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https://www.readbyqxmd.com/read/27914083/antibody-guided-molecular-imaging-of-infective-endocarditis
#1
Kenneth L Pinkston, Peng Gao, Kavindra V Singh, Ali Azhdarinia, Barbara E Murray, Eva M Sevick-Muraca, Barrett R Harvey
In this protocol, we describe the application of using a high affinity monoclonal antibody generated against the major pilin protein component of the pilin structure of Enterococcus faecalis as a PET imaging agent for enterococcal endocarditis detection. The anti-pilin -mAb 64Cu conjugate was able to specifically label enterococcal endocarditis vegetation in vivo in a rodent endocarditis model. By targeting pili, a covalently linked surface antigen extending from the bacterial surface, we provided evidence that gram-positive pilin represent a logical surface antigen to define or target an infectious agent for molecularly guided imaging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914064/computational-tools-for-aiding-rational-antibody-design
#2
Konrad Krawczyk, James Dunbar, Charlotte M Deane
Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#3
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#4
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#5
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914057/bindml-bindml-detecting-protein-protein-interaction-interface-propensity-from-amino-acid-substitution-patterns
#6
Qing Wei, David La, Daisuke Kihara
Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914052/applications-of-normal-mode-analysis-methods-in-computational-protein-design
#7
Vincent Frappier, Matthieu Chartier, Rafael Najmanovich
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#8
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914048/geometric-potentials-for-computational-protein-sequence-design
#9
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#10
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914008/igf1r-dental-pulp-stem-cells-enhanced-neuroplasticity-in-hypoxia-ischemia-model
#11
Hsiao-Yu Chiu, Chen-Huan Lin, Chung Y Hsu, John Yu, Chia-Hung Hsieh, Woei-Cherng Shyu
Until now, the surface markers of multipotent mesenchymal stem cells (MSCs) had not been fully identified. Here, we found that the IGF1 receptor (IGF1R), regarded as a pluripotent marker of embryonic stem cells (ESCs), was also expressed in human dental pulp derived-mesenchymal stem cells (hDSCs), which displayed a potential for both self-renewal and multipotency. hDSC-secreted IGF1 interacted with IGF1R through an autocrine signaling pathway to maintain this self-renewal and proliferation potential. Stereotaxic implantation of immunosorted IGF1R(+) hDSCs in rats with neonatal hypoxia-ischemia (NHI) promoted neuroplasticity, improving the neurological outcome by increasing expression of the anti-apoptotic protein Bcl-2, which enhanced both neurogenesis and angiogenesis...
December 2, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27913964/intracerebroventricular-streptozotocin-as-a-model-of-alzheimer-s-disease-neurochemical-and-behavioral-characterization-in-mice
#12
Katherine Garcia Ravelli, Barbara Dos Anjos Rosário, Rosana Camarini, Marina Sorrentino Hernandes, Luiz Roberto Britto
Streptozotocin has been widely used to mimic some aspects of Alzheimer's disease (AD). However, especially in mice, several characteristics involved in the streptozotocin (STZ)-induced AD pathology are not well known. The main purpose of this study was to evaluate temporally the expression of AD-related proteins, such as amyloid-β (Aβ), choline acetyltransferase (ChAT), synapsin, axonal neurofilaments, and phosphorylated Tau in the hippocampus following intracerebroventricular (icv) administration of STZ in adult mice...
December 2, 2016: Neurotoxicity Research
https://www.readbyqxmd.com/read/27913862/prognostic-impact-of-her3-based-on-protein-and-mrna-expression-in-high-grade-serous-ovarian-carcinoma
#13
Ulrike Unger, Carsten Denkert, Ioana Braicu, Jalid Sehouli, Manfred Dietel, Sibylle Loibl, Silvia Darb-Esfahani
HER3 is a member of the epidermal growth factor family and was predominantly described as a negative prognostic factor in various solid tumors as well as in ovarian cancer. In this study, we investigated HER3 on protein and mRNA expression in histologically defined subtypes of ovarian cancer looking for an influence on patient's survival. Altogether, we examined HER3 in ovarian high-grade serous (HGSC, n = 320), low-grade serous (LGSC, n = 55), endometrioid (EC, n = 33), and clear cell (CCC, n = 48) carcinomas using immunohistochemistry (IHC) and quantitative real-time reverse transcription PCR (qRT-PCR)...
