ω-芋螺毒素MVIIC的N及C端修饰对折叠及活性影响

 合成了 ω-芋螺毒素 MVIIC的三种 N及 C端修饰肽 ,应用高压液相色谱、CD及生物体内活性实验 ,研究了其 N及 C端修饰对折叠及活性的影响 .结果表明 :MVIIC N端用 Phe及 Ser修饰后降低其线性肽形成正确折叠的比例及结构的稳定性 ,对小鼠的脑室给药活性也相应降低 ;C端酰胺转为电负性羧基端后活性降低 ,CD谱存在显著差异 .     

Organization of connectin/titin filaments in sarcomeres of differentiating chicken skeletal muscle cells

Very long, elastic connectin/titin molecules position the myosin filaments at the center of a sarcomere by linking them to the Z line. The behavior of the connectin filaments during sarcomere formation in differentiating chicken skeletal muscle cells was observed under a fluorescent microscope using the antibodies to the N terminal (located in the Z line), C terminal (M line), and C zone (myosin filament) regions of connectin and was compared to the incorporation of -actinin and myosin into forming sarcomeres. In early stages of differentiating muscle cells, the N terminal region of connectin was incorporated into a stress fiber-like structure (SFLS) together with -actinin to form dots, whereas the C terminal region was diffusely distributed in the cytoplasm. When both the C and N terminal regions formed striations in young myofibrils, the epitope to the C zone of A-band region, that is the center between the A-I junction and the M-line, initially was diffuse in appearance and later formed definite striations. It appears that it took some time for the N and C terminal regions of connectin to form a regular organization in a sarcomere. Thus the two ends of the connectin filaments were first fixed followed by the specific binding of the middle portion onto the myosin filament during sarcomere formation.     

Structure of α-tropomyosin magnesium paracrystals: II. Simulation of staining patterns from the sequence and some observations on the mechanism of positive staining

Electron micrographs of magnesium paracrystals of α-tropomyosin stained with uranyl acetate show a repeating pattern of 14 dark bands. Previous studies (Caspar et al., 1969; Ohtsuki, 1974) have shown that the molecules in the paracrystal lie antiparallel with their ends near two prominent white bands. These white lines divide the pattern into two zones containing nine and five dark bands, respectively, with the longer zone corresponding to the overlap between C termini. The present study shows that the intensity of the prominent white lines is reduced after digesting tropomyosin with carboxypeptidase A. This implies that, even in supposedly positively stained material, the white lines result from the exclusion of residual negative stain by the local thickening associated with the overlap of the ends of consecutive parallel molecules (NC overlap). Computer image processing and least-squares analysis have been employed to relate the positively stained patterns observed in both digested and undigested material to molecular positions and the amino acid sequence. Over a range of different staining criteria, it is shown that the pattern is fitted best when the C termini overlap by 176 ± 5 residues and the ends of consecutive parallel molecules overlap by 11 ± 5 residues. Uranyl ions appear to bind to carboxyl groups in the structure unless they form salt bridges with basic residues or they lie in the innermost positions of the tropomyosin coiled coil. Systematic differences between predicted and observed patterns near the molecular ends suggest that the conformation of the NC overlap may not be completely α-helical. A model with a globular N terminus and an extended C terminus is more consistent with the observed staining patterns and also offers an explanation for some other observations.     

Protein structure prediction begins well but ends badly

The accurate prediction of protein structure, both secondary and tertiary, is an ongoing problem. Over the years, many approaches have been implemented and assessed. Most prediction algorithms start with the entire amino acid sequence and treat all residues in an identical fashion independent of sequence position. Here, we analyze blind prediction data to investigate whether predictive capability varies along the chain. Free modeling results from recent critical assessment of techniques for protein structure prediction (CASP) experiments are evaluated; as is the most up‐to‐date data from EVA, a fully automated blind test of secondary structure prediction servers. The results demonstrate that structure prediction accuracy is dependent on sequence position. Both secondary structure and tertiary structure predictions are more accurate in regions near the amino(N)‐terminus when compared with analogous regions near the carboxy(C)‐terminus. Eight of 10 secondary structure prediction algorithms assessed by EVA perform significantly better in regions at the N‐terminus. CASP data shows a similar bias, with N‐terminal fragments being predicted more accurately than fragments from the C‐terminus. Two analogous fragments are taken from each model, the N‐terminal fragment begins at the start of the most N‐terminal secondary structure element (SSE), whereas the C‐terminal fragment finishes at the end of the most C‐terminal SSE. Each fragment is locally superimposed onto its respective native fragment. The relative terminal prediction accuracy (RMSD) is calculated on an intramodel basis. At a fragment length of 20 residues, the N‐terminal fragment is predicted with greater accuracy in 79% of cases. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Computational modeling of the N‐terminus of the human dopamine transporter and its interaction with PIP2‐containing membranes

