Hongwei Yao

Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea

Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a β-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex

Cren7 is a crenarchaeal conserved chromatin protein discovered recently. To explore the mechanism of the DNA packaging in Crenarchaeota, the crystal structure of Cren7–GCGATCGC complex has been determined and refined at 1.6 Å resolution. Cren7 kinks the dsDNA sharply similar to Sul7d, another chromatin protein existing only in Sulfolobales, which reveals that the “bending and unwinding” compacting mechanism is conserved in Crenarchaeota. Significant structural differences are revealed by comparing both protein–dsDNA complexes. The kinked sites on the same dsDNA in the complexes with Sul7d and Cren7 show one base pair shift. For Cren7, fewer charged residues in the β‐barrel structural region bind to DNA, and additionally, the flexible loop Lβ3β4 is also involved in the binding. Electrophoretic mobility shift assays indicate that loop Lβ3β4 is essential for DNA‐binding of Cren7. These differences provide insight into the functional difference of both chromatin proteins, suggesting that Cren7 may be more regulative than Sul7d in the DNA‐binding affinity by the methylation in the flexible loop Lβ3β4 in vivo.

Anti-apoptosis proteins Mcl-1 and Bcl-xL have different p53-binding profiles.

One of the transcription-independent mechanisms of the tumor suppressor p53 discovered in recent years involves physical interaction between p53 and proteins of the Bcl-2 family. In this paper, significant differences between the interaction of p53 with Mcl-1 and Bcl-xL were demonstrated by NMR spectroscopy and isothermal titration calorimetry. Bcl-xL was found to bind strongly to the p53 DNA-binding domain (DBD) with a dissociation constant (Kd) of ~600 nM, whereas Mcl-1 binds to the p53 DBD weakly with a dissociation constant in the mM range. In contrast, the p53 transactivation domain (TAD) binds weakly to Bcl-xL with a Kd ~ 300-500 μM and strongly to Mcl-1 with a Kd ~ 10-20 μM. NMR titrations indicate that although the p53 TAD binds to the BH3-binding grooves of both Bcl-xL and Mcl-1, Bcl-xL prefers to bind to the first subdomain (TAD1) in the p53 TAD, and Mcl-1 prefers to bind to the second subdomain (TAD2). Therefore, Mcl-1 and Bcl-xL have different p53-binding profiles. This indicates that the detailed interaction mechanisms are different, although both Mcl-1 and Bcl-xL can mediate transcription-independent cytosolic roles of p53. The revealed differences in binding sites and binding affinities should be considered when BH3 mimetics are used in cancer therapy development.

The N-terminal 26-residue fragment of human programmed cell death 5 protein can form a stable α-helix having unique electrostatic potential character

PDCD5-(1-26) is a N-terminal 26-residue fragment of human PDCD5 (programmed cell death 5) protein. PDCD5 is an important novel protein that regulates both apoptotic and non-apoptotic programmed cell death. The conformation of PDCD5 protein is a stable helical core consisting of a triple-helix bundle and two dissociated terminal regions. The N-terminal region is ordered and contains abundant secondary structure. Overexpression and purification of the N-terminal 26-residure fragment, PDCD5-(1-26), was performed in this study to better understand its tertiary structure. The spectroscopic studies using CD and hetero- and homo-nuclear NMR methods determine a stable alpha-helix formed by Asp3-Ala19 of PDCD5-(1-26). The N-terminal residues Asp3-Ala19 of PDCD5 were then affirmed to have the capacity to form a stable alpha-helix independently of the core of the protein. Analysis of the helical peptide of PDCD5-(1-26) indicates that the surface of this well-formed alpha-helix has a unique electrostatic potential character. This may provide an environment for the N-terminal alpha-helix of PDCD5 to serve as an independent functional entity of the protein. The apoptosis activity assay shows that the deletion of the N-terminal alpha-helix of PDCD5 significantly attenuates the apoptosis-promoting effects on HL-60 cells induced by serum withdrawal.

