Temperature‐Modulated Water Filtration Using Microgel‐Functionalized Hollow‐Fiber Membranes

In the present work, we investigate the potential of aqueous polymer microgels in membrane technology, especially for filtration applications. The poly(N‐vinylcaprolactam)‐based microgels exhibit thermoresponsive behavior and were employed to coat hollow‐fiber membranes used for micro‐ and ultrafiltration. We discuss the preparation of microgel‐modified membranes (by “inside‐out” as well as “outside‐in” filtration in dead‐end mode). The clean‐water permeability and stability of these membranes was studied not only as a function of time, but also of temperature. The microgel‐modified membranes exhibit a reversible thermoresponsive behavior whereby both the resistance and the retention increased with decreasing temperature.     

A novel approach to tag and identify geranylgeranylated proteins

A recently developed proteomic strategy, the “GG‐azide”‐labeling approach, is described for the detection and proteomic analysis of geranylgeranylated proteins. This approach involves metabolic incorporation of a synthetic azido‐geranylgeranyl analog and chemoselective derivatization of azido‐geranylgeranyl‐modified proteins by the “click” chemistry, using a tetramethylrhodamine‐alkyne. The resulting conjugated proteins can be separated by 1‐D or 2‐D and pH fractionation, and detected by fluorescence imaging. This method is compatible with downstream LC‐MS/MS analysis. Proteomic analysis of conjugated proteins by this approach identified several known geranylgeranylated proteins as well as Rap2c, a novel member of the Ras family. Furthermore, prenylation of progerin in mouse embryonic fibroblast cells was examined using this approach, demonstrating that this strategy can be used to study prenylation of specific proteins. The “GG‐azide”‐labeling approach provides a new tool for the detection and proteomic analysis of geranylgeranylated proteins, and it can readily be extended to other post‐translational modifications.     

Structure‐based redesign of proteins for minimal T‐cell epitope content

The protein universe displays a wealth of therapeutically relevant activities, but T‐cell driven immune responses to non‐“self” biological agents present a major impediment to harnessing the full diversity of these molecular functions. Mutagenic T‐cell epitope deletion seeks to mitigate the immune response, but can typically address only a small number of epitopes. Here, we pursue a “bottom‐up” approach that redesigns an entire protein to remain native‐like but contain few if any immunogenic epitopes. We do so by extending the Rosetta flexible‐backbone protein design software with an epitope scoring mechanism and appropriate constraints. The method is benchmarked with a diverse panel of proteins and applied to three targets of therapeutic interest. We show that the deimmunized designs indeed have minimal predicted epitope content and are native‐like in terms of various quality measures, and moreover that they display levels of native sequence recovery comparable to those of non‐deimmunized designs. © 2013 Wiley Periodicals, Inc.     

Chemodivergent Metathesis of Dienynes Catalyzed by Ruthenium–Indenylidene Complexes: An Experimental and Computational Study

A study on the enyne metathesis reaction leading to the formation cyclic compounds using ruthenium–indenylidene complexes is presented. Several 1,11‐dien‐6‐ynes have been subjected to ruthenium metathesis cyclization by using ruthenium–indenylidene complexes bearing various phosphine and N‐heterocyclic carbene (NHC) ligands. Interestingly, for some substrates chemodivergent metathesis occurs and is a function of the catalyst employed. This led us to investigate the competing “ene‐then‐yne” or “yne‐then‐ene” reaction pathways apparently at play in these systems using both experimental observations and DFT calculations. Experimental and computational studies were found in good agreement and permit to conclude that for phosphine‐containing catalysts, the “ene‐then‐yne” pathway is exclusively adopted. On the other hand, for catalysts bearing NHC ligands, both pathways are possible.     

“One‐step” Preparation of Thiol‐Ene Clickable PEG‐Based Thermoresponsive Hyperbranched Copolymer for In Situ Crosslinking Hybrid Hydrogel

A well‐defined poly(ethylene glycol) based hyperbranched thermoresponsive copolymer with high content of acrylate vinyl groups was synthesized via a “one‐pot and one‐step” deactivation enhanced atom transfer radical polymerization approach, which provided an injectable and in situ crosslinkable system via Michael‐type thiol‐ene reaction with a thiol‐modified hyaluronan biopolymer. The hyperbranched structure, molecular weight, and percentage of vinyl content of the copolymer were characterized by gel permeation chromatography and ¹H NMR. The lower critical solution temperature of this copolymer is close to body temperature, which can result in a rapid thermal gelation at 37 °C. The scanning electron microscopy analysis of crosslinked hydrogel showed the network formation with porous structure, and 3D cell culture study demonstrated the good cell viability after the cells were embedded inside the hydrogel. This injectable and in situ crosslinking hybrid hydrogel system offers great promise as a new class of hybrid biomaterials for tissue engineering.     

