Biomedical subjects

Linxi Zhang

Publications and source records attributed to Linxi Zhang.

9 recordsLinked to original sources

PubMed2005

Folding rate prediction using n-order contact distance for proteins with two- and three-state folding kinetics.

It is a challenging task to understand the relationship between sequences and folding rates of proteins. Previous studies are found that one of contact order (CO), long-range order (LRO), total contact distance (TCD), chain topology parameter (CTP), and effective length (Leff) has a significant correlation with folding rate of proteins. In this paper, we introduce a new parameter called n-order contact distance (nOCD) and use it to predict folding rate of proteins with two- and three-state folding kinetics. A good linear correlation between the folding rate logarithm lnkf and nOCD with n=1.2, alpha=0.6 is found for two-state folders (correlation coefficient is -0.809, P-value<0.0001) and n=2.8, alpha=1.5 for three-state folders (correlation coefficient is -0.816, P-value<0.0001). However, this correlation is completely absent for three-state folders with n=1.2, alpha=0.6 (correlation coefficient is 0.0943, P-value=0.661) and for two-state folders with n=2.8, alpha=1.5 (correlation coefficient is -0.235, P-value=0.2116). We also find that the average number of contacts per residue Pm in the interval of m for two-state folders is smaller than that for three-state folders. The probability distribution P(gamma) of residue having gamma pairs of contacts fits a Gaussian distribution for both two- and three-state folders. We observe that the correlations between square radius of gyration S2 and number of residues for two- and three-state folders are both good, and the correlation coefficient is 0.908 and 0.901, and the slope of the fitting line is 1.202 and 0.795, respectively. Maybe three-state folders are more compact than two-state folders. Comparisons with nTCD and nCTP are also made, and it is found that nOCD is the best one in folding rate prediction.

Databases, Protein↗

PubMed2004

Elastic behavior of adsorbed polymer chains.

Elastic behaviors of single polymer chains adsorbed on the attractive surface are first investigated using Monte Carlