2010 Vol. 1, No. 4

News and views
Zebrafishing for tuberculosis infection
Liwei Wang
2010, 1(4): 309-311. doi: 10.1007/s13238-010-0055-5
Amyloid and Alzheimer's disease
Hongxing Lei
2010, 1(4): 312-314. doi: 10.1007/s13238-010-0046-6
Shizhang Bei (Sitsan Pai) and his theory of cell reformation
Guyan Wang
2010, 1(4): 315-318. doi: 10.1007/s13238-010-0050-x
Monoclonal antibodies-a proven and rapidly expanding therapeutic modality for human diseases
Zhiqiang An
2010, 1(4): 319-330. doi: 10.1007/s13238-010-0052-8
The study of antibodies has been a focal point in modern biology and medicine since the early 1900s. However, progress in therapeutic antibody development was slow and intermittent until recently. The first antibody therapy, murine-derived murononab OKT3 for acute organ rejection, was approved by the US Food and Drug Administration (FDA) in 1986, more than a decade after César Milstein and Georges Köhler developed methods for the isolation of mouse monoclonal antibodies from hybridoma cells in 1975. As a result of the scientific, technological, and clinical breakthroughs in the 1980s and 1990s, the pace of therapeutic antibody discovery and development accelerated. Antibodies are becoming a major drug modality with more than two dozen therapeutic antibodies in the clinic and hundreds more in development. Despite the progress, need for improvement exists at every level. Antibody therapeutics provides fertile ground for protein scientists to fulfill the dream of personalized medicine through basic scientific discovery and technological innovation.
Molecular mechanism of the Neurospora circadian oscillator
Jinhu Guo, Yi Liu
2010, 1(4): 331-341. doi: 10.1007/s13238-010-0053-7
Circadian clocks are the internal time-keeping mechanisms for organisms to synchronize their cellular and physiological processes to the daily light/dark cycles. The molecular mechanisms underlying circadian clocks are remarkably similar in eukaryotes. Neurospora crassa, a filamentous fungus, is one of the best understood model organisms for circadian research. In recent years, accumulating data have revealed complex regulation in the Neurospora circadian clock at transcriptional, posttranscriptional, post-translational and epigenetic levels. Here we review the recent progress towards our understanding of the molecular mechanism of the Neurospora circadian oscillator. These advances have provided novel insights and furthered our understanding of the mechanism of eukaryotic circadian clocks.
Roles of the hemagglutinin of influenza A virus in viral entry and development of antiviral therapeutics and vaccines
Shibo Jiang, Runming Li, Lanying Du, Shuwen Liu
2010, 1(4): 342-354. doi: 10.1007/s13238-010-0054-6
Seasonal influenza epidemics and influenza pandemics caused by influenza A virus (IAV) has resulted in millions of deaths in the world. The development of anti-IAV vaccines and therapeutics is urgently needed for prevention and treatment of IAV infection and for controlling future influenza pandemics. Hemagglutinin (HA) of IAV plays a critical role in viral binding, fusion and entry, and contains the major neutralizing epitopes. Therefore, HA is an attractive target for developing anti-IAV drugs and vaccines. Here we have reviewed the recent progress in study of conformational changes of HA during viral fusion process and development of HA-based antiviral therapeutics and vaccines.
Cellular models for disease exploring and drug screening
Zhi-kun Li, Qi Zhou
2010, 1(4): 355-362. doi: 10.1007/s13238-010-0027-9
The biopharmaceutical industry has been greatly promoted by the application of drug and disease models, including both animal and cellular models. In particular, the emergence of induced pluripotent stem cells (iPSC) makes it possible to create a large number of diseasespecific cells in vitro. This review introduces the most widely applied models and their specialties.
Crystal structures of catalytic core domain of BIV integrase: implications for the interaction between integrase and target DNA
Xue Yao, Shasha Fang, Wentao Qiao, Yunqi Geng, Yuequan Shen
2010, 1(4): 363-370. doi: 10.1007/s13238-010-0047-5
Integrase plays a critical role in the recombination of viral DNA into the host genome. Therefore, over the past decade, it has been a hot target of drug design in the fight against type 1 human immunodeficiency virus (HIV-1). Bovine immunodeficiency virus (BIV) integrase has the same function as HIV-1 integrase. We have determined crystal structures of the BIV integrase catalytic core domain (CCD) in two different crystal forms at a resolution of 2.45 Å and 2.2 Å, respectively. In crystal form I, BIV integrase CCD forms a back-to-back dimer, in which the two active sites are on opposite sides. This has also been seen in many of the CCD structures of HIV-1 integrase that were determined previously. However, in crystal form Ⅱ, BIV integrase CCD forms a novel face-toface dimer in which the two active sites are close to each other. Strikingly, the distance separating the two active sites is approximately 20 Å, a distance that perfectly matches a 5-base pair interval. Based on these data, we propose a model for the interaction of integrase with its target DNA, which is also supported by many published biochemical data. Our results provide important clues for designing new inhibitors against HIV-1.
