In all six members of TRPV channel subfamily, there is an ankyrin repeat domain (ARD) in their intracellular N-termini. Ankyrin (ANK) repeat, a common motif with typically 33 residues in each repeat, is primarily involved in protein-protein interactions. Despite the sequence similarity among the ARDs of TRPV channels, the structure of TRPV3-ARD, however, remains unknown. Here, we report the crystal structure of TRPV3-ARD solved at 1.95 Å resolution, which reveals six-ankyrin repeats. While overall structure of TRPV3-ARD is similar to ARDs from other members of TRPV subfamily; it, however, features a noticeable finger 3 loop that bends over and is stabilized by a network of hydrogen bonds and hydrophobic packing, instead of being flexible as seen in known TRPV-ARD structures. Electrophysiological recordings demonstrated that mutating key residues R225, R226, Q255, and F249 of finger 3 loop altered the channel activities and pharmacology. Taken all together, our findings show that TRPV3-ARD with characteristic finger 3 loop likely plays an important role in channel function and pharmacology.
Amino Acid Sequence ; Ankyrin Repeat ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Models, Molecular ; Molecular Sequence Data ; Patch-Clamp Techniques ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; TRPV Cation Channels ; chemistry ; physiology

The transition metal cobalt, an essential cofactor for many enzymes in prokaryotes, is taken up by several specific transport systems. The CbiMNQO protein complex belongs to type-1 energy-coupling factor (ECF) transporters and is a widespread group of microbial cobalt transporters. CbiO is the ATPase subunit (A-component) of the cobalt transporting system in the gram-negative thermophilic bacterium Thermoanaerobacter tengcongensis. Here we report the crystal structure of a nucleotide-free CbiO at a resolution of 2.3 Å. CbiO contains an N-terminal canonical nucleotide-binding domain (NBD) and C-terminal helical domain. Structural and biochemical data show that CbiO forms a homodimer mediated by the NBD and the C-terminal domain. Interactions mainly via conserved hydrophobic amino acids between the two C-terminal domains result in formation of a four-helix bundle. Structural comparison with other ECF transporters suggests that non-conserved residues outside the T-component binding groove in the A component likely act as a specificity determinant for T components. Together, our data provide information on understanding of the structural organization and interaction of the CbiMNQO system.
Adenosine Triphosphatases ; chemistry ; Amino Acids ; chemistry ; Biological Transport ; Catalytic Domain ; Cobalt ; chemistry ; Crystallography, X-Ray ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Structure-Activity Relationship ; Thermoanaerobacter ; enzymology

KM-HN-1 is a C-terminal coiled-coil domain containing protein previously referred to as image clone MGC33607. This protein has been previously identified as a cancer/testis antigen and reported as nuclear and chromatin localizing protein. We raised polyclonal antisera with the GST fusion protein and identified them as a 105 kDa protein. Motif analysis showed that this protein harbors the leucine zipper motif in internal 1/3 region and the coiled-coil domain in the C-terminal region. Using the full length and various deletion mutants, we determined the motif that governs the subcellular localization of KM-HN-1. Immunofluorescence staining of the endogenous KM-HN-1 and various kinds of GFP-tagged KM-HN-1 revealed that KM-HN-1 localizes to the centrosomes as well as nucleus. The centrosomal localization-determining region of this protein is C-terminal coiled-coil domain in which the leucine zipper motif and the nuclear export signal (NES) harbor.
Amino Acid Motifs/physiology ; Amino Acid Sequence ; Antigens, Neoplasm/chemistry/*metabolism ; Cells, Cultured ; Centrosome/*metabolism ; Fluorescent Antibody Technique ; Humans ; Leucine Zippers/*physiology ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Sequence Analysis, Protein

