Protein loop compaction and the origin of the effect of arginine and glutamic acid mixtures on solubility, stability and transient oligomerization of proteins

Addition of a 50 mM mixture of l-arginine and l-glutamic acid (RE) is extensively used to improve protein solubility and stability, although the origin of the effect is not well understood. We present Small Angle X-ray Scattering (SAXS) and Nuclear Magnetic Resonance (NMR) results showing that RE induces protein compaction by collapsing flexible loops on the protein core. This is suggested to be a general mechanism preventing aggregation and improving resistance to proteases and to originate from the polyelectrolyte nature of RE. Molecular polyelectrolyte mixtures are expected to display long range correlation effects according to dressed interaction site theory. We hypothesize that perturbation of the RE solution by dissolved proteins is proportional to the volume occupied by the protein. As a consequence, loop collapse, minimizing the effective protein volume, is favored in the presence of RE

Individual & Collective Human Intelligence in Drug Design: Evaluating the Search Strategy

In recent years, individual and collective human intelligence, defined as the knowledge, skills, reasoning and intuition of individuals and groups, have been used in combination with computer algorithms to solve complex scientific problems. Such approach was successfully used in different research fields such as: structural biology, comparative genomics, macromolecular crystallography and RNA design. Herein we describe an attempt to use a similar approach in small-molecule drug discovery, specifically to drive search strategies of de novo drug design. This is assessed with a case study that consists of a series of public experiments in which participants had to explore the huge chemical space in silico to find predefined compounds by designing molecules and analyzing the score associate with them. Such a process may be seen as an instantaneous surrogate of the classical design-make-test cycles carried out by medicinal chemists during the drug discovery hit to lead phase but not hindered by long synthesis and testing times. The objectives of this case study are to give the first insights towards: the assessment of human intelligence in chemical space exploration problems; compare the performance of individual and collective human intelligence in such a problems; and also contrast some human and artificial intelligence achievements in de novo drug design.</p

An Extended Winged Helix Domain in General Transcription Factor E/IIE&alpha

Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. Here we define a conserved and functionally essential N−terminal domain in TFE, the archaeal homolog of the large TFIIE subunit {alpha}. X−ray crystallography shows that this TFE domain adopts a winged helix−turn−helix (winged helix) fold, extended by specific {alpha}−helices at the N and C termini. Although the winged helix fold is often found in DNA−binding proteins, we show that TFE is not a typical DNA−binding winged helix protein, because its putative DNA−binding face shows a negatively charged groove and an unusually long wing, and because the domain lacks DNA−binding activity in vitro. The groove and a conserved hydrophobic surface patch on the additional N−terminal {alpha}−helix may, however, allow for interactions with other general transcription factors and RNA polymerase. Homology modeling shows that the TFE domain is conserved in TFIIE{alpha}, including the potential functional surface

Protein loop compaction and the origin of the effect of arginine and glutamic acid mixtures on solubility, stability and transient oligomerization of proteins

Addition of a 50 mM mixture of l-arginine and l-glutamic acid (RE) is extensively used to improve protein solubility and stability, although the origin of the effect is not well understood. We present Small Angle X-ray Scattering (SAXS) and Nuclear Magnetic Resonance (NMR) results showing that RE induces protein compaction by collapsing flexible loops on the protein core. This is suggested to be a general mechanism preventing aggregation and improving resistance to proteases and to originate from the polyelectrolyte nature of RE. Molecular polyelectrolyte mixtures are expected to display long range correlation effects according to dressed interaction site theory. We hypothesize that perturbation of the RE solution by dissolved proteins is proportional to the volume occupied by the protein. As a consequence, loop collapse, minimizing the effective protein volume, is favored in the presence of RE