Elucidating the origin of diastereoselectivity in a self-replicating system: selfishness versus altruism

We have investigated a diastereoselective self‐replicating system based on a cycloaddition of a fulvene derivative and a maleimide using a two‐pronged approach of combining NMR spectroscopy with computational modelling. Two diastereomers are formed with identical rates in the absence of replication. When replication is enabled, one diastereomer takes over the resources as a “selfish” autocatalyst, while exploiting the competitor as a weak “altruist”, resulting in a diastereoselectivity of 16:1. We applied 1D and 2D NMR spectroscopic techniques supported by ab initio chemical shifts as well as ab initio molecular dynamics simulations to study the structure and dynamics of the underlying network. This powerful combination allowed us to decipher the energetic and structural rationale behind the observed behaviour, while static computational methods currently used in the field did not.     

GPCR‐CA: A cellular automaton image approach for predicting G‐protein–coupled receptor functional classes

Given an uncharacterized protein sequence, how can we identify whether it is a G‐protein–coupled receptor (GPCR) or not? If it is, which functional family class does it belong to? It is important to address these questions because GPCRs are among the most frequent targets of therapeutic drugs and the information thus obtained is very useful for “comparative and evolutionary pharmacology,” a technique often used for drug development. Here, we present a web‐server predictor called “GPCR‐CA,” where “CA” stands for “Cellular Automaton” (Wolfram, S. Nature 1984, 311, 419), meaning that the CA images have been utilized to reveal the pattern features hidden in piles of long and complicated protein sequences. Meanwhile, the gray‐level co‐occurrence matrix factors extracted from the CA images are used to represent the samples of proteins through their pseudo amino acid composition (Chou, K.C. Proteins 2001, 43, 246). GPCR‐CA is a two‐layer predictor: the first layer prediction engine is for identifying a query protein as GPCR on non‐GPCR; if it is a GPCR protein, the process will be automatically continued with the second‐layer prediction engine to further identify its type among the following six functional classes: (a) rhodopsin‐like, (b) secretin‐like, (c) metabotrophic/glutamate/pheromone; (d) fungal pheromone, (e) cAMP receptor, and (f) frizzled/smoothened family. The overall success rates by the predictor for the first and second layers are over 91% and 83%, respectively, that were obtained through rigorous jackknife cross‐validation tests on a new‐constructed stringent benchmark dataset in which none of proteins has ≥40% pairwise sequence identity to any other in a same subset. GPCR‐CA is freely accessible at http://218.65.61.89:8080/bioinfo/GPCR‐CA , by which one can get the desired two‐layer results for a query protein sequence within about 20 seconds. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Rung 3.5 density functionals: Another step on Jacob's ladder

Applications of density functional theory (DFT) to computational chemistry and solid‐state physics rely on a “Jacob's Ladder” of progressively more complicated approximations to the many‐body exchange‐correlation (XC) density functional. Accurate, computationally tractable DFT calculations on large and periodic systems remain challenging for existing XC functionals. Simple XC functionals on the three lowest rungs of Jacob's Ladder are insufficiently accurate for many properties, while fourth‐rung hybrid functionals incorporating nonlocal information can be prohibitively expensive. This perspective presents our work toward a compromise, a new class of “Rung 3.5” functionals that incorporate a linear dependence on the nonlocal one‐particle density matrix. This work reviews these functionals' formal underpinning, numerical performance, and prospects for modeling solids and surfaces. © 2012 Wiley Periodicals, Inc.     

A highly sensitive “turn‐on” fluorescent sensor for the detection of human serum proteins based on the size exclusion of the polyacrylamide gel

A highly sensitive “turn‐on” fluorescent sensor based on the size exclusion of the polyacrylamide gel was developed for the on‐gels detection of human serum proteins after PAGE. The possible mechanism of this fluorescence sensor was illustrated and validated by utilizing five kinds of colloidal silver nanoparticles with different particle size distribution and six kinds of polyacrylamide gels with different pore size. It was attributed to that silver nanoparticles (<5 nm in diameter) had been selectively absorbed into the gel and formed the small silver nanoclusters, resulting in the red fluorescence. Using this new technique for the detection of human serum proteins after PAGE, a satisfactory sensitivity was achieved and some relatively low‐abundance proteins (e.g. zinc‐alpha‐2‐glycoprotein), which are the significant proteinic markers of certain diseases can be easily detected, but not with traditional methods. Furthermore, it was also successfully applied to distinguish between serums from hepatoma patient and healthy people. As a new protein detection technique, the colloidal silver nanoparticles based “turn‐on” fluorescent sensor offers a rapid, economic, low background, and sensitive way for direct detection of human serum proteins, showing available potential and significance in the development of nanobiotechnology and proteome research.     

