A Generic Program for Multistate Protein Design

Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate design, where a single sequence is threaded onto multiple backbones (states) and evaluated for its strengths and weaknesses on each backbone. For example, to design a protein that can switch between two specific conformations, it is necessary to to find a sequence that is compatible with both backbone conformations. We present in this paper a generic implementation of multistate design that is suited for a wide range of protein design tasks and demonstrate in silico its capabilities at two design tasks: one of redesigning an obligate homodimer into an obligate heterodimer such that the new monomers would not homodimerize, and one of redesigning a promiscuous interface to bind to only a single partner and to no longer bind the rest of its partners. Both tasks contained negative design in that multistate design was asked to find sequences that would produce high energies for several of the states being modeled. Success at negative design was assessed by computationally redocking the undesired protein-pair interactions; we found that multistate design's accuracy improved as the diversity of conformations for the undesired protein-pair interactions increased. The paper concludes with a discussion of the pitfalls of negative design, which has proven considerably more challenging than positive design

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

Natural proteins often partake in several highly specific protein-protein interactions. They are thus subject to multiple opposing forces during evolutionary selection. To be functional, such multispecific proteins need to be stable in complex with each interaction partner, and, at the same time, to maintain affinity toward all partners. How is this multispecificity acquired through natural evolution? To answer this compelling question, we study a prototypical multispecific protein, calmodulin (CaM), which has evolved to interact with hundreds of target proteins. Starting from high-resolution structures of sixteen CaM-target complexes, we employ state-of-the-art computational methods to predict a hundred CaM sequences best suited for interaction with each individual CaM target. Then, we design CaM sequences most compatible with each possible combination of two, three, and all sixteen targets simultaneously, producing almost 70,000 low energy CaM sequences. By comparing these sequences and their energies, we gain insight into how nature has managed to find the compromise between the need for favorable interaction energies and the need for multispecificity. We observe that designing for more partners simultaneously yields CaM sequences that better match natural sequence profiles, thus emphasizing the importance of such strategies in nature. Furthermore, we show that the CaM binding interface can be nicely partitioned into positions that are critical for the affinity of all CaM-target complexes and those that are molded to provide interaction specificity. We reveal several basic categories of sequence-level tradeoffs that enable the compromise necessary for the promiscuity of this protein. We also thoroughly quantify the tradeoff between interaction energetics and multispecificity and find that facilitating seemingly competing interactions requires only a small deviation from optimal energies. We conclude that multispecific proteins have been subjected to a rigorous optimization process that has fine-tuned their sequences for interactions with a precise set of targets, thus conferring their multiple cellular functions

Gendered self-views across 62 countries: a test of competing models

Social role theory posits that binary gender gaps in agency and communion should be larger in less egalitarian countries, reflecting these countries’ more pronounced sex-based power divisions. Conversely, evolutionary and self-construal theorists suggest that gender gaps in agency and communion should be larger in more egalitarian countries, reflecting the greater autonomy support and flexible self-construction processes present in these countries. Using data from 62 countries (N = 28,640), we examine binary gender gaps in agentic and communal self-views as a function of country-level objective gender equality (the Global Gender Gap Index) and subjective distributions of social power (the Power Distance Index). Findings show that in more egalitarian countries, gender gaps in agency are smaller and gender gaps in communality are larger. These patterns are driven primarily by cross-country differences in men’s self-views and by the Power Distance Index (PDI) more robustly than the Global Gender Gap Index (GGGI). We consider possible causes and implications of these findings

Functionalized periodic mesoporous organosilicas for enhanced and selective peptide enrichment

Nitroxide radical polymers can undergo both excellent electrochemical redox reactions and a rapid "click" coupling reaction with carbon-centered radicals (i.e., nitroxide radical coupling (NRC) reaction). In this work, we report a strategy to functionalize poly(2,2,6,6,-tetramethylpiperidinyl-1-oxyl methacrylate) (PTMA) with pyrene side groups through a rapid and near quantitative NRC reaction. This resulted in P(TMA-co-PyMA) random copolymers with near quantitative amounts of pyrene along the PTMA chain for greater π-π interaction with rGO, while the nitroxide radicals on the polymer could simultaneously be used for energy storage. These copolymers can bind with reduced graphene oxide (rGO) and form layered composites through noncovalent π-π stacking, attaining molecular-level dispersion. Electrochemical performance of the composites with different polymer contents (24, 35, and 45 wt %), tested in lithium ion batteries, indicated that the layered structures consisting of P(TMA-co-PyMA) maintained greater capacities at high C-rates. This simple and efficient strategy to synthesize pyrene-functionalized polymers will provide new opportunities to fabricate many other polymer composite electrodes for desired electrochemical performance

Country-level and individual-level predictors of men's support for gender equality in 42 countries

Men sometimes withdraw support for gender equality movements when their higher gender status is threatened. Here, we expand the focus of this phenomenon by examining it cross-culturally, to test if both individual- and country-level variables predict men's collective action intentions to support gender equality. We tested a model in which men's zero-sum beliefs about gender predict reduced collective action intentions via an increase in hostile sexism. Because country-level gender equality may threaten men's higher gender status, we also examined whether the path from zero-sum beliefs to collective action intentions was stronger in countries higher in gender equality. Multilevel modeling on 6,734 men from 42 countries supported the individual-level mediation model, but found no evidence of moderation by country-level gender equality. Both country-level gender equality and individual-level zero-sum thinking independently predicted reductions in men's willingness to act collectively for gender equality