pinecone/core-2020-05-10-deduplication huggingface dataset:
Automated protein structure modeling in CASP9 by I‐TASSER pipeline combined with QUARK‐based  ab initio  folding and FG‐MD‐based structure refinement

I‐TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment‐guided molecular dynamics (FG‐MD), were added to the I‐TASSER pipeline for improving the structural modeling accuracy. QUARK is a  de novo  structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I‐TASSER structure assembly simulations. FG‐MD is an atomic‐level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen‐bonding networks, torsion angles, and steric clashes. Despite considerable progress in both the template‐based and template‐free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and  ab initio  folding of β‐proteins are still needed to further improve the I‐TASSER pipeline. Proteins 2011; © 2011 Wiley‐Liss, Inc
Fibril elongation mechanisms of HET-s prion-forming domain: Topological
  evidence for growth polarity

The prion-forming C-terminal domain of the fungal prion HET-s forms
infectious amyloid fibrils at physiological pH. The conformational switch from
the non-prion soluble form to the prion fibrillar form is believed to have a
functional role, since HET-s in its prion form participates in a recognition
process of different fungal strains. Based on the knowledge of the
high-resolution structure of HET-s(218-289) (the prion forming-domain) in its
fibrillar form, we here present a numerical simulation of the fibril growth
process which emphasizes the role of the topological properties of the
fibrillar structure. An accurate thermodynamic analysis of the way an
intervening HET-s chain is recruited to the tip of the growing fibril suggests
that elongation proceeds through a dock and lock mechanism. First, the chain
docks onto the fibril by forming the longest $\beta$-strands. Then, the
re-arrangement in the fibrillar form of all the rest of molecule takes place.
Interestingly, we predict also that one side of the HET-s fibril is more
suitable for substaining its growth with respect to the other. The resulting
strong polarity of fibril growth is a consequence of the complex topology of
HET-s fibrillar structure, since the central loop of the intervening chain
plays a crucially different role in favouring or not the attachment of the
C-terminus tail to the fibril, depending on the growth side.Comment: 16 pages, 10 figure
Prots: A fragment based protein thermo‐stability potential

Designing proteins with enhanced thermo‐stability has been a main focus of protein engineering because of its theoretical and practical significance. Despite extensive studies in the past years, a general strategy for stabilizing proteins still remains elusive. Thus effective and robust computational algorithms for designing thermo‐stable proteins are in critical demand. Here we report PROTS, a sequential and structural four‐residue fragment based protein thermo‐stability potential. PROTS is derived from a nonredundant representative collection of thousands of thermophilic and mesophilic protein structures and a large set of point mutations with experimentally determined changes of melting temperatures. To the best of our knowledge, PROTS is the first protein stability predictor based on integrated analysis and mining of these two types of data. Besides conventional cross validation and blind testing, we introduce hypothetical reverse mutations as a means of testing the robustness of protein thermo‐stability predictors. In all tests, PROTS demonstrates the ability to reliably predict mutation induced thermo‐stability changes as well as classify thermophilic and mesophilic proteins. In addition, this white‐box predictor allows easy interpretation of the factors that influence mutation induced protein stability changes at the residue level. Proteins 2012; © 2011 Wiley Periodicals, Inc
BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures

We developed BSP‐SLIM, a new method for ligand–protein blind docking using low‐resolution protein structures. For a given sequence, protein structures are first predicted by I‐TASSER; putative ligand binding sites are transferred from holo‐template structures which are analogous to the I‐TASSER models; ligand–protein docking conformations are then constructed by shape and chemical match of ligand with the negative image of binding pockets. BSP‐SLIM was tested on 71 ligand–protein complexes from the Astex diverse set where the protein structures were predicted by I‐TASSER with an average RMSD 2.92 Å on the binding residues. Using I‐TASSER models, the median ligand RMSD of BSP‐SLIM docking is 3.99 Å which is 5.94 Å lower than that by AutoDock; the median binding‐site error by BSP‐SLIM is 1.77 Å which is 6.23 Å lower than that by AutoDock and 3.43 Å lower than that by LIGSITE CSC . Compared to the models using crystal protein structures, the median ligand RMSD by BSP‐SLIM using I‐TASSER models increases by 0.87 Å, while that by AutoDock increases by 8.41 Å; the median binding‐site error by BSP‐SLIM increase by 0.69Å while that by AutoDock and LIGSITE CSC  increases by 7.31 Å and 1.41 Å, respectively. As case studies, BSP‐SLIM was used in virtual screening for six target proteins, which prioritized actives of 25% and 50% in the top 9.2% and 17% of the library on average, respectively. These results demonstrate the usefulness of the template‐based coarse‐grained algorithms in the low‐resolution ligand–protein docking and drug‐screening. An on‐line BSP‐SLIM server is freely available at  http://zhanglab.ccmb.med.umich.edu/BSP‐SLIM . Proteins 2012. © 2011 Wiley Periodicals, Inc
Predicting extreme p K  a  shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