The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N‐ and C‐terminal domains that are strongly implicated in the transporter function. The N‐terminus (N‐term), in particular, regulates the reverse transport (efflux) of the substrate through DAT. Currently, the molecular mechanisms of the efflux remain elusive in large part due to lack of structural information on the N‐terminal segment. Here we report a computational model of the N‐term of the human DAT (hDAT), obtained through an ab initio structure prediction, in combination with extensive atomistic molecular dynamics (MD) simulations in the context of a lipid membrane. Our analysis reveals that whereas the N‐term is a highly dynamic domain, it contains secondary structure elements that remain stable in the long MD trajectories of interactions with the bilayer (totaling >2.2 μs). Combining MD simulations with continuum mean‐field modeling we found that the N‐term engages with lipid membranes through electrostatic interactions with the charged lipids PIP₂ (phosphatidylinositol 4,5‐Biphosphate) or PS (phosphatidylserine) that are present in these bilayers. We identify specific motifs along the N‐term implicated in such interactions and show that differential modes of N‐term/membrane association result in differential positioning of the structured segments on the membrane surface. These results will inform future structure‐based studies that will elucidate the mechanistic role of the N‐term in DAT function. Proteins 2015; 83:952–969. © 2015 Wiley Periodicals, Inc.     

Searching for remote homologs of CAML among eukaryotes

The tryptophan rich basic protein/calcium signal‐modulating cyclophilin ligand (WRB/CAML) and Get1p/Get2p complexes, in vertebrates and yeast, respectively, mediate the final step of tail‐anchored protein insertion into the endoplasmic reticulum membrane via the Get pathway. While WRB appears to exist in all eukaryotes, CAML homologs were previously recognized only among chordates, raising the question as to how CAML's function is performed in other phyla. Furthermore, whereas WRB was recognized as the metazoan homolog of Get1, CAML and Get2, although functionally equivalent, were not considered to be homologous. CAML contains an N‐terminal basic, TRC40/Get3‐interacting, region, three transmembrane segments near the C‐terminus, and a poorly conserved region between these domains. Here, I searched the NCBI protein database for remote CAML homologs in all eukaryotes, using position‐specific iterated‐basic local alignment search tool, with the C‐terminal, the N‐terminal or the full‐length sequence of human CAML as query. The N‐terminal basic region and full‐length CAML retrieved homologs among metazoa, plants and fungi. In the latter group several hits were annotated as GET2. The C‐terminal query did not return entries outside of the animal kingdom, but did retrieve over one hundred invertebrate metazoan CAML‐like proteins, which all conserved the N‐terminal TRC40‐binding domain. The results indicate that CAML homologs exist throughout the eukaryotic domain of life, and suggest that metazoan CAML and yeast GET2 share a common evolutionary origin. They further reveal a tight link between the particular features of the metazoan membrane‐anchoring domain and the TRC40‐interacting region. The list of sequences presented here should provide a useful resource for future studies addressing structure‐function relationships in CAML proteins.     

Condensation of polynucleosome by histone H1 binding

The complete amino acid sequence of the oligomycin sensitivity-conferring protein (OSCP) of beef-heart mitochondria is reported. The protein contains 190 amino acids and has a molecular mass of 20 967. Its structure is characterized by a concentration of charged amino acids in the two terminal segments (N 1-77 and C 128-190) of the protein, whereas its central region is more hydrophobic. The earlier reported homology of the protein with the delta-subunit of E. coli F1, based on the terminal amino acid sequences of OSCP, is further substantiated.     

