Publications by authors named "Chengdong Huang"

17 Publications

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Sandwiched-fusion strategy facilitates recombinant production of small labile proteins.

Protein Sci 2021 03 29;30(3):650-662. Epub 2021 Jan 29.

Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Efficient production of large quantities of soluble, properly folded proteins is of high demand in modern structural and functional genomics. Despite much advancement toward improving recombinant protein expression, many eukaryotic proteins especially small peptides often fail to be recovered due to rapid proteolytic degradation. Here we show that the sandwiched-fusion strategy, which is based on two protein tags incorporated both at the amino- and carboxyl-terminus of target protein, could be employed to overcome this obstacle. We have exploited this strategy on heterologous expression in Escherichia coli of eight small degradation-prone eukaryotic proteins, whose successful recombinant productions have yet to be achieved. These include seven mitochondria-derived peptides (MDPS), a class of unique metabolic regulators of human body, and a labile mosquito transcription factor, Guy1. We show here that the sandwiched-fusion strategy, which provides robust protection against proteolysis, affords an economical method to obtain large quantities of pure five MDPs and the transcription factor Guy1, in sharp contrast to otherwise unsuccessful recovery using the traditional amino-fusion method. Further biophysical characterization and interaction studies by NMR spectroscopy confirmed that the proteins produced by this novel approach are properly folded into their biologically active structures. We anticipate this strategy could be widely utilized in production of other labile protein systems.
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http://dx.doi.org/10.1002/pro.4024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7888576PMC
March 2021

Pursuing sustainable productivity with millions of smallholder farmers.

Nature 2018 03 7;555(7696):363-366. Epub 2018 Mar 7.

Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China.

Sustainably feeding a growing population is a grand challenge, and one that is particularly difficult in regions that are dominated by smallholder farming. Despite local successes, mobilizing vast smallholder communities with science- and evidence-based management practices to simultaneously address production and pollution problems has been infeasible. Here we report the outcome of concerted efforts in engaging millions of Chinese smallholder farmers to adopt enhanced management practices for greater yield and environmental performance. First, we conducted field trials across China's major agroecological zones to develop locally applicable recommendations using a comprehensive decision-support program. Engaging farmers to adopt those recommendations involved the collaboration of a core network of 1,152 researchers with numerous extension agents and agribusiness personnel. From 2005 to 2015, about 20.9 million farmers in 452 counties adopted enhanced management practices in fields with a total of 37.7 million cumulative hectares over the years. Average yields (maize, rice and wheat) increased by 10.8-11.5%, generating a net grain output of 33 million tonnes (Mt). At the same time, application of nitrogen decreased by 14.7-18.1%, saving 1.2 Mt of nitrogen fertilizers. The increased grain output and decreased nitrogen fertilizer use were equivalent to US$12.2 billion. Estimated reactive nitrogen losses averaged 4.5-4.7 kg nitrogen per Megagram (Mg) with the intervention compared to 6.0-6.4 kg nitrogen per Mg without. Greenhouse gas emissions were 328 kg, 812 kg and 434 kg CO equivalent per Mg of maize, rice and wheat produced, respectively, compared to 422 kg, 941 kg and 549 kg CO equivalent per Mg without the intervention. On the basis of a large-scale survey (8.6 million farmer participants) and scenario analyses, we further demonstrate the potential impacts of implementing the enhanced management practices on China's food security and sustainability outlook.
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http://dx.doi.org/10.1038/nature25785DOI Listing
March 2018

Enhancing the sensitivity of multidimensional NMR experiments by using triply-compensated π pulses.

J Biomol NMR 2017 Dec 21;69(4):237-243. Epub 2017 Nov 21.

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.