Accurate computational methods of determining protein and nucleic acid p K  a  values are vital to understanding pH‐dependent processes in biological systems. In this article, we use the recently developed method constant pH molecular dynamics (CPHMD) to explore the calculation of highly perturbed p K  a  values in variants of staphylococcal nuclease (SNase). Simulations were performed using the replica exchange (REX) protocol for improved conformational sampling with eight temperature windows, and yielded converged proton populations in a total sampling time of 4 ns. Our REX‐CPHMD simulations resulted in calculated p K  a  values with an average unsigned error (AUE) of 0.75 pK units for the acidic residues in Δ + PHS, a hyperstable variant of SNase. For highly p K  a ‐perturbed SNase mutants with known crystal structures, our calculations yielded an AUE of 1.5 pK units and for those mutants based on modeled structures an AUE of 1.4 pK units was found. Although a systematic underestimate of pK shifts was observed in most of the cases for the highly perturbed pK mutants, correlations between conformational rearrangement and plasticity associated with the mutation and error in p K  a  prediction was not evident in the data. This study further extends the scope of electrostatic environments explored using the REX‐CPHMD methodology and suggests that it is a reliable tool for rapidly characterizing ionizable amino acids within proteins even when modeled structures are employed. Proteins 2011; © 2011 Wiley‐Liss, Inc
On the molecular structure of human neuroserpin polymers

The polymerization of serpins is at the root of a large class of diseases; the molecular structure of serpin polymers has been recently debated. Here, we study the polymerization kinetics of human neuroserpin by Fourier Transform Infra Red spectroscopy and by time-lapse Size Exclusion Chromatography. Firstly we show that two distinct neuroserpin polymers, formed at 45 and 85 °C, display the same isosbestic points in the Amide I′ band, and therefore share common secondary structure features. We also find a concentration independent polymerization rate at 45 °C, suggesting that the polymerization rate-limiting step is the formation of an activated monomeric\ud
species. The polymer structures are consistent with a model that predicts the bare insertion of portions of the reactive center loop into the A β-sheet of neighboring serpin molecule, although with different extents at 45 and 85 °C
STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2011
Predicting nucleic acid binding interfaces from structural models of proteins

The function of DNA‐ and RNA‐binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure‐based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high‐resolution three‐dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I‐TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high‐resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I‐TASSER produces high‐quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low‐resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Proteins 2012. © 2011 Wiley Periodicals, Inc
Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics.

Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free approach and reduced spectral density mapping. Comparison of predictions, based on 77 ns molecular dynamics simulations, with the observed relaxation rates gives insight into dynamical properties of the protein and their alteration on ligand binding. Data indicate dynamics changes in the vicinity of the binding site. More interesting is the presence of perturbations located in remote regions of this well-structured globular protein in which no large-amplitude motions are involved. This suggests that delocalized changes in dynamics that occur upon binding could be a general feature of proteintarget interactions. Proteins 2012; (c) 2011 Wiley Periodicals, Inc
Molecular modeling of hair keratin/peptide complex : using MM-PBSA calculations to describe experimental binding results

Molecular dynamics simulations of a keratin/peptide complex have been conducted to predict the binding affinity of four different peptides toward human hair. Free energy calculations on the peptides' interaction with the keratin model demonstrated that electrostatic interactions are believed to be the main driving force stabilizing the complex. The molecular mechanics–Poisson-Boltzmann surface area methodology used for the free energy calculations demonstrated that the dielectric constant in the protein's interior plays a major role in the free energy calculations, and the only way to obtain accordance between the free energy calculations and the experimental binding results was to use the average dielectric constant.Grant sponsor: Contract Research Program "Compromisso com a Ciencia''; Grant number: C2008-UMINHO-CQ-03; Grant sponsor: FCT "Fundacao para a Ciencia e Tecnologia'' (PhD); Grant number: SFRH/BD/38363/200
Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations

The HIV Rev protein mediates the nuclear export of viral mRNA, and is thereby essential for the production of late viral proteins in the replication cycle. Rev forms a large organized multimeric protein-protein complex for proper functioning. Recently, the three-dimensional structures of a Rev dimer and tetramer have been resolved and provide the basis for a thorough structural analysis of the binding interaction. Here, molecular dynamics (MD) and binding free energy calculations were performed to elucidate the forces thriving dimerization and higher order multimerization of the Rev protein. It is found that despite the structural differences between each crystal structure, both display a similar behavior according to our calculations. Our analysis based on a molecular mechanics-generalized Born surface area (MM/GBSA) and a configurational entropy approach demonstrates that the higher order multimerization site is much weaker than the dimerization site. In addition, a quantitative hot spot analysis combined with a mutational analysis reveals the most contributing amino acid residues for protein interactions in agreement with experimental results. Additional residues were found in each interface, which are important for the protein interaction. The investigation of the thermodynamics of the Rev multimerization interactions performed here could be a further step in the development of novel antiretrovirals using structure based drug design. Moreover, the variability of the angle between each Rev monomer as measured during the MD simulations suggests a role of the Rev protein in allowing flexibility of the arginine rich domain (ARM) to accommodate RNA binding. Proteins 2012; © 2012 Wiley Periodicals, Inc.status: publishe
All‐atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone‐binding element