河蚌C反应蛋白一级结构分析

经亲和层析纯化的河蚌 C反应蛋白 ( CRP)具有 SDS- PAGE纯度 ,用经改进的双偶联 Ed-man方法测得其 N端残基为谷氨酸 ,而不是高等动物 (人与家兔 ) C反应蛋白 N端的焦谷氨酸 .河蚌 C反应蛋白 N端的一级结构由固相 Edman方法测得 ,依次为 H2 N- E- T- A- Y- S- C- I- T- A- V- ;C端的一级结构由羧肽酶 A降解法测得 ,依次为 - L/V- S- S- T- Y- COOH,也不同于人和家兔的 C反应蛋白 .在河蚌 CRP的胰蛋白酶酶解肽段中 ,其 N端及 C端的结构也得到了证实 .河蚌 C反应蛋白经 V8蛋白内切酶酶解 ,溴化氰裂解 ,肽段经 HPLC反相柱分离 ,共得到 35个肽段 ,所有肽段的氨基酸序列均由气相氨基酸自动分析仪测得 .结合河蚌 C反应蛋白的胰蛋白酶酶解肽段的分析结果 ,其一级结构已初步拼接完成 .在其一级结构中发现有类似于其它 CRP的 Ca2 + 结合部位和磷酸胆碱结合部位 .河蚌 C反应蛋白的分子结构中存在微观不均一性 .从已知河蚌 C反应蛋白的分子特点 ,包括分子量 ,糖基化比例 ,一级结构不均一等特点 ,可以推测它与高等动物的免疫蛋白有许多相关之处 .对于河蚌 C反应蛋白分子结构的分析 ,将有助于免疫系统蛋白的发生 ,进化等方面的研究     

Temperature-, SDS-, and pH-induced conformational changes in protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus: a dynamic simulation and fourier transform infrared spectroscopic study

The effect of SDS, pD, and temperature on the structure and stability of the protein disulfide oxidoreductase from Pyrococcus furiosus (PfPDO) was investigated by molecular dynamic (MD) simulations and FT-IR spectroscopy. pD affects the thermostability of alpha-helices and beta-sheets differently, and 0.5% or higher SDS concentration influences the structure significantly. The experiments allowed us to detect a secondary structural reorganization at a definite temperature and pD which may correlate with a high ATPase activity of the protein. The MD simulations supported the infrared data and revealed the different behavior of the N and C terminal segments, as well as of the two active sites.     

Ultrastructure of the calcium release channel of sarcoplasmic reticulum

This study is concerned with the characterization of the morphology of the calcium release channel of sarcoplasmic reticulum (SR) from fast-twitch skeletal muscle, which is involved in excitation-contraction coupling. We have previously purified the ryanodine receptor and found it to be equivalent to the feet structures, which are involved, in situ, in the junctional association of transverse tubules with terminal cisternae of SR. The receptor is an oligomer of a single high molecular weight polypeptide and when incorporated into phospholipid bilayers, has channel conductance which is characteristic of calcium release in terminal cisternae of SR. The purified channel can be observed by electron microscopy using different methods of sample preparation, with complementary views being observed by negative staining, double staining, thin section and rotary shadowing electron microscopy. Three views can be observed and interpreted: (a) a square face which, in situ, is junctionally associated with the transverse tubule or junctional face membrane; (b) a rectangle equivalent to the side view; and (c) a diamond shape equivalent to the side view, of which the base portion appears to be equivalent to the transmembrane segment. Negative staining reveals detailed substructure of the channel. A computer averaged view of the receptor displays fourfold symmetry and ultrastructural detail. The dense central mass is divided into four domains with a 2-nm hole in the center, and is enclosed within an outer frame which has a pinwheel appearance. Double staining shows substructure of the square face in the form of parallel linear arrays (six/face). The features of the isolated receptor can be correlated with the structure observed in terminal cisternae vesicles. Sections tangential to the junctional face membrane reveal that the feet structures (23-nm squares) overlap so as to enclose smaller square spaces of approximately 14 nm/side. We suggest that this is equivalent to the transverse tubule face and that the terminal cisternae face is smaller (approximately 17 nm/face) and has larger alternating spaces as a consequence of the tapered sides of the foot structures. Image reconstruction analysis appears to be feasible and should provide the three-dimensional structure of the channel.     

