Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability

Structural comparison of in vitro evolved proteins with biological proteins will help determine the extent to which biological proteins sample the structural diversity available in protein sequence space. We have previously isolated a family of nonbiological ATP binding proteins from an unconstrained random sequence library. One of these proteins was further optimized for high-affinity binding to ATP, but biophysical characterization proved impossible due to poor solubility. To determine if such nonbiological proteins can be optimized for improved folding stability, we performed multiple rounds of mRNA-display selection under increasingly denaturing conditions. Starting from a pool of protein variants, we evolved a population of proteins capable of binding ATP in 3 M guanidine hydrochloride. One protein was chosen for further characterization. Circular dichroism, tryptophan fluorescence, and (1)H-(15)N correlation NMR studies show that this protein has a unique folded structure.     

Tunable and Photoswitchable Chemically Induced Dimerization for Chemo‐optogenetic Control of Protein and Organelle Positioning

The spatiotemporal dynamics of proteins and organelles play an important role in controlling diverse cellular processes. Optogenetic tools using photosensitive proteins and chemically induced dimerization (CID), which allow control of protein dimerization, have been used to elucidate the dynamics of biological systems and to dissect the complicated biological regulatory networks. However, the inherent limitations of current optogenetic and CID systems remain a significant challenge for the fine‐tuning of cellular activity at precise times and locations. Herein, we present a novel chemo‐optogenetic approach, photoswitchable chemically induced dimerization (psCID), for controlling cellular function by using blue light in a rapid and reversible manner. Moreover, psCID is tunable; that is, the dimerization and dedimerization degrees can be fine‐tuned by applying different doses of illumination. Using this approach, we control the localization of proteins and positioning of organelles in live cells with high spatial (μm) and temporal (ms) precision.     

Measuring in vivo protein half-life

Protein turnover critically influences many biological functions, yet methods have been lacking to assess this parameter in?vivo. Here, we demonstrate how chemical labeling of SNAP-tag fusion proteins can be exploited to measure the half-life of resident intracellular and extracellular proteins in living mice. First, we demonstrate that SNAP-tag substrates have wide?bioavailability in mice and can be used for the specific in?vivo labeling of SNAP-tag fusion proteins. We then apply near-infrared probes to perform noninvasive imaging of in?vivo-labeled tumors. Finally, we use SNAP-mediated chemical pulse-chase labeling to perform measurement of the in?vivo half-life of different extra- and intracellular proteins. These results open broad perspectives for studying protein function in living animals.     

Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels

Progress in the field of proteomics is dependent upon an ability to visualise close to an entire protein complement via a given array technology. These efforts have previously centred upon two-dimensional gel electrophoresis in association with immobilised pH gradients in the first dimension. However, limitations in this technology, including the inability to separate hydrophobic, basic, and low copy number proteins have hindered the analysis of complete proteomes. The challenge is now to overcome these limitations through access to new technology and improvements in existing methodologies. Proteomics can no longer be equated with a single two-dimensional electrophoresis gel. Greater information can be obtained using targeted biological approaches based upon sample prefractionation into specific cellular compartments to determine protein location, while novel immobilised pH gradients spanning single pH units can be used to display poorly abundant proteins due to their increased resolving power and loading capacity. In this study, we show the effectiveness of a combined use of two differential subproteomes (as defined by relative solubilities, cellular location and narrow-range immobilised pH gradients) to increase the resolution of proteins contained on two-dimensional gels. We also present new results confirming that this method is capable of displaying up to a further 45% of a given microbial proteome. Subproteomics, utilising up to 40 two-dimensional gels per sample will become a powerful tool for near-to-total proteome analysis in the postgenome era. Furthermore, this new approach can direct biological focus towards molecules of specific interest within complex cells and thus simplify efforts in discovery-based proteome research.     

Genetic Incorporation of a Reactive Isothiocyanate Group into Proteins

Methods for the site‐specific modification of proteins are useful for introducing biological probes into proteins and engineering proteins with novel activities. Herein, we genetically encode a novel noncanonical amino acid (ncAA) that contains an aryl isothiocyanate group which can form stable thiourea crosslinks with amines under mild conditions. We show that this ncAA (pNCSF) allows the selective conjugation of proteins to amine‐containing molecular probes through formation of a thiourea bridge. pNCSF was also used to replace a native salt bridge in myoglobin with an intramolecular crosslink to a proximal Lys residue, leading to increased thermal stability. Finally, we show that pNCSF can form stable intermolecular crosslinks between two interacting proteins.     