In multidimensional solution NMR experiments, π pulses are used extensively for inversion and refocusing operations on H, C and N nuclei. Pulse miscalibration, off-resonance effects, and J-coupling evolution during π pulse execution result in severe signal losses that are exacerbated at high magnetic fields. Here, we report the implementation of a triply-compensated π pulse (G5) optimized for both inversion and refocusing in widely used 2- and 3-dimensional experiments. By replacing most of the hard π pulses, adiabatic or composite pulses on the H, C and N channels with G5 pulses, we obtained signal enhancements ranging from 80 to 240%. We anticipate that triply-compensated pulses will be crucial for improving the performance of multidimensional and multinuclear pulse sequences at ultra-high fields.
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http://dx.doi.org/10.1007/s10858-017-0153-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738291PMC
December 2017

Automatic methyl assignment in large proteins by the MAGIC algorithm.

J Biomol NMR 2017 Dec 2;69(4):215-227. Epub 2017 Nov 2.

Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.

Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25-50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.
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http://dx.doi.org/10.1007/s10858-017-0149-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764113PMC
December 2017

Optimization of H decoupling eliminates sideband artifacts in 3D TROSY-based triple resonance experiments.

J Biomol NMR 2017 Sep 8;69(1):45-52. Epub 2017 Sep 8.

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.

TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality and hamper data analysis. Specifically, these experiments produce sidebands in the C(t ) dimension with inverted phase corresponding to H resonance frequencies, with approximately 5% intensity of the parent C crosspeaks. These artifacts originate from the modulation of the H frequency onto the resonance frequency of Cα and/or Cβ and are due to 180° pulses imperfections used for H decoupling during the C(t ) evolution period. These sidebands can become severe for CA, CA and/or CB, CB correlation experiments such as TROSY-HNCACB. Here, we implement three alternative decoupling strategies that suppress these artifacts and, depending on the scheme employed, boost the sensitivity up to 14% on Bruker spectrometers. A class of comparable Agilent/Varian pulse sequences that use WALTZ16 H decoupling can also be improved by this method resulting in up to 60-80% increase in sensitivity.
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http://dx.doi.org/10.1007/s10858-017-0133-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693675PMC
September 2017

Structures of Large Protein Complexes Determined by Nuclear Magnetic Resonance Spectroscopy.

Annu Rev Biophys 2017 05 17;46:317-336. Epub 2017 Mar 17.

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; email:

Nuclear magnetic resonance (NMR) spectroscopy has been instrumental during the past two decades in providing high-resolution structures of protein complexes. It has been the method of choice for determining the structure of dynamic protein complexes, which are typically recalcitrant to other structural techniques. Until recently, NMR spectroscopy has yielded structures of small or medium-sized protein complexes, up to approximately 30-40 kDa. Major breakthroughs during the past decade, especially in isotope-labeling techniques, have enabled NMR characterization of large protein systems with molecular weights of hundreds of kDa. This has provided unique insights into the binding, dynamic, and allosteric properties of large systems. Notably, there is now a slowly but steadily growing list of large, dynamic protein complexes whose atomic structure has been determined by NMR. Many of these complexes are characterized by a high degree of flexibility and, thus, their structures could not have been obtained using other structural methods. Especially in the field of molecular chaperones, NMR has recently provided the first-ever high-resolution structures of their complexes with unfolded proteins. Further technological advances will establish NMR as the primary tool for obtaining atomic structures of challenging systems with even higher complexity.
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http://dx.doi.org/10.1146/annurev-biophys-070816-033701DOI Listing
May 2017

Structural basis for the antifolding activity of a molecular chaperone.

Nature 2016 09 8;537(7619):202-206. Epub 2016 Aug 8.

Department of Biochemistry, Molecular Biology &Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.
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http://dx.doi.org/10.1038/nature18965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161705PMC
September 2016

Correlation between weighted spectral distribution and average path length in evolving networks.

Chaos 2016 Feb;26(2):023110

Luoyang Electronic Equipment Test Center, Luoyang 471003, China.

