共查询到20条相似文献,搜索用时 31 毫秒
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Sandeep Yadav Jun Liu Thomas M. Scherer Yatin Gokarn Barthélemy Demeule Sonoko Kanai James D. Andya Steven J. Shire 《Biophysical reviews》2013,5(2):121-136
Early development of protein biotherapeutics using recombinant DNA technology involved progress in the areas of cloning, screening, expression and recovery/purification. As the biotechnology industry matured, resulting in marketed products, a greater emphasis was placed on development of formulations and delivery systems requiring a better understanding of the chemical and physical properties of newly developed protein drugs. Biophysical techniques such as analytical ultracentrifugation, dynamic and static light scattering, and circular dichroism were used to study protein–protein interactions during various stages of development of protein therapeutics. These studies included investigation of protein self-association in many of the early development projects including analysis of highly glycosylated proteins expressed in mammalian CHO cell cultures. Assessment of protein–protein interactions during development of an IgG1 monoclonal antibody that binds to IgE were important in understanding the pharmacokinetics and dosing for this important biotherapeutic used to treat severe allergic IgE-mediated asthma. These studies were extended to the investigation of monoclonal antibody–antigen interactions in human serum using the fluorescent detection system of the analytical ultracentrifuge. Analysis by sedimentation velocity analytical ultracentrifugation was also used to investigate competitive binding to monoclonal antibody targets. Recent development of high concentration protein formulations for subcutaneous administration of therapeutics posed challenges, which resulted in the use of dynamic and static light scattering, and preparative analytical ultracentrifugation to understand the self-association and rheological properties of concentrated monoclonal antibody solutions. 相似文献
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Tomohide Saio Masashi Yokochi Hiroyuki Kumeta Fuyuhiko Inagaki 《Journal of biomolecular NMR》2010,46(4):271-280
A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 Å) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure determination of the p62 PB1-PB1 complex, which forms a front-to-back 20 kDa homo-oligomer. As p62 PB1 does not intrinsically bind metal ions, the lanthanide binding peptide tag was attached to one subunit of the dimer at two anchoring points. Each monomer was treated as a rigid body and was docked based on the backbone PCS and backbone chemical shift perturbation data. Unlike NOE-based structural determination, this method only requires resonance assignments of the backbone 1HN/15N signals and the PCS data obtained from several sets of two-dimensional 15N-heteronuclear single quantum coherence spectra, thus facilitating rapid structure determination of the protein–protein complex. 相似文献
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The ATP-binding cassette (ABC) transporters are a large family of proteins responsible for the translocation of a variety
of compounds across the membranes of both prokaryotes and eukaryotes. The inter-protein and intra-protein interactions in
these traffic ATPases are still only poorly understood. In the present study we describe, for the first time, an extensive
yeast two-hybrid (Y2H)-based analysis of the interactions of the cytoplasmic loops of the yeast pleiotropic drug resistance
(Pdr) protein, Pdr5p, an ABC transporter of Saccharomyces
cerevisiae. Four of the major cytosolic loops that have been predicted for this protein [including the two nucleotide-binding domain
(NBD)-containing loops and the cytosolic C-terminal region] were subjected to an extensive inter-domain interaction study
in addition to being used as baits to identify potential interacting proteins within the cell using the Y2H system. Results
of these studies have revealed that the first cytosolic loop (CL1) – containing the first NBD domain – and also the C-terminal
region of Pdr5p interact with several candidate proteins. The possibility of an interaction between the CL1 loops of two neighboring
Pdr5p molecules was also indicated, which could possibly have implications for dimerization of this protein.
Electronic Publication 相似文献
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Valerio Ferrario 《Journal of biomolecular structure & dynamics》2019,37(6):1534-1544
Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (RS), which was derived from the diffusion coefficient and the viscosity. RS was compared to the geometric radius (RG) of CALB, which was derived from the protein density. RS and RG differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient. 相似文献
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Src homology 3 (SH3) domains are involved in the regulation of important cellular pathways, such as cell proliferation, migration and cytoskeletal modifications. Recognition of polyproline and a number of noncanonical sequences by SH3 domains has been extensively studied by crystallography, nuclear magnetic resonance and other methods. High-affinity peptides that bind SH3 domains are used in drug development as candidates for anticancer treatment. This review summarizes the latest achievements in deciphering structural determinants of SH3 function. 相似文献
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Sumonja Neven Gemovic Branislava Veljkovic Nevena Perovic Vladimir 《Amino acids》2019,51(8):1187-1200
Amino Acids - Over the last decade, various machine learning (ML) and statistical approaches for protein–protein interaction (PPI) predictions have been developed to help annotating... 相似文献
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This paper describes efforts of the structural genomics project in the nuclear magnetic resonance (NMR) laboratory at the
University of Science and Technology of China. This structural genomics project is biological-functional driven. Targets are
mainly selected from two systems: proteins related with regulation of gene expression in humans and other eukaryotes, and
proteins existing in the cell junction in humans. The majority of proteins selected from these two systems are related with
human health and diseases, and some are potential drug targets. Twenty-five protein structures from Homo sapiens and other
eukaryotes have been determined during last 5 years in this laboratory. Nuclear magnetic resonance (NMR) spectroscopy is highly
suited to investigate molecular interactions at a close physiological condition and is particularly suited for the study of
low-affinity, transient complexes. It can provide information on protein surface interaction, their complex structure, and
their dynamic properties during protein recognition. Several examples are given in this paper. 相似文献
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It is currently believed that the protein folding rate is related to the protein structures and its amino acid sequence. However, few studies have been done on the problem that whether the protein folding rate is influenced by its corresponding mRNA sequence. In this paper, we analyzed the possible relationship between the protein folding rates and the corresponding mRNA sequences. The content of guanine and cytosine (GC content) of palindromes in protein coding sequence was introduced as a new parameter and added in the Gromiha's model of predicting protein folding rates to inspect its effect in protein folding process. The multiple linear regression analysis and jack-knife test show that the new parameter is significant. The linear correlation coefficient between the experimental and the predicted values of the protein folding rates increased significantly from 0.96 to 0.99, and the population variance decreased from 0.50 to 0.24 compared with Gromiha's results. The results show that the GC content of palindromes in the corresponding protein coding sequence really influences the protein folding rate. Further analysis indicates that this kind of effect mostly comes from the synonymous codon usage and from the information of palindrome structure itself, but not from the translation information from codons to amino acids. 相似文献
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Tino Wilson Sanchez Bikash Debnath Frauke Christ Hiroyuki Otake Zeger Debyser Nouri Neamati 《Bioorganic & medicinal chemistry》2013,21(4):957-963
Human lens epithelium-derived growth factor (LEDGF)/p75 plays an important role in the HIV life cycle by stimulating integrase (IN)-led viral DNA integration into cellular chromosomes. Mechanistic studies show the majority of IN inhibitors chelate magnesium ions in the catalytic active site, a region topologically distant from the LEDGF/p75 binding site. Compounds disrupting the formation of LEDGF/p75 and IN complexes serve as a novel mechanistic approach different from current antiretroviral therapies. We previously built pharmacophore models mimicking LEDGF/p75 residues and identified four classes of LEDGF/p75-IN inhibitors. Substructure and similarity searches yielded additional LEDGF/p75-IN inhibitors containing an acylhydrazone moiety. The most potent of the acylhydrazones inhibited LEDGF/p75-IN interaction with an IC50 value of 400 nM. We explored structure–activity relationships (SAR) and identified new acylhydrazones, hydrazines, and diazenes as lead molecules for further optimization. Two lead LEDGF/p75-IN inhibitors showed antiviral activity. 相似文献