Are formalin‐fixed and paraffin‐embedded tissues fit for proteomic analysis?

Formalin‐fixed and paraffin‐embedded (FFPE)–tissue archives are potential treasure troves in the search for clinically interesting specimens. However, while the FFPE‐treatment provides excellent conservation of the three‐dimensional structure of the tissue and prevents degradation over decades, it also introduces numerous nonspecific and irreversible protein modifications. In this study, we have evaluated several published workflows for FFPE‐tissue by fit‐for‐purpose proteomics technologies. We demonstrate that many protein modifications and cross‐links remain after treatment and conclude that the proteomics of FFPE‐tissue is of value, but clear‐cut limitations must be kept in mind. The analysis of abundant proteins in FFPE is straightforward, but confident identification of low‐level proteins and/or biologically relevant modifications is seriously hampered by the FFPE‐treatment. Peptide assignment should only be performed on high‐quality spectra, even if this is at the cost of lower numbers of protein IDs. As Yergey and Coorssen stated in 2015: “Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis.”     

Response to “comment on density functional theory study of 1,2‐dioxetanone decomposition in condensed phase”

Roca‐Sanjuan et al. commented on our paper “Density Functional Theory Study of 1,2‐Dioxetanone Decomposition in Condensed Phase”, by criticizing the use of a closed‐shell approach and the differences encountered regarding other previous studies. However, our suggested reaction mechanism was in line with experimental findings, contrary to other computational studies. Moreover, we have presented data to support our use of a closed‐shell approach. © 2012 Wiley Periodicals, Inc.     

Recursion formula for electron repulsion integrals over Hermite polynomials

A method for computing electron repulsion integrals over contracted Gaussian functions is described in which intermediate integrals over Hermite polynomials are generated by a “pre‐Hermite” recursion (PHR) step before the conversion to regular integrals. This greatly reduces the floating‐point operation counts inside the contraction loops, where only simple “scaling”‐type operations are required, making the method efficient for contracted Gaussians, particularly of high angular momentum. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Flexible protein‐protein docking based on Best‐First search algorithm

We developed a new high resolution protein‐protein docking method based on Best‐First search algorithm that loosely imitates protein‐protein associations. The method operates in two stages: first, we perform a rigid search on the unbound proteins. Second, we search alternately on rigid and flexible degrees of freedom starting from multiple configurations from the rigid search. Both stages use heuristics added to the energy function, which causes the proteins to rapidly approach each other and remain adjacent, while optimizing on the energy. The method deals with backbone flexibility explicitly by searching over ensembles of conformations generated before docking. We ran the rigid docking stage on 66 complexes and grouped the results into four classes according to evaluation criteria used in Critical Assessment of Predicted Interactions (CAPRI; “high,” “medium,” “acceptable,” and “incorrect”). Our method found medium binding conformations for 26% of the complexes and acceptable for additional 44% among the top 10 configurations. Considering all the configurations, we found medium binding conformations for 55% of the complexes and acceptable for additional 39% of the complexes. Introducing side‐chains flexibility in the second stage improves the best found binding conformation but harms the ranking. However, introducing side‐chains and backbone flexibility improve both the best found binding conformation and the best found conformation in the top 10. Our approach is a basis for incorporating multiple flexible motions into protein‐protein docking and is of interest even with the current use of a simple energy function. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Toward the complete range separation of non‐hybrid exchange–correlation functional

In this study, we use a very simple scheme to achieve range separation of a total exchange–correlation functional. We have utilized this methodology to combine a short‐range pure density functional theory (DFT) functional with a corresponding long‐range pure DFT, leading to a “Range‐separated eXchange–Correlation” (RXC) scheme. By examining the performance of a range of standard exchange–correlation functionals for prototypical short‐ and long‐range properties, we have chosen B‐LYP as the short‐range functional and PBE‐B95 as the long‐range counterpart. The results of our testing using a more diverse range of data sets show that, for properties that we deem to be short‐range in nature, the performance of this prescribed RXC‐DFT protocol does resemble that of B‐LYP in most cases, and vice versa. Thus, this RXC‐DFT protocol already provides meaningful numerical results. Furthermore, we envisage that the general RXC scheme can be easily implemented in computational chemistry software packages. This study paves a way for further refinement of such a range‐separation technique for the development of better performing DFT procedures. © 2015 Wiley Periodicals, Inc.     