December 2, 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27913859/complex-genetics-architecture-contributes-to-salmonella-resistance-in-acb60-mice
#14
Sean Beatty, Leïla Rached-D'Astous, Danielle Malo
Human infection with Salmonella is of global public health concern. In low- and middle-income countries, Salmonella infection is a major source of disease in terms of both mortality and morbidity, while in high-income nations, the pathogen is an ongoing threat to food security. The outcome of infection with Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) in mouse models is dependent upon a coordinated and complex immune response. A panel of recombinant congenic strains (RCS) derived from the reciprocal double backcross of A/J and C57BL/6J mice has been screened for their susceptibility to Salmonella infection, and the RCS AcB60 was identified to be the most resistant strain to Salmonella infection, more resistant than the parental strain A/J...
December 2, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/27913854/the-role-of-macromolecules-in-the-formation-of-kidney-stones
#15
REVIEW
Jeffrey D Rimer, Ann M Kolbach-Mandel, Michael D Ward, Jeffrey A Wesson
The formation of crystal aggregates, one of the critical processes in kidney stone pathogenesis, involves interactions between crystals (predominantly calcium oxalate monohydrate, COM) and urinary constituents (e.g., proteins), which serve as an adhesive "glue" between crystals in stones. To develop a better understanding of the protein-crystal interactions that lead to crystal aggregation, we have measured the effect of model proteins on bulk COM crystal properties as well as their adsorption on crystal surfaces using three synthetic polyanions: poly(aspartic acid) (polyD), poly(glutamic acid) (polyE), and poly(acrylic acid) (polyAA)...
December 2, 2016: Urolithiasis
https://www.readbyqxmd.com/read/27913845/mitogen-activated-protein-kinases-are-involved-in-hepatocanalicular-dysfunction-and-cholestasis-induced-by-oxidative-stress
#16
Flavia D Toledo, Cecilia L Basiglio, Ismael R Barosso, Andrea C Boaglio, Andrés E Zucchetti, Enrique J Sánchez Pozzi, Marcelo G Roma
In previous studies, we showed that the pro-oxidant model agent tert-butyl hydroperoxide (tBuOOH) induces alterations in hepatocanalicular secretory function by activating Ca(2+)-dependent protein kinase C isoforms (cPKC), via F-actin disorganization followed by endocytic internalization of canalicular transporters relevant to bile formation (Mrp2, Bsep). Since mitogen-activated protein kinases (MAPKs) may be downstream effectors of cPKC, we investigated here the involvement of the MAPKs of the ERK1/2, JNK1/2, and p38(MAPK) types in these deleterious effects...
December 2, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27913822/more-than-just-scanning-the-importance-of-cap-independent-mrna-translation-initiation-for-cellular-stress-response-and-cancer
#17
REVIEW
Rafaela Lacerda, Juliane Menezes, Luísa Romão
The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5' end of the mRNA and scans the 5' untranslated region (5'UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment...
December 2, 2016: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/27913816/genetic-ablation-or-pharmacologic-inhibition-of-autophagy-mitigated-nsaid-associated-gastric-damages
#18
Chan Young Ock, Jong-Min Park, Young-Min Han, Migyeong Jeong, Mi-Young Kim, Ho Jae Lee, Ki Baik Hahm
: Non-steroidal anti-inflammatory drug (NSAID)-associated endoplasmic reticulum (ER) stress (a cyclooxygenase-2-independent mechanism) and consequent autophagic cell death are responsible for NSAID-associated gastric damage. Therefore, alleviating cytotoxicity executed via ER stress and autophagy can be a strategy to prevent NSAID-associated gastric damage. Here, we explored whether genetic or pharmacologic inhibition of autophagy can mitigate NSAID-associated gastric damage in in vitro and in vivo models...
December 2, 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/27913751/new-fungal-defensin-like-peptides-provide-evidence-for-fold-change-of-proteins-in-evolution
#19
Yucheng Wu, Bin Gao, Shunyi Zhu
Defensins containing a consensus cystine framework, Cys[1]..Cys[2]X3Cys[3]..Cys[4]..Cys[5]X1Cys[6] ("X", any amino acids normally except Cys; "...", variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming a cystine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation...
December 2, 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#20
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
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