The Most Severe Test for Hydrophobicity Scales: Two Proteins with 88% Sequence Identity but Different Structure and Function

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD) concluded that the "simplicity and graphic nature of hydrophobicity scales make them very useful tools for the evaluation of protein structures". In practice, however, attempts to develop hydrophobicity scales (for example, compatible with classical force fields (CFF) in calculating the energetics of protein folding) have encountered many difficulties. Here we suggest an entirely different approach, based on the idea that proteins are self-organized networks, subject to finite-scale criticality (like some network glasses). We test this proposal against two small proteins that are delicately balanced between alpha and alpha/beta structures, with different functions encoded with only 12% of their amino acids. This example explains why protein structure prediction is so challenging, and it provides a severe test for the accuracy and content of hydrophobicity scales. The new method confirms KD's evaluation, and at the same time suggests that protein structure, dynamics and function can be best discussed without using CFF

Universal geometrical factor of protein conformations as a consequence of energy minimization

The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V/(A)) of the van der Waals volume V to the surface area A and average atomic radius of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491\pm0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.Comment: 6 pages, 1 table, 4 figure

Hydrophobic gating of mechanosensitive channel of large conductance evidenced by single-subunit resolution

Mechanosensitive (MS) ion channels are membrane proteins that detect and respond to membrane tension in all branches of life. In bacteria, MS channels prevent cells from lysing upon sudden hypoosmotic shock by opening and releasing solutes and water. Despite the importance of MS channels and ongoing efforts to explain their functioning, the molecular mechanism of MS channel gating remains elusive and controversial. Here we report a method that allows single-subunit resolution for manipulating and monitoring “mechanosensitive channel of large conductance” from Escherichia coli. We gradually changed the hydrophobicity of the pore constriction in this homopentameric protein by modifying a critical pore residue one subunit at a time. Our experimental results suggest that both channel opening and closing are initiated by the transmembrane 1 helix of a single subunit and that the participation of each of the five identical subunits in the structural transitions between the closed and open states is asymmetrical. Such a minimal change in the pore environment seems ideal for a fast and energy-efficient response to changes in the membrane tension.

Sustainability, pandemia and women in academia: breaking the “good girl” culture to enhance sustainability in engineering education

We would all agree that the role of sustainable development is to enable all people throughout the world to satisfy their basic needs and enjoy a better quality of life, without compromising quality of life for future generations. We would agree that sustainable development relies on ending discrimination towards women and providing equal opportunities for education and employment. Gender equality has been conclusively shown to stimulate economic growth, which is crucial for low-income countries. We would also agree that there has been a lot of research in relation to sustainable development in engineering education, indicating that the subject of sustainability may help increase participation of women in engineering. But in reality, how can we teach our students sustainable development and promote the role of females in engineering, when the engineering education is so unsustainable for female academics? Academic women have long made the compromises in terms of the double burden of domestic and paid work, as well as to their personal life choices and well-being, yet academia and higher education institutions have simply not made the working environment a more just and sustainable space for women. During the pandemic, these inequities were exacerbated by the loss of educational provision, now delivered online and facilitated by, in the majority of cases, mothers. The precarity of childcare, now makes the question of the unsustainability of female academic’s lives unavoidable. Women have been literally and figuratively left holding the baby during this crisis. We are at a critical juncture where we have the opportunity as academics, to reimagine the post-pandemic community, and create a more socially just and sustainable balance in our lives. This issue exceeds academia; it is actually the culture that dictates women to be “good girls”; to comply with the patriarchal system. While there is nothing wrong about being a good person, the “good girl” label has a completely different meaning and impact on the life and career of women. “Good girl” is the one who cares about the others, seeks their approval, has no needs or ambitions, is quiet, kind, willing to please everyone, to get everything right the first time, is not allowed to make mistakes, has to sacrifice herself, and to be perfect and above all else, not to challenge the system or to call out all the specifically gendered ways in which the impact of the system marginalises and hurts women. The “good girl” culture has been a big burden for women in academia in general, having a detrimental impact to the career development of female academics in particular in the male dominated sector of engineering education. During the pandemic, it has been taken for granted that women would deliver on all fronts. It is well document that women’s work is often invisible, both in the domestic and public spheres [1]. Although common to all disciplines, the impacts of bias and stereotypes are particularly pronounced in engineering [2]. Female academics please their students, line managers, colleagues and family, leaving behind themselves, their research and other necessary elements for their progression. They are never considered equally good, impactful, and successful, as their male colleagues. As a matter of fact, women in engineering education experience more grade appeals and receive lower course evaluations than their white male counterparts [3], being discriminated by students, administrators and academics, while their efforts and ideas are being constantly discounted. There is nothing sustainable about this. This paper proposes effective actions to tackle the “good girl” expectations for female academics, enhancing sustainability, implementing a fit-for-purpose change of the culture system across school, with targeted and consistent actions, actively promoting the needs of female academics

A Small Conductance Calcium-Activated K⁺ Channel in C. elegans, KCNL-2, Plays a Role in the Regulation of the Rate of Egg-Laying

In the nervous system of mice, small conductance calcium-activated potassium (SK) channels function to regulate neuronal excitability through the generation of a component of the medium afterhyperpolarization that follows action potentials. In humans, irregular action potential firing frequency underlies diseases such as ataxia, epilepsy, schizophrenia and Parkinson's disease. Due to the complexity of studying protein function in the mammalian nervous system, we sought to characterize an SK channel homologue, KCNL-2, in C. elegans, a genetically tractable system in which the lineage of individual neurons was mapped from their early developmental stages. Sequence analysis of the KCNL-2 protein reveals that the six transmembrane domains, the potassium-selective pore and the calmodulin binding domain are highly conserved with the mammalian homologues. We used widefield and confocal fluorescent imaging to show that a fusion construct of KCNL-2 with GFP in transgenic lines is expressed in the nervous system of C. elegans. We also show that a KCNL-2 null strain, kcnl-2(tm1885), demonstrates a mild egg-laying defective phenotype, a phenotype that is rescued in a KCNL-2-dependent manner. Conversely, we show that transgenic lines that overexpress KCNL-2 demonstrate a hyperactive egg-laying phenotype. In this study, we show that the vulva of transgenic hermaphrodites is highly innervated by neuronal processes and by the VC4 and VC5 neurons that express GFP-tagged KCNL-2. We propose that KCNL-2 functions in the nervous system of C. elegans to regulate the rate of egg-laying. © 2013 Chotoo et al