Insulin regulates blood glucose levels in higher organisms by binding to and activating insulin receptor (IR), a constitutively homodimeric glycoprotein of the receptor tyrosine kinase (RTK) superfamily. Therapeutic efforts in treating diabetes have been significantly impeded by the absence of structural information on the activated form of the insulin/IR complex. Mutagenesis and photo‐crosslinking experiments and structural information on insulin and apo‐IR strongly suggest that the dual‐chain insulin molecule, unlike the related single‐chain insulin‐like growth factors, binds to IR in a very different conformation than what is displayed in storage forms of the hormone. In particular, hydrophobic residues buried in the core of the folded insulin molecule engage the receptor. There is also the possibility of plasticity in the receptor structure based on these data, which may in part be due to rearrangement of the so‐called CT‐peptide, a tandem hormone‐binding element of IR. These possibilities provide opportunity for large‐scale molecular modeling to contribute to our understanding of this system. Using various atomistic simulation approaches, we have constructed all‐atom structural models of hormone/receptor complexes in the presence of CT in its crystallographic position and a thermodynamically favorable displaced position. In the “displaced‐CT” complex, many more insulin–receptor contacts suggested by experiments are satisfied, and our simulations also suggest that R‐insulin potentially represents the receptor‐bound form of hormone. The results presented in this work have further implications for the design of receptor‐specific agonists/antagonists. Proteins 2013; © 2012 Wiley Periodicals, Inc
Interplay of I‐TASSER and QUARK for template‐based and ab initio protein structure prediction in CASP10

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I‐TASSER and QUARK for both free‐modeling (FM) and template‐based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK‐based ab initio models as probes allows the detection of distant‐homology templates which might be ignored by the traditional sequence profile‐based threading alignment algorithms. Further template assembly refinement by I‐TASSER resulted in successful folding of two medium‐sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I‐TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading‐constrained ab initio folding models can consistently improve the quality of the full‐length models as assessed by the GDT‐HA and hydrogen‐bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium‐size proteins (especially beta‐proteins) for nonhomologous targets. Further developments of sensitive fold‐recognition and ab initio folding methods are critical for solving these problems. Proteins 2014; 82(Suppl 2):175–187. © 2013 Wiley Periodicals, Inc
Optimized E.coli expression strain LOBSTR eliminates common contaminants from His-tag purification

His-tag affinity purification is one of the most commonly used methods to purify recombinant proteins expressed in E. coli. One drawback of using the His-tag is the co-purification of contaminating histidine-rich E. coli proteins. We engineered a new E. coli expression strain, LOBSTR (low background strain), which eliminates the most abundant contaminants. LOBSTR is derived from the E. coli BL21(DE3) strain and carries genomically modified copies of arnA and slyD, whose protein products exhibit reduced affinities to Ni and Co resins, resulting in a much higher purity of the target protein. The use of LOBSTR enables the pursuit of challenging low-expressing protein targets by reducing background contamination with no additional purification steps, materials, or costs, and thus pushes the limits of standard His-tag purifications.Lundbeck FoundationDanish Council for Independent Research (Postdoctoral Grant)National Institutes of Health (U.S.) (Pew Scholar Award Grant GM077537
Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations

HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that is targeted by nucleoside analogs (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). NNRTIs are allosteric inhibitors of RT, and constitute an integral part of several highly active antiretroviral therapy regimens. Under selective pressure, HIV-1 acquires resistance against NNRTIs primarily by selecting mutations around the NNRTI pocket. Complete RT sequencing of clinical isolates revealed that spatially distal mutations arising in connection and the RNase H domain also confer NNRTI resistance and contribute to NRTI resistance. However, the precise structural mechanism by which the connection domain mutations confer NNRTI resistance is poorly understood. We performed 50-ns molecular dynamics (MD) simulations, followed by essential dynamics, free-energy landscape analyses, and network analyses of RT-DNA, RT-DNA-nevirapine (NVP), and N348I/T369I mutant RT-DNA-NVP complexes. MD simulation studies revealed altered global motions and restricted conformational landscape of RT upon NVP binding. Analysis of protein structure network parameters demonstrated a dissortative hub pattern in the RT-DNA complex and an assortative hub pattern in the RT-DNA-NVP complex suggesting enhanced rigidity of RT upon NVP binding. The connection subdomain mutations N348I/T369I did not induce any significant structural change; rather, these mutations modulate the conformational dynamics and alter the long-range allosteric communication network between the connection subdomain and NNRTI pocket. Insights from the present study provide a structural basis for the biochemical and clinical findings on drug resistance caused by the connection and RNase H mutations.status: publishe