The weighted spectral distribution (WSD) is a metric defined on the normalized Laplacian spectrum. In this study, synchronic random graphs are first used to rigorously analyze the metric's scaling feature, which indicates that the metric grows sublinearly as the network size increases, and the metric's scaling feature is demonstrated to be common in networks with Gaussian, exponential, and power-law degree distributions. Furthermore, a deterministic model of diachronic graphs is developed to illustrate the correlation between the slope coefficient of the metric's asymptotic line and the average path length, and the similarities and differences between synchronic and diachronic random graphs are investigated to better understand the correlation. Finally, numerical analysis is presented based on simulated and real-world data of evolving networks, which shows that the ratio of the WSD to the network size is a good indicator of the average path length.
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http://dx.doi.org/10.1063/1.4941727DOI Listing
February 2016

Economic Performance and Sustainability of a Novel Intercropping System on the North China Plain.

PLoS One 2015 14;10(8):e0135518. Epub 2015 Aug 14.

Center for Resources, Environment and Food Security, China Agricultural University, Beijing, China.

Double cropping of wheat and maize is common on the North China Plain, but it provides limited income to rural households due to the small farm sizes in the region. Local farmers in Quzhou County have therefore innovated their production system by integration of watermelon as a companion cash crop into the system. We examine the economic performance and sustainability of this novel intercropping system using crop yield data from 2010 to 2012 and farm household survey data collected in 2012. Our results show that the gross margin of the intercropping system exceeded that of the double cropping system by more than 50% in 2012. Labor use in the intercropping system was more than three times that in double cropping. The lower returns per labor hour in intercropping, however, exceeded the average off-farm wage in the region by a significant margin. Nutrient surpluses and irrigation water use are significant larger under the intercropping system. We conclude that the novel wheat-maize/watermelon intercropping system contributes to rural poverty alleviation and household-level food security, by raising farm incomes and generating more employment, but needs further improvement to enhance its sustainability.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135518PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537243PMC
May 2016

Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis.

Proc Natl Acad Sci U S A 2013 Dec 18;110(49):E4790-7. Epub 2013 Nov 18.

Departments of Immunology and Microbiology and Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065.

Mycobacterium tuberculosis (Mtb) restrains immune responses well enough to escape eradication but elicits enough immunopathology to ensure its transmission. Here we provide evidence that this host-pathogen relationship is regulated in part by a cytosolic, membrane-associated protein with a unique structural fold, encoded by the Mtb gene rv0431. The protein acts by regulating the quantity of Mtb-derived membrane vesicles bearing Toll-like receptor 2 ligands, including the lipoproteins LpqH and SodC. We propose that rv0431 be named "vesiculogenesis and immune response regulator."
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http://dx.doi.org/10.1073/pnas.1320118110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856836PMC
December 2013

Eukaryotic N-glycosylation occurs via the membrane-anchored C-terminal domain of the Stt3p subunit of oligosaccharyltransferase.

J Biol Chem 2012 Sep 3;287(39):32450-8. Epub 2012 Aug 3.

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.

N-glycosylation is an essential and highly conserved protein modification. In eukaryotes, it is catalyzed by a multisubunit membrane-associated enzyme, oligosaccharyltransferase (OT). We report the high resolution structure of the C-terminal domain of eukaryotic Stt3p. Unlike its soluble β-sheet-rich prokaryotic counterparts, our model reveals that the C-terminal domain of yeast Stt3p is highly helical and has an overall oblate spheroid-shaped structure containing a membrane-embedded region. Anchoring of this protein segment to the endoplasmic reticulum membrane is likely to bring the membrane-embedded donor substrate closer, thus facilitating glycosylation efficiency. Structural comparison of the region near the WWDYG signature motif revealed that the acceptor substrate-binding site of yeast OT strikingly resembles its prokaryotic counterparts, suggesting a conserved mechanism of N-glycosylation from prokaryotes to eukaryotes. Furthermore, comparison of the NMR and cryo-EM structures of yeast OT revealed that the molecular architecture of this acceptor substrate-recognizing domain has interesting spatial specificity for interactions with other essential OT subunits.
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http://dx.doi.org/10.1074/jbc.M112.342253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463301PMC
September 2012

Dynamic flexibility of the ATPase p97 is important for its interprotomer motion transmission.

Proc Natl Acad Sci U S A 2012 Jun 6;109(25):9792-7. Epub 2012 Jun 6.

Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.