Sequence design of biomimetic copolymers: modeling of membrane proteins and globular proteins with active enzymatic center

The biomimetic approach to the sequence design of synthetic AB‐copolymers has been developed further by means of new series of Monte Carlo computer simulation. The approach is based on using of some particular conformation of a homopolymer chain for “coloring” of monomeric units into two “colors” (or types) A and B depending on the spatial position of particular monomeric unit. We present recent data of our Monte Carlo computer simulation studies of properties of designed AB‐copolymers which mimic membrane proteins, and designed ABC‐copolymers which mimic proteins with active enzymatic center. We have found further evidences for the fact that designed copolymer chain preserves the “memory” about its “parent” spatial conformation and shows the well‐pronounced tendency to restore main features of the “parent” conformation.     

Nanorobots: The Ultimate Wireless Self‐Propelled Sensing and Actuating Devices

Natural motor proteins, “bionanorobots,” have inspired researchers to develop artificial nanomachines (nanorobots) able to move autonomously by the conversion of chemical to mechanical energy. Such artificial nanorobots are self‐propelled by the electrochemical decomposition of the fuel (up to now, hydrogen peroxide). Several approaches have been developed to provide nanorobots with some functionality, such as for controlling their movement, increasing their power output, or transporting different cargo. In this Focus Review we will discuss the recent advances in nanorobots based on metallic nanowires, which can sense, deliver, and actuate in complex environments, looking towards real applications in the not‐too‐distant future.     

Polyproline as a Minimal Antifreeze Protein Mimic That Enhances the Cryopreservation of Cell Monolayers

Tissue engineering, gene therapy, drug screening, and emerging regenerative medicine therapies are fundamentally reliant on high‐quality adherent cell culture, but current methods to cryopreserve cells in this format can give low cell yields and require large volumes of solvent “antifreezes”. Herein, we report polyproline as a minimum (bio)synthetic mimic of antifreeze proteins that is accessible by solution, solid‐phase, and recombinant methods. We demonstrate that polyproline has ice recrystallisation inhibition activity linked to its amphipathic helix and that it enhances the DMSO cryopreservation of adherent cell lines. Polyproline may be a versatile additive in the emerging field of macromolecular cryoprotectants.     

Generation of Pseudocontact Shifts in Proteins with Lanthanides Using Small “Clickable” Nitrilotriacetic Acid and Iminodiacetic Acid Tags

Pseudocontact shifts (PCS) induced by paramagnetic lanthanide ions provide unique long‐range structural information in nuclear magnetic resonance (NMR) spectra, but the site‐specific attachment of lanthanide tags to proteins remains a challenge. Here we incorporated p‐azido‐phenylalanine (AzF) site‐specifically into the proteins ubiquitin and GB1, and ligated the AzF residue with alkyne derivatives of small nitrilotriacetic acid and iminodiacetic acid tags using the Cu^I‐catalysed “click” reaction. These tags form lanthanide complexes with no or only a small net charge and produced sizeable PCSs with paramagnetic lanthanide ions in all mutants tested. The PCSs were readily fitted by single magnetic susceptibility anisotropy tensors. Protein precipitation during the click reaction was greatly alleviated by the presence of 150 mM NaCl.     

A Glimpse of Our Journey into the Design of Optical Probes in Self‐assembled Surfactant Aggregates

Dynamic self‐assembling amphiphilic surfactant molecules, popularly known as “micelles”, have received widespread attention, due to their ability to modulate the photophysical properties of various organic dyes upon encapsulation. Along with their well‐known use as cleaning agents, catalysts in organic reactions, and even for drug delivery purposes, these surfactant assemblies also show promising pertinence in the recognition of both ionic and nonionic targeted analytes. Low micropolarity and relatively hydrophobic environments promote their interaction with ionic analytes, whereas neutral species mostly affect the aggregation pattern of the probe molecules upon partitioning inside the micellar hydrophobic milieu. The environment‐sensitive nature of micelle‐based self‐assembled probes also prompts us to devise new sensor arrays for the recognition of multiple analytes. While this account will largely focus on our own work in developing surfactant‐triggered self‐assembled sensors, our findings have been placed in the context of the relevant contributions from others during their strategic evolution.