ORGANIZING FORCES AND CONFORMATIONAL ACCESSIBILITY IN THE UNFOLDED STATE OF PROTEINS

For over fifty years, the unfolded state of proteins had been thought to be featureless and random. Experiments by Tanford and Flory confirmed that unfolded proteins possessed the same dimensions as those predicted of a random flight chain in good solvent. In the late eighties and early nineties, however, researchers began to notice structural trends in unfolded proteins. Some experiments showed that the unfolded state was very similar to the native state, while others indicated a conformational preference for the polyproline II helix in unfolded proteins. As a result, a paradox developed. How can unfolded proteins be both random and nonrandom at the same time? Current experiments and most theoretical simulations cannot characterize the unfolded state in high detail, so we have used the simplified hard sphere model of Richards to address this question. By modeling proteins as hard spheres, we can not only determine what interactions are important in the unfolded state of proteins, but we can address the paradox directly by investigating whether nonrandom behavior is in conflict with random coil statistics. Our simulations identify hundreds of disfavored conformations in short peptides, each of which proves that unfolded proteins are not at all random. Some interactions are important for the folded state of proteins as well. For example, we find that an α-helix cannot be followed directly by a β-strand because of steric considerations. The interactions outlined here limit the conformational possibilities of an unfolded protein far beyond what would be expected for a random coil. For a 100-residue protein, we find that approximately 9 orders of magnitude of conformational freedom are lost because of iii local chain organization alone. Furthermore, we show that the existence of this organization is compatible with random coil statistics. Although our simulations cannot settle the controversy surrounding the unfolded state, we can conclude that new methods of characterizing the unfolded state are needed. Since unfolded proteins are not random coils, the methods developed for describing random coils cannot adequately describe the complexities of this diverse structural ensemble

1928 Ruby Yearbook

A digitized copy of the 1928 Ruby, the Ursinus College yearbook.https://digitalcommons.ursinus.edu/ruby/1030/thumbnail.jp

Unstructured intermediate states in single protein force experiments

Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native state. Here we investigate on-lattice protein-like heteropolymer models that lead to a three-state mechanism and show that force experiments can be useful to determine the structure of I. We have mostly found that I is composed of a core stabilized by a high number of native contacts, plus an unstructured extended chain. The lifetime of I is shown to be sensitive to modifications of the protein that spoil the core. We then propose three types of modifications--point mutations, cuts, and circular permutations--aiming at: (1) confirming the presence of the core and (2) determining its location, within one amino acid accuracy, along the polypeptide chain. We also propose force jump protocols aiming to probe the on/off-pathway nature of I.Comment: 10 page

\u3csup\u3e1\u3c/sup\u3eH, \u3csup\u3e15\u3c/sup\u3eN, and \u3csup\u3e13\u3c/sup\u3eC Chemical Shift Assignments of the Regulatory Domain of Human Calcineurin

Calcineurin (CaN) plays an important role in T-cell activation, cardiac system development and nervous system function. Previous studies have demonstrated that the regulatory domain (RD) of CaN binds calmodulin (CaM) towards the N-terminal end. Calcium-loaded CaM activates the serine/threonine phosphatase activity of CaN by binding to the RD, although the mechanistic details of this interaction remain unclear. It is thought that CaM binding at the RD displaces the auto-inhibitory domain (AID) from the active site of CaN, activating phosphatase activity. In the absence of calcium-loaded CaM, the RD is disordered, and binding of CaM induces folding in the RD. In order to provide mechanistic detail about the CaM–CaN interaction, we have undertaken an NMR study of the RD of CaN. Complete 13C, 15N and 1H assignments of the RD of CaN were obtained using solution NMR spectroscopy. The backbone of RD has been assigned using a combination of 13C-detected CON-IPAP experiments as well as traditional HNCO, HNCA, HNCOCA and HNCACB-based 3D NMR spectroscopy. A 15N-resolved TOCSY experiment has been used to assign Hα and Hβ chemical shifts

BriX: a database of protein building blocks for structural analysis, modeling and design

High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments

Empirical Potential Function for Simplified Protein Models: Combining Contact and Local Sequence-Structure Descriptors