The hexameric protein p97, a very abundant type II AAA ATPase (ATPase associated with various cellular activities), is involved in a diverse range of cellular functions. During its ATPase cycle p97 functions as an ATP motor, converting the chemical energy released upon hydrolysis of ATP to ADP into mechanical work, which is then directed toward the proteins that serve as substrates. A key question in this process is: How is the nucleotide-induced motion transmitted from the C-terminal ATPase domain (the D2 domain) of p97 to the distant N-terminal substrate-processing domain? We have previously reported the surprising finding that motion transmission between the two ATPase domains (the D2 and D1 domains) is mediated by the D1-D2 linker region of its neighboring protomer. In this study we report efforts to better understand this process. Our findings suggest that the amino acid sequence containing Gly-Gly that is located at the C terminus of the D1-D2 linker functions as a pivoting point that allows the dynamic movement of the D1-D2 linker. Furthermore, we found that locking the D1-D2 linker to the D2 domain by introducing disulfide bonds significantly impaired the motion-transmission process. These results support our previous model for interprotomer motion transmission, and provide more detailed information on how the motion transmission between the two ATPase domains of p97 is relayed by the flexible movement of the D1-D2 linker from its neighboring protomer.
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http://dx.doi.org/10.1073/pnas.1205853109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382474PMC
June 2012

Interprotomer motion-transmission mechanism for the hexameric AAA ATPase p97.

Proc Natl Acad Sci U S A 2012 Mar 21;109(10):3737-41. Epub 2012 Feb 21.

Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.

Multimeric AAA ATPases represent a structurally homologous yet functionally diverse family of proteins. The essential and highly abundant hexameric AAA ATPase p97 is perhaps the best studied AAA protein, playing an essential role in various important cellular activities. During ATP-hydrolysis process, p97 undergoes dramatic conformational changes, and these changes are initiated in the C-terminal ATPase domain and transmitted across the entire length of the molecule to the N-terminal effector domain. However, the detailed mechanism of the motion transmission remains unclear. Here, we report an interprotomer motion-transmission mechanism to explain this process: The nucleotide-dependent motion transmission between the two ATPase domains of one protomer is mediated by its neighboring protomer. This finding reveals a strict requirement for interprotomer coordination of p97 during the motion-transmission process and may shed light on studies of other AAA ATPases.
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http://dx.doi.org/10.1073/pnas.1200255109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309748PMC
March 2012

Challenging the limit: NMR assignment of a 31 kDa helical membrane protein.

J Am Chem Soc 2010 Mar;132(11):3662-3

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.

Structural determination of membrane proteins by NMR spectroscopy remains a challenge, especially for helical membrane proteins. Here we report the NMR assignment and secondary structure of a 31 kDa helical membrane protein, the C-terminal domain of Stt3p. The C-terminal domain of Stt3p has been proposed to be the catalytic domain of yeast oligosaccharyl transferase (OT), a multisubunit membrane-associated enzyme complex catalyzing N-glycosylation, which is an essential and highly conserved protein modification. NMR assignment is the first critical step in the determination of the high-resolution solution structure and further structure-function studies.
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http://dx.doi.org/10.1021/ja100078zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862971PMC
March 2010

A novel method of production and biophysical characterization of the catalytic domain of yeast oligosaccharyl transferase.

Biochemistry 2010 Feb;49(6):1115-26

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.

Oligosaccharyl transferase (OT) is a multisubunit enzyme that catalyzes N-linked glycosylation of nascent polypeptides in the lumen of the endoplasmic reticulum. In the case of Saccharomyces cerevisiae, OT is composed of nine integral membrane protein subunits. Defects in N-linked glycosylation cause a series of disorders known as congenital disorders of glycosylation (CDG). The C-terminal domain of the Stt3p subunit has been reported to contain the acceptor protein recognition site and/or catalytic site. We report here the subcloning, overexpression, and a robust but novel method of production of the pure C-terminal domain of Stt3p at 60-70 mg/L in Escherichia coli. CD spectra indicate that the C-terminal Stt3p is highly helical and has a stable tertiary structure in SDS micelles. The well-dispersed two-dimensional (1)H-(15)N HSQC spectrum in SDS micelles indicates that it is feasible to determine the atomic structure by NMR. The effect of the conserved D518E mutation on the conformation of the C-terminal Stt3p is particularly interesting. The replacement of a key residue, Asp(518), located within the WWDYG signature motif (residues 516-520), led to a distinct tertiary structure, even though both proteins have similar overall secondary structures, as demonstrated by CD, fluorescence and NMR spectroscopies. This observation strongly suggests that Asp(518) plays a critical structural role, in addition to the previously proposed catalytic role. Moreover, the activity of the protein was confirmed by saturation transfer difference and nuclear magnetic resonance titration studies.
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http://dx.doi.org/10.1021/bi902181vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838725PMC
February 2010