NMR Studies of the Interaction between Human Programmed Cell Death 5 and Human p53

Human programmed cell death 5 (PDCD5) is a protein playing a significant role in regulating both the apoptotic and paraptotic cell deaths. Resent findings show that PDCD5 is a positive regulator of Tip60 and also has a potential ability to interact with p53. Here we aim to experimentally characterize the nature of the interactions between PDCD5 and the p53 N-terminal domain (NTD) and to depict the binding mode between two proteins. The interprotein binding interfaces were determined by NMR experiments performed with PDCD5 and various fragments of p53 NTD. The binding affinity was investigated using the NMR titration experiments. Analysis revealed that the PDCD5 binding site on p53 is localized within residues 41-56 of p53 TAD2 subdomain while p53 binds preferentially to the positively charged surface region around the C-terminals of helices α3 and α5 and the N-terminal of helix α4 of PDCD5. The binding is mainly mediated through electrostatic interactions. The present data suggested a model for the interaction between PDCD5 and the p53 NTD.

Structure-function correlation of human programmed cell death 5 protein

Human programmed cell death 5 (PDCD5) is a translocatory protein playing an important role in the apoptotic process of cells. Although there are accumulated data about PDCD5 function, the correlation of the structure with the function of PDCD5 has not been investigated. Here, we report the studies of structure-function relationship of PDCD5 by multidimensional NMR methods and by FACScan flow cytometer and fluorescence microscope. The 3D structure of intact PDCD5 and the internal motions of PDCD5 have been determined. PDCD5 has a compact core structure of low flexibility with two mobile alpha-helices at N-terminal region and a flexible unstructured C-terminal region. The flow cytometry and internalization measurements of different PDCD5 fragments indicate that the charged residues are crucial for the ability of apoptosis-promoting and cell translocation of the protein. Combined analyses reveal a fact that the regions that seem to be most involved in the function also are more flexible in PDCD5.

Solution structure and calcium binding of protein SSO6904 from the hyperthermophilic archaeon Sulfolobus solfataricus

Calcium signaling in bacteria and archaea has been believed to be as important as it in eukaryotes for many years, but calcium-binding proteins identified in prokaryotes are much less than those in eukaryotes.1–3 A calcium-gated potassium channel discovered in the archaeon Methanobacterium thermoautotrophicum indicated the importance of calcium in archaea.4 So far, several calcium-binding proteins, such as pullulanase,5 MTH1880,6 Ulilysin,7 Tk-subtilisin,8 and M-Crystallin,9 have been identified from various archaea. Of them only a few structures were solved by X-ray crystallography or NMR spectroscopy. The physiological significance of most of these calcium-binding proteins is still unclear to date. Sulfolobus solfataricus is a hyperthermophilic archaeon used as a model system for researches on genetics, evolution, and hyperthermophilic mechanism.10–12 S. solfataricus genome encodes about 3000 proteins, in which about 25% proteins are exclusive to Sulfolobus.11 Calcium-binding proteins in S. solfataricus were rarely investigated up to now. SSO6904 (UniProt ID: Q97ZE1) is a predicted protein conserved in Sulfolobales [Fig. 1(A)] and has no sequence homology to any of other protein families. We determined the solution structure of SSO6904 from S. solfataricus P2 and found that it is a helical protein. The tertiary fold of SSO6904 is similar to that of saposin-fold proteins and some calcium-binding proteins. Although SSO6904 has no EF-hand sequence, which is the most common calcium-binding sequence, NMR titration experiments showed that SSO6904 can bind with calcium weakly at its unique binding site.

Cloning, expression and purification of DNA-binding protein Mvo10b from Methanococcus voltae

Mvo10b from the mesophilic archaeon Methanococcus voltae is a member of the Sac10b family which may play an important role in the organization and accessibility of genetic information in Archaea. Since Mvo10b is a DNA-binding protein as the other member in the Sac10b family, to obtain a recombinant Mvo10b requires an efficient and inexpensive expression and purification system for producing the protein free of nucleic acid contamination. Previously, the hyperthermophilic archaeal Ssh10b of the Sac10b family was successfully purified. However, the protocol adopted to purify Ssh10b is not appropriate for purifying the mesophilic Mvo10b. This study describes the successful expression and purification of the recombinant Mvo10b. The expression of recombinant Mvo10b was carried out in Escherichia coli, and the target protein was expressed in the soluble form. The protein was purified by polyethyleneimine (PEI) precipitation followed by nickel ion metal affinity chromatography. The purity of Mvo10b was checked to insure being free of nucleic acid contamination. The final protein yield is about 30mg/l of LB culture. The ensemble of NMR and far-UV CD data shows that the purified Mvo10b has abundant regular secondary structures and is correctly folded, which may have similar 3D structure as its hyperthermophilic counterpart [P62A]Ssh10b. The developed protocol has potential application in the production of the other thermophilic and mesophilic proteins in the Sac10b family.