Research articles
Three-dimensional domain swapping as a mechanism to lock the active conformation in a super-active octamer of SARS-CoV main protease
Shengnan Zhang, Nan Zhong, Fei Xue, Xue Kang, Xiaobai Ren, Jiaxuan Chen, Changwen Jin, Zhiyong Lou, Bin Xia
2010, 1(4): 371-383. doi: 10.1007/s13238-010-0044-8
Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses. The main protease (Mpro) of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the polyprotein processing. Mpro is initially produced as part of viral polyproteins and it is matured by autocleavage. Here, we report that, with the addition of an N-terminal extension peptide, Mpro can form a domain-swapped dimer. After complete removal of the extension peptide from the dimer, the mature Mpro self-assembles into a novel super-active octamer (AO-Mpro). The crystal structure of AO-Mpro adopts a novel fold with four domainswapped dimers packing into four active units with nearly identical conformation to that of the previously reported Mpro active dimer, and 3D domain swapping serves as a mechanism to lock the active conformation due to entanglement of polypeptide chains. Compared with the previously well characterized form of Mpro, in equilibrium between inactive monomer and active dimer, the stable AO-Mpro exhibits much higher proteolytic activity at low concentration. As all eight active sites are bound with inhibitors, the polyvalent nature of the interaction between AO-Mpro and its polyprotein substrates with multiple cleavage sites, would make AO-Mpro functionally much more superior than the Mpro active dimer for polyprotein processing. Thus, during the initial period of SARS-CoV infection, this novel active form AOMpro should play a major role in cleaving polyproteins as the protein level is extremely low. The discovery of AOMpro provides new insights about the functional mechanism of Mpro and its maturation process.
Probing the architecture of the Mycobacterium marinum arylamine N-acetyltransferase active site
Areej M. Abuhammad, Edward D. Lowe, Elizabeth Fullam, Martin Noble, Elspeth F. Garman, Edith Sim
2010, 1(4): 384-392. doi: 10.1007/s13238-010-0037-7
Treatment of latent tuberculosis infection remains an important goal of global TB eradication. To this end, targets that are essential for intracellular survival of Mycobacterium tuberculosis are particularly attractive. Arylamine N-acetyltransferase (NAT) represents such a target as it is, along with the enzymes encoded by the associated gene cluster, essential for mycobacterial survival inside macrophages and involved in cholesterol degradation. Cholesterol is likely to be the fuel for M. tuberculosis inside macrophages. Deleting the nat gene and inhibiting the NAT enzyme prevents survival of the microorganism in macrophages and induces cell wall alterations, rendering the mycobacterium sensitive to antibiotics to which it is normally resistant. To date, NAT from M. marinum (MMNAT) is considered the best available model for NAT from M. tuberculosis (TBNAT). The enzyme catalyses the acetylation and propionylation of arylamines and hydrazines. Hydralazine is a good acetyl and propionyl acceptor for both MMNAT and TBNAT. The MMNAT structure has been solved to 2.1 Å resolution following crystallisation in the presence of hydralazine and is compared to available NAT structures. From the mode of ligand binding, features of the binding pocket can be identified, which point to a novel mechanism for the acetylation reaction that results in a 3-methyltriazolo[3,4-a]phthalazine ring compound as product.
Interaction of the α2A domain of integrin with small collagen fragments
Hans-Christian Siebert, Monika Burg-Roderfeld, Thomas Eckert, Sabine Stötzel, Ulrike Kirch, Tammo Diercks, Martin J. Humphries, Martin Frank, Rainer Wechselberger, Emad Tajkhorshid, Steffen Oesser
2010, 1(4): 393-405. doi: 10.1007/s13238-010-0038-6
We here present a detailed study of the ligand-receptor interactions between single and triple-helical strands of collagen and the α2A domain of integrin (α2A), providing valuable new insights into the mechanisms and dynamics of collagen-integrin binding at a sub-molecular level. The occurrence of single and triple-helical strands of the collagen fragments was scrutinized with atom force microscopy (AFM) techniques. Strong interactions of the triple-stranded fragments comparable to those of collagen can only be detected for the 42mer triple-helical collagen-like peptide under study (which contains 42 amino acid residues per strand) by solid phase assays as well as by surface plasmon resonance (SPR) measurements. However, changes in NMR signals during titration and characteristic saturation transfer difference (STD) NMR signals are also detectable when α2A is added to a solution of the 21mer single-stranded collagen fragment. Molecular dynamics (MD) simulations employing different sets of force field parameters were applied to study the interaction between triple-helical or single-stranded collagen fragments with α2A. It is remarkable that even single-stranded collagen fragments can form various complexes with α2A showing significant differences in the complex stability with identical ligands. The results of MD simulations are in agreement with the signal alterations in our NMR experiments, which are indicative of the formation of weak complexes between single-stranded collagen and α2A in solution. These results provide useful information concerning possible interactions of α2A with small collagen fragments that are of relevance to the design of novel therapeutic A-domain inhibitors.
Crystal structures of NAC domains of human nascent polypeptide-associated complex (NAC) and its αNAC subunit
Lanfeng Wang, Wenchi Zhang, Lu Wang, Xuejun C. Zhang, Xuemei Li, Zihe Rao
2010, 1(4): 406-416. doi: 10.1007/s13238-010-0049-3
Nascent polypeptide associated complex (NAC) and its two isolated subunits, αNAC and βNAC, play important roles in nascent peptide targeting. We determined a 1.9 Å resolution crystal structure of the interaction core of NAC heterodimer and a 2.4 Å resolution crystal structure of αNAC NAC domain homodimer. These structures provide detailed information of NAC heterodimerization and αNAC homodimerization. We found that the NAC domains of αNAC and βNAC share very similar folding despite of their relative low identity of amino acid sequences. Furthermore, different electric charge distributions of the two subunits at the NAC interface provide an explanation to the observation that the heterodimer of NAC complex is more stable than the single subunit homodimer. In addition, we successfully built a βNAC NAC domain homodimer model based on homologous modeling, suggesting that NAC domain dimerization is a general property of the NAC family. These 3D structures allow further studies on structurefunction relationship of NAC.