azobenzene. These studies reveal that steric interactions influence the extent of PPV emission quenching by trans-azobenzene but do not affect the efficient quenching by cis-azobenzene. The difference in dynamic quenching efficiencies between trans- and cis-azobenzene isomers is consistent with fluorescence resonance energy transfer. These results show that it is possible to control the efficiency of photoswitchable fluorescence modulation through specific structural variations designed to encourage or block quenching by trans-azobenzene. This is a promising approach to providing useful general guidelines for designing photomodulated PPV derivatives.     

Simplifying the setup for vacuum‐outlet GC: Using a restriction inside the injection port

The application of vacuum GC has several advantages over pressurized GC. One of the key characteristics is that the optimal gas velocity is very high. Combined with short capillary columns of wide internal diameter, this results in short analysis times using standard GC‐MS equipment. To make vacuum GC possible using a GC‐MS system, a restriction must be positioned at the injection side of the column. This restriction is usually made of deactivated 0.1 mm i.d. fused‐silica tubing which is coupled to the analytical column. Such restrictions will work, but practical challenges are found in coupling, reducing dead volume and robustness. A new way of making restrictions is by incorporating the restriction into the injection port. Using well‐defined short pieces of fused silica with internal diameter of 0.025 mm, one can make a restriction using a Press‐Tight® type connector, and position this inside the injection port. By doing this, the restriction is very short and at high temperature all the time. Activity plays a minimal role, and also leaks will not be an issue as the coupling is in 100% inert gas. Data obtained using this concept is promising as vacuum GC becomes easier and more robust.