Degenerate PCR primers were designed by multiple alignment of the protein sequences of known structural genes encoding the catalytic subunits of NiFe-hydrogenases obtained from Swiss-Prot Protein Sequence Database through CLUSTAL-W software and compared for conserved sequence motifs. An amplified PCR product 1 kb in size was obtained from the genomic DNA of Klebsiella pneumoniae using a set of degenerate primers, and then inverse PCR technique was used to obtain the full hydrogenase coding region. A predicted secondary structure and 3D structural model were constructed by homology modeling and docking. On the basis of these results, it was inferred that NiFe-hydrogenase from Klebsiella pneumoniae belongs to the membrane-bound H2 evolving hydrogenase group (Ech hydrogenase group).
Bacterial Proteins ; chemistry ; genetics ; Cloning, Molecular ; Codon ; genetics ; DNA, Bacterial ; chemistry ; genetics ; Databases, Protein ; Hydrogen Bonding ; Hydrogenase ; chemistry ; genetics ; Klebsiella pneumoniae ; enzymology ; genetics ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Analysis, DNA

Transient receptor potential (TRP) channels are widely found throughout the animal kingdom. By serving as cellular sensors for a wide spectrum of physical and chemical stimuli, they play crucial physiological roles ranging from sensory transduction to cell cycle modulation. TRP channels are tetrameric protein complexes. While most TRP subunits can form functional homomeric channels, heteromerization of TRP channel subunits of either the same subfamily or different subfamilies has been widely observed. Heteromeric TRP channels exhibit many novel properties compared to their homomeric counterparts, indicating that co-assembly of TRP channel subunits has an important contribution to the diversity of TRP channel functions.
Animals ; Ankyrin Repeat ; Humans ; Models, Molecular ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits ; TRPC Cation Channels ; chemistry ; genetics ; physiology

Collagen is the most abundant protein in human body and a periodic helix, i. e. , triple helix, fibrous protein, which provides the scaffold structures for the cell adhesion and macromolecule aggregation, etc. With the development of gene engineering and biomaterial technologies, and the incessant studies on the technique to obtain the proteins with special functions, the collagen protein has been one of the third generation biomaterials that attract more attention than others. In this paper, we reviewed the recent structure-based design and biosynthesis of collagen.
Animals ; Biotechnology ; methods ; Collagen ; biosynthesis ; chemistry ; genetics ; Humans ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Stability ; Protein Structure, Secondary ; Temperature

Firstly, parathyroid hormone (1-14) [PTH (1-14)] analogue containing various alpha-amino-iso-butyric acid residue (Aib) was synthesized by exchanging the 1st and 3rd Ala residues of alpha carbon of PTH (1-14). This analogue revealed to have the quite tight and stable alpha-helical structure using the nuclear magnetic resonance (NMR) analysis. The biological activities of these analogues were examined using a cAMP-generating assay in LLC-PK1 cell lines stably transfected with the wild-type human PTH1 receptor. Only the PTH analogue substituted with methyl moiety without acetylation showed significant cAMP generating action with 15.0 +/- 3.414 of EC50. Then, we used an ovariectomized rat model system to compare the in vivo effects of parathyroid hormone analogue with that of PTH (1-84). Daily subcutaneous administration of the unacetylated Aib1,3PTH (1-14) for 5 weeks in 30 nM/kg subcutaneously with positive control group receiving PTH (1-84) with 8 nM/ kg were performed. However, there was no significant change in spinal or femoral bone mineral density assessed by dual x-ray absorptiometry (DXA) in the Aib1,3PTH (1-14) group where definite increase of these parameters shown in the PTH (1-84) group (p < 0.001). Assessment of bone strength was evaluated with no significant differences among all groups. It was quite disappointing to see the actual discrepancies between the result of significant pharmacokinetic potency and the in vivo clinical effect of the Aib1,3PTH (1-14). However, there are several limitations to mention, such as the short duration of treatment, matter of dosage, and insufficient effect of tight alpha-helical structures with absence of C-terminus. In conclusion, our findings suggest that unacetylated Aib1,3PTH (1-14) did not exhibit any anabolic effects at the bones of ovariectomized rats.
Transfection ; Time Factors ; Structure-Activity Relationship ; Stress, Mechanical ; Spectrometry, X-Ray Emission ; Rats ; Protein Structure, Tertiary ; Protein Structure, Secondary ; Protein Conformation ; Protein Binding ; Peptides/chemistry ; Parathyroid Hormone/*analogs & derivatives/chemistry/*metabolism ; Molecular Sequence Data ; Molecular Conformation ; Models, Statistical ; Models, Molecular ; Magnetic Resonance Spectroscopy ; LLC-PK1 Cells ; Humans ; Female ; Dose-Response Relationship, Drug ; Densitometry ; Cyclic AMP/metabolism ; Cell Line ; Bone and Bones/metabolism ; Bone Density ; Biomechanics ; Animals ; Aminoisobutyric Acids/*metabolism ; Amino Acid Sequence ; Alanine/chemistry

TRAF4 is a unique member of TRAF family, which is essential for innate immune response, nervous system and other systems. In addition to be an adaptor protein, TRAF4 was identified as a regulator protein in recent studies. We have determined the crystal structure of TRAF domain of TRAF4 (residues 292-466) at 2.60 Å resolution by X-ray crystallography method. The trimericly assembled TRAF4 resembles a mushroom shape, containing a super helical "stalk" which is made of three right-handed intertwined α helixes and a C-terminal "cap", which is divided at residue L302 as a boundary. Similar to other TRAFs, both intermolecular hydrophobic interaction in super helical "stalk" and hydrogen bonds in "cap" regions contribute directly to the formation of TRAF4 trimer. However, differing from other TRAFs, there is an additional flexible loop (residues 421-426), which contains a previously identified phosphorylated site S426 exposing on the surface. This S426 was reported to be phosphorylated by IKKα which is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation. Therefore, the crystal structure of TRAF4-TRAF is valuable for understanding its molecular basis for its special function and provides structural information for further studies.
Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Phosphorylation ; Protein Conformation, alpha-Helical ; Protein Domains ; Protein Structure, Quaternary ; Recombinant Proteins ; chemistry ; Sequence Homology, Amino Acid ; TNF Receptor-Associated Factor 4 ; chemistry

To predict the B cell epitopes for major outer membrane protein (MOMP) of Chlamydia trachomatis (CT), the secondary structure of CT MOMP was predicted by the methods of GOR based on the sequence of amino acids of E serotype CT MOMP. By combining the comprehensive analysis of transmembrane domain, hydrophilicity profile, surface probability, antigenic index and average flexibility, the B cell predominant epitopes of CT MOMP were further predicted. The N-terminal No. 73-81, 217-225, 377-386, 261-270 and 161-175 were the predominant B cell epitopes. Prediction of the B cell epitopes for the CT MOMP by the multi-parameters is helpful for the identification of B cell epitopes.
Amino Acid Sequence ; Antigens, Bacterial ; immunology ; Chlamydia trachomatis ; classification ; immunology ; Epitopes, B-Lymphocyte ; immunology ; Molecular Sequence Data ; Porins ; immunology ; Protein Conformation ; Protein Structure, Secondary ; Serotyping

Arrestins are soluble relatively small 44-46 kDa proteins that specifically bind hundreds of active phosphorylated GPCRs and dozens of non-receptor partners. There are binding partners that demonstrate preference for each of the known arrestin conformations: free, receptor-bound, and microtubule-bound. Recent evidence suggests that conformational flexibility in every functional state is the defining characteristic of arrestins. Flexibility, or plasticity, of proteins is often described as structural disorder, in contrast to the fixed conformational order observed in high-resolution crystal structures. However, protein-protein interactions often involve highly flexible elements that can assume many distinct conformations upon binding to different partners. Existing evidence suggests that arrestins are no exception to this rule: their flexibility is necessary for functional versatility. The data on arrestins and many other multi-functional proteins indicate that in many cases, "order" might be artificially imposed by highly non-physiological crystallization conditions and/or crystal packing forces. In contrast, conformational flexibility (and its extreme case, intrinsic disorder) is a more natural state of proteins, representing true biological order that underlies their physiologically relevant functions.
Animals ; Arrestins ; chemistry ; metabolism ; Humans ; Protein Conformation