Constructing real-time,wash-free,and reiterative sensors for cell surface proteins using binding-induced dynamic DNA assembly

Cell surface proteins are an important class of biomarkers for fundamental biological research and for disease diagnostics and treatment. In this communication, we report a universal strategy to construct sensors that can achieve rapid imaging of cell surface proteins without any separation by using binding-induced dynamic DNA assembly. As a proof-of-principle, we developed a real-time and wash-free sensor for an important breast cancer biomarker, human epidermal growth factor receptor-2 (HER2). We then demonstrated that this sensor could be used for imaging and sensing HER2 on both fixed and live breast cancer cells. Additionally, we have also incorporated toehold-mediated DNA strand displacement reactions into the HER2 sensor, which allows for reiterating (switching on/off) fluorescence signals for HER2 from breast cancer cells in real-time.     

Enhancing the stability of kinesin motors for microscale transport applications

Biomolecular motors, such as kinesins, have great potential for micro-actuation and micro- or nanoscale active transport when integrated into microscale devices. However, the stability and limited shelf life of these motor proteins and their associated protein filaments is a barrier to their implementation. Here we demonstrate that freeze-drying or critical point-drying kinesins adsorbed to glass surfaces extends their lifetime from days to more than four months. Further, photoresist deposition and removal can be carried out on these motor-adsorbed surfaces without loss of motor function. The methods developed here are an important step towards realizing the integration of biological motors into practical devices, and these approaches can be extended to patterning and preserving other proteins immobilized on surfaces.     

Controlling crystallization and its absence: proteins, colloids and patchy models

The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and technological importance. Much can be learnt from the exquisite control that biological systems exert over the behaviour of proteins, where protein crystallization and aggregation are generally suppressed, but where in particular instances complex crystalline assemblies can be formed that have a functional purpose. We also explore the insights that can be obtained from computational modelling, focussing on the subtle interplay between the interparticle interactions, the preferred local order and the resulting crystallization kinetics. In particular, we highlight the role played by "frustration", where there is an incompatibility between the preferred local order and the global crystalline order, using examples from atomic glass formers and model anisotropic particles.     

Near-ultraviolet photolysis of L-mandelate, formation of reactive oxygen species, inactivation of phage T7 and implications on human health

Compared with ultraviolet B and C, UVA is considered to have little direct effects on biological systems. However, damaging effects of UVA on biological systems are often synergistically enhanced in the presence of sensitizers. Production of reactive oxygen species (ROS) has been implicated in the process. Several ROS have been identified but their involvement in inducing cellular damage is yet to be fully evaluated. Although membranes and proteins are affected, DNA is an important target and a variety of types of damage have been reported. Here, we present evidence that L-mandelate can act as a near UV (NUV) sensitizer, when activated by a lamp emitting 99% UVA and 1% UVB. Although evidence is available that H(2)O(2) and a small amount of *OH are produced, an alternative effect of the sensitization reaction may involve direct electron transfer. Studies have shown that NUV photolysis of mandelate can inactivate phage T7. Employment of tetrazolium blue test to detect superoxide anion may not be sufficient evidence as this agent may be reduced by alternative routes.     

Quantum dot-conjugated anti-GRP78 scFv inhibits cancer growth in mice

Semiconductor quantum dots (Qdots) have recently been shown to offer significant advantages over conventional fluorescent probes to image and study biological processes. The stability and low toxicity of QDs are well suited for biological applications. Despite this, the potential of Qdots remains limited owing to the inefficiency of existing delivery methods. By conjugating Qdots with small antibody fragments targeting membrane-bound proteins, such as GRP78, we demonstrate here that the Quantum dot- Anti-GRP78 scFv (Qdot-GRP78) retains its immunospecificity and its distribution can be monitored by visualization of multi-color fluorescence imaging both in vitro and in vivo. Moreover we demonstrate here for the first time that Qdot-GRP78 scFv bioconjugates can be efficiently internalized by cancer cells, thus upregulate phophosphate-AKT-ser473 and possess biological anti-tumour activity as shown by inhibition of breast cancer growth in a xenograft model. This suggests that nanocarrier-conjugated scFvs can be used as a therapeutic antibody for cancer treatment.     

Optochemical Control of Biological Processes in Cells and Animals

Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.     