Probing the structure and function of human glutaminase-interacting protein: a possible target for drug design.

Biochemistry 2008 Sep 9;47(35):9208-19. Epub 2008 Aug 9.

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.

PDZ domains are one of the most ubiquitous protein-protein interaction modules found in living systems. Glutaminase interacting protein (GIP), also known as Tax interacting protein 1 (TIP-1), is a PDZ domain-containing protein, which plays pivotal roles in many aspects of cellular signaling, protein scaffolding and modulation of tumor growth. We report here the overexpression, efficient refolding, single-step purification, and biophysical characterization of recombinant human GIP with three different C-terminal target protein recognition sequence motifs by CD, fluorescence, and high-resolution solution NMR methods. It is clear from our NMR analysis that GIP contains 2 alpha-helices and 6 beta-strands. The three target protein C-terminal recognition motifs employed in our interaction studies are glutaminase, beta-catenin and FAS. This is the first report of GIP recognition of the cell surface protein FAS, which belongs to the tumor necrosis factor (TNF) receptor family and mediates cell apoptosis. The dissociation constant ( K D) values for the binding of GIP with different interacting partners as measured by fluorescence spectroscopy range from 1.66 to 2.64 microM. Significant chemical shift perturbations were observed upon titration of GIP with above three ligands as monitored by 2D {(1)H, (15)N}-HSQC NMR spectroscopy. GIP undergoes a conformational change upon ligand binding.
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http://dx.doi.org/10.1021/bi800287vDOI Listing
September 2008

Probing the conformation and dynamics of allatostatin neuropeptides: a structural model for functional differences.

Peptides 2008 Mar 29;29(3):375-85. Epub 2007 Nov 29.

Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA.

Allatostatins are a family of related neuropeptides that play an important role in development, reproduction, and digestion in insects. The cockroach Diploptera punctata has 13 allatostatin neuropeptides, with pleiotropic functions, two of which are: inhibition of juvenile hormone (JH) production and inhibition of gut muscle contraction. In this study, the conformation and dynamics of D. punctata allatostatin 5 (Dippu-AST 5) and allatostatin 8 (Dippu-AST 8) are investigated by CD, NMR, and molecular dynamics simulations. These peptides contain eight and nine residues, respectively, and the identical six-residue C-terminal motif. Yet Dippu-AST 5 and Dippu-AST 8 affect juvenile hormone production and hindgut contraction with different potencies. Dippu-AST 5 is one of the most potent inhibitors of juvenile hormone production and one of the least potent inhibitors of gut contraction, whereas Dippu-AST 8 has the opposite potencies with respect to these tissues. From the NMR structure, it is clear that Dippu-AST 5 has a 3(10) helix involving three of its residues and a "gamma" turn at the end of its C-terminal motif. In contrast Dippu-AST 8 has an open "pi" turn among five of its central residues. In addition, the orientation preferences within the membrane of the two peptides were simulated. Our simulation results show that the C-terminal segment of Dippu-AST 5 orients in the membrane surface with an average angle of 17.5 degrees, whereas Dippu-AST 8 orients with an average angle of 5.1 degrees. Taken together, from the structures and orientation preferences of these peptides within the membrane, it appears that these peptides may interact with the receptor very differently.
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http://dx.doi.org/10.1016/j.peptides.2007.11.016DOI Listing
March 2008