An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of the conformational space. We show residue specific reduced discrete state models can represent the backbone conformations of proteins with small RMSD values. However, no potential functions exist that are designed for such simplified protein models. In this study, we develop optimal potential functions by combining contact interaction descriptors and local sequence-structure descriptors. The form of the potential function is a weighted linear sum of all descriptors, and the optimal weight coefficients are obtained through optimization using both native and decoy structures. The performance of the potential function in test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. Our potential function requiring only backbone atoms or $C_\alpha$ atoms have comparable or better performance than several residue-based potential functions that require additional coordinates of side chain centers or coordinates of all side chain atoms. By reducing the residue alphabets down to size 5 for local structure-sequence relationship, the performance of the potential function can be further improved. Our results also suggest that local sequence-structure correlation may play important role in reducing the entropic cost of protein folding.Comment: 20 pages, 5 figures, 4 tables. In press, Protein

Blink and you'll miss it: The role of blinking in the perception of magic tricks

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed.Magicians use several techniques to deceive their audiences, including, for example, the misdirection of attention and verbal suggestion. We explored another potential stratagem, namely the relaxation of attention. Participants watched a video of a highly skilled magician whilst having their eye-blinks recorded. The timing of spontaneous eye-blinks was highly synchronized across participants. In addition, the synchronized blinks frequency occurred immediately after a seemingly impossible feat, and often coincided with actions that the magician wanted to conceal from the audience. Given that blinking is associated with the relaxation of attention, these findings suggest that blinking plays an important role in the perception of magic, and that magicians may utilize blinking and the relaxation of attention to hide certain secret actions.Peer reviewedFinal Published versio

Magic in the machine: a computational magician's assistant

A human magician blends science, psychology and performance to create a magical effect. In this paper we explore what can be achieved when that human intelligence is replaced or assisted by machine intelligence. Magical effects are all in some form based on hidden mathematical, scientific or psychological principles; often the parameters controlling these underpinning techniques are hard for a magician to blend to maximise the magical effect required. The complexity is often caused by interacting and often conflicting physical and psychological constraints that need to be optimally balanced. Normally this tuning is done by trial and error, combined with human intuitions. Here we focus on applying Artificial Intelligence methods to the creation and optimisation of magic tricks exploiting mathematical principles. We use experimentally derived data about particular perceptual and cognitive features, combined with a model of the underlying mathematical process to provide a psychologically valid metric to allow optimisation of magical impact. In the paper we introduce our optimisation methodology and describe how it can be flexibly applied to a range of different types of mathematics based tricks. We also provide two case studies as exemplars of the methodology at work: a magical jigsaw, and a mind reading card trick effect. We evaluate each trick created through testing in laboratory and public performances, and further demonstrate the real world efficacy of our approach for professional performers through sales of the tricks in a reputable magic shop in London

Surface Plasmon Resonance, Formation Mechanism, and Surface Enhanced Raman Spectroscopy of Ag+-Stained Gold Nanoparticles

A series of recent works have demonstrated the spontaneous Ag+ adsorption onto gold surfaces. However, a mechanistic understanding of the Ag+ interactions with gold has been controversial. Reported herein is a systematic study of the Ag+ binding to AuNPs using several in-situ and ex-situ measurement techniques. The time-resolved UV-vis measurements of the AuNP surface plasmonic resonance revealed that the silver adsorption proceeds through two parallel pseudo-first order processes with a time constant of 16(±2) and 1,000(±35) s, respectively. About 95% of the Ag+ adsorption proceeds through the fast adsorption process. The in-situ zeta potential data indicated that this fast Ag+ adsorption is driven primarily by the long-range electrostatic forces that lead to AuNP charge neutralization, while the time-dependent pH data shows that the slow Ag+ binding process involves proton-releasing reactions that must be driven by near-range interactions. These experimental data, together with the ex-situ XPS measurement indicates that adsorbed silver remains cationic, but not as a charged-neutral silver atom proposed by the anti-galvanic reaction mechanism. The surface-enhanced Raman activities of the Ag+-stained AuNPs are slightly higher than that for AuNPs, but significantly lower than that for the silver nanoparticles (AgNPs). The SERS feature of the ligands on the Ag+-stained AuNPs can differ from that on both AuNPs and AgNPs. Besides the new insights to formation mechanism, properties, and applications of the Ag+-stained AuNPs, the experimental methodology presented in this work can also be important for studying nanoparticle interfacial interactions