基于大体积循环进样的低丰度蛋白质富集

发展了一种大体积循环进样方法,用于富集低丰度蛋白质。在优化的色谱分离条件下,通过增加蛋白质样品的上样体积提高低丰度蛋白质的绝对含量;进一步采用增加样品进样循环次数的方法提高蛋白质的富集效率。以猪肝提取蛋白质为样品,每次上样量500 μL的大体积11次循环进样。根据色谱峰的信号强弱,选择了在原始谱图中看不到色谱峰、有较少小峰和有较多小峰出现的时间段等有代表性的馏分进行研究。在中等极性的组分中,保留时间为11.38 min和12.58 min组分的富集效率分别提高了52倍和61倍,实验结果与理论富集效率相近。所发展的方法为生物蛋白质样品研究提供了一种新的富集制备及检测方法。     

Electron Transfer Mechanisms in Heme Proteins

Recent years have seen substantial progress in our understanding of biological electron-transfer mechanisms. Of particular value have been soluble c-type cytochromes, due to the large structural base available. Using structurally homologous families of simple redox proteins, the contribution of driving force, electrostatics, and sterics to the kinetics of electron transfer has been quantified. Importantly, because Marcus' theory for outer-sphere electron transfer is applicable, we have been able to develop an approach termed “kinetic taxonomy.” That is, based on the correlations obtained with a large number of redox proteins in different structural families, we can predict structural features from the kinetic properties of redox proteins of unknown structure. More recently, we have been able to establish a role for dynamics, orientation, and intervening media in intracomplex electron transfer when two redox proteins form a long-lived complex.     

Genetic Encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions

Rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists. Enzyme-mediated labeling approaches may be rapid but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many "bioorthogonal" reactions for which a component can be genetically encoded are too slow to effect quantitative site-specific labeling of proteins on a time scale that is useful for studying many biological processes. We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines that is 3-7 orders of magnitude faster than many bioorthogonal reactions. Unlike the reactions of strained alkenes, including trans-cyclooctenes and norbornenes, with tetrazines, the BCN-tetrazine reaction gives a single product of defined stereochemistry. We have discovered aminoacyl-tRNA synthetase/tRNA pairs for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli , and in live mammalian cells. These approaches may be extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on labeling and imaging studies.     

Identification of functional modules in a PPI network by clique percolation clustering

Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein–protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein–protein interaction data for any species and even other biological networks.     

Selective formation of covalent protein heterodimers with an unnatural amino acid

We report a strategy for the generation of heterodimeric protein conjugates using an unnatural amino acid with orthogonal reactivity. This paper addresses the challenges of site-specificity and homogeneity with respect to the synthesis of bivalent proteins and antibody-drug conjugates. There are numerous antibody-drug conjugates in preclinical and clinical development, yet these are based either on nonspecific lysine coupling chemistry or on disulfide modification made difficult by the large number of cysteines in antibodies. Here, we describe a recombinant approach that can be used to rapidly generate a variety of constructs with defined conjugation sites. Moreover, this methodology results in homogeneous antibody conjugates whose biological, physical, and pharmacological properties can be quantitatively assessed and subsequently optimized. As proof of concept, we have generated anti-Her2 Fab-Saporin conjugates that demonstrate excellent potency in vitro.     

Proteomics of metal transport and metal-associated diseases

Proteomics technology has the potential to identify groups of proteins that have similar biological function. However, few attempts have been made to identify and characterize metal-binding proteins by using proteomics strategies. Many transition metals are essential to sustain life. Copper, iron, and zinc are the most abundant transition metals relevant to biological systems. In addition to their important biological functions, metals can also catalyze the formation of damaging free radical species. Hence, their intracellular transport is tightly regulated. Despite recent insights into the intracellular transport of copper and other metals, our overall understanding of intracellular metal metabolism remains incomplete and it is likely that many metal-binding proteins remain undiscovered. Furthermore, the protein targets for metals during metal-associated disease states or during exposure to toxic levels of environmental metals are yet to be unravelled. A proteomics strategy for the analysis of metal-transporting or metal-binding proteins has the potential to uncover how a large number of proteins function in normal or metal-associated diseased states. Here we discuss the principal aspects of metal metabolism, and the recent developments in the area of the proteomics of metal transport.     

A General Strategy to Access Structural Information at Atomic Resolution in Polyglutamine Homorepeats

Homorepeat (HR) proteins are involved in key biological processes and multiple pathologies, however their high‐resolution characterization has been impaired due to their homotypic nature. To overcome this problem, we have developed a strategy to isotopically label individual glutamines within HRs by combining nonsense suppression and cell‐free expression. Our method has enabled the NMR investigation of huntingtin exon1 with a 16‐residue polyglutamine (poly‐Q) tract, and the results indicate the presence of an N‐terminal α‐helix at near neutral pH that vanishes towards the end of the HR. The generality of the strategy was demonstrated by introducing a labeled glutamine into a pathological version of huntingtin with 46 glutamines. This methodology paves the way to decipher the structural and dynamic perturbations induced by HR extensions in poly‐Q‐related diseases. Our approach can be extended to other amino acids to investigate biological processes involving proteins containing low‐complexity regions (LCRs).