An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C‐terminal stable core

Autotransporter (AT) proteins are a broad class of virulence factors from Gram‐negative pathogens. AT outer membrane (OM) secretion appears simple in many regards, yet the mechanism that enables transport of the central AT ‘passenger’ across the OM remains unclear. OM secretion efficiency for two AT passengers is enhanced by a ～ 20 kDa stable core at the C‐terminus of the passenger, but studies on a broader range of AT proteins are needed in order to determine whether a stability difference between the passenger N‐ and C‐terminus represents a truly common mechanistic feature. Yersinia pestis YapV is homologous to Shigella flexneri IcsA, and like IcsA, YapV recruits mammalian neural Wiskott–Aldrich syndrome protein (N‐WASP). In vitro, the purified YapV passenger is functional and rich in β‐sheet structure, but lacks a ～ 20 kDa C‐terminal stable core. However, the N‐terminal 49 residues of the YapV passenger globally destabilize the entire YapV passenger, enhancing its OM secretion efficiency. These results indicate that the contributions of AT passenger sequences to OM secretion efficiency extend beyond a C‐terminal stable core, and highlight a role of the passenger N‐terminus in reducing passenger stability in order to facilitate OM secretion of some AT proteins.     

Folding and membrane insertion of amyloid‐beta (25–35) peptide and its mutants: Implications for aggregation and neurotoxicity

The mechanisms of interfacial folding and membrane insertion of the Alzheimer's amyloid‐β fragment Aβ(25–35) and its less toxic mutant, N27A‐Aβ(25–35) and more toxic mutant, M35A‐Aβ(25–35), are investigated using replica–exchange molecular dynamics in an implicit water‐membrane environment. This study simulates the processes of interfacial folding and membrane insertion in a spontaneous fashion to identify their general mechanisms. Aβ(25–35) and N27A‐Aβ(25–35) peptides share similar mechanisms: the peptides are first located in the membrane hydrophilic region where their C‐terminal residues form helical structures. The peptides attempt to insert themselves into the membrane hydrophobic region using the C‐terminal or central hydrophobic residues. A small portion of peptides can successfully enter the membrane's hydrophobic core, led by their C‐terminal residues, through the formation of continuous helical structures. No detectable amount of M35A‐Aβ(25–35) peptides appeared to enter the membrane's hydrophobic core. The three studied peptides share a similar helical structure for their C‐terminal five residues, and these residues mainly buried within the membrane's hydrophobic region. In contrast, their N‐terminal properties are markedly different. With respect to the Aβ(25–35), the N27A‐Aβ(25–35) forms a more structured helix and is buried deeper within the membrane, which may result in a lower degree of aggregation and a lower neurotoxicity; in contrast, the less structured and more water‐exposed M35A‐Aβ(25–35) is prone to aggregation and has a higher neurotoxicity. Understanding the mechanisms of Aβ peptide interfacial folding and membrane insertion will provide new insights into the mechanisms of neurodegradation and may give structure‐based clues for rational drug design preventing amyloid associated diseases. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases

Xaa‐Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa‐Pro iminopeptide bond with a trans‐proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 Å resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N‐terminal domains such that their C‐terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N‐terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N‐terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.     

Structural characterization of α‐synuclein in an aggregation prone state

The relation of α‐synuclein (αS) aggregation to Parkinson's disease has long been recognized, but the pathogenic species and its molecular properties have yet to be identified. To obtain insight into the properties of αS in an aggregation‐prone state, we studied the structural properties of αS at acidic pH using NMR spectroscopy and computation. NMR demonstrated that αS remains natively unfolded at lower pH, but secondary structure propensities were changed in proximity to acidic residues. The ensemble of conformations of αS at acidic pH is characterized by a rigidification and compaction of the Asp and Glu‐rich C‐terminal region, an increased probability for proximity between the NAC‐region and the C‐terminal region and a lower probability for interactions between the N‐ and C‐terminal regions.     

Crystal structure of the N‐terminal methyltransferase‐like domain of anamorsin

Anamorsin is a recently identified molecule that inhibits apoptosis during hematopoiesis. It contains an N‐terminal methyltransferase‐like domain and a C‐terminal Fe‐S cluster motif. Not much is known about the function of the protein. To better understand the function of anamorsin, we have solved the crystal structure of the N‐terminal domain at 1.8 Å resolution. Although the overall structure resembles a typical S‐adenosylmethionine (SAM) dependent methyltransferase fold, it lacks one α‐helix and one β‐strand. As a result, the N‐terminal domain as well as the full‐length anamorsin did not show S‐adenosyl‐l ‐methionine (AdoMet) dependent methyltransferase activity. Structural comparisons with known AdoMet dependent methyltransferases reveals subtle differences in the SAM binding pocket that preclude the N‐terminal domain from binding to AdoMet. The N‐terminal methyltransferase‐like domain of anamorsin probably functions as a structural scaffold to inhibit methyl transfers by out‐competing other AdoMet dependant methyltransferases or acts as bait for protein–protein interactions.Proteins 2014; 82:1066–1071. © 2013 Wiley Periodicals, Inc.     

大肠杆菌的蛋白分泌机制

大肠杆菌的分泌蛋白定位于内膜、外膜、周质空间和胞外环境,它们在N端或C端带有一定的结构包含着分泌信号,这两类分泌蛋白在各自特定的一组蛋白因子的协助下跨越内膜,再通过目前尚不清楚的方式实现其最终定位.N端带有信号肽的分子在跨越内膜时得到Sec家族蛋白因子协助,信号肽在跨膜过程中可能被切除,该过程由ATP和电化学势提供能量.C端带分泌信号的分子主要受到Hly家族分子协助,一次穿过内膜和外膜而不经过周质空间.     

Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution.

Lactoferrin is a monomeric glycoprotein with a molecular mass of approximately 80 kDa. The three-dimensional structure of mare diferric lactoferrin (mlf) has been determined at 2.6 A resolution. The protein crystallizes in the space group P 212121with a=85.2 A, b=99.5 A, c=103.1 A with a solvent content of 55 % (v/v). The structure was solved by the molecular replacement method using human diferric lactoferrin as the model. The structure has been refined using XPLOR to a final R -factor of 0.194 for all data in the 15-2.6 A resolution range. The amino acid sequence of mlf was determined using a cDNA method. The final refined model comprises 5281 protein atoms, 2 Fe3+, 2 CO32-and 112 water molecules. The overall folding of mlf is similar to that of other proteins of the transferrin family. The protein folds into two globular lobes, N and C. The lobes are further divided into two domains, N1 and N2, and C1 and C2. The iron-binding cleft is situated between the domains in each lobe. The N lobe appears to be well ordered and is more stable than the C lobe in mlf unlike in other lactoferrins, where the C lobe is the more stable. The opening of the binding cleft in the N lobe of mlf is narrower than those in other proteins of the transferrin family. This is very unusual and is found only in mare lactoferrin. Apart from certain hydrophobic interactions at the mouth of the cleft, one salt-bridge (Lys301 . . . . . . . . Glu216) crosses between the two walls of the cleft. The two lobes are connected covalently by a three-turn alpha-helix involving residues 334-344. The N lobe displays a highly ordered structure with appreciably low temperature factors. The iron coordination is more symmetrical in the N lobe than in the C lobe. There are only 16 intermolecular hydrogen bonds in the structure of mlf.     

Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A

Despite extensive study, the molecular structure of the chromophore-binding pocket of phytochrome A (phyA), the principal photoreceptor controlling photomorphogenesis in plants, has not yet been successfully resolved. Here, we report a series of two-dimensional (2-D) magic-angle spinning solid-state NMR experiments on the recombinant N-terminal, 65-kDa PAS-GAF-PHY light-sensing module of phytochrome A3 from oat (Avena sativa), assembled with uniformly 13C- and 15N-labeled phycocyanobilin (u-[13C,15N]-PCB-As.phyA3). The Pr state of this protein was studied regarding the electronic structure of the chromophore and its interactions with the proximal amino acids. Using 2-D 13C-13C and 1H-15N experiments, a complete set of 13C and 15N assignments for the chromophore were obtained. Also, a large number of 1H-13C distance restraints between the chromophore and its binding pocket were revealed by interfacial heteronuclear correlation spectroscopy. 13C doublings of the chromophore A-ring region and the C-ring carboxylate moiety, together with the observation of two Pr isoforms, Pr-I and Pr-II, demonstrate the local mobility of the chromophore and the plasticity of its protein environment. It appears that the interactions and dynamics in the binding pocket of phyA in the Pr state are remarkably similar to those of cyanobacterial phytochrome (Cph1). The N-terminus of the region modeled (residues 56-66 of phyA) is highly mobile. Differences in the regulatory processes involved in plant and Cph1 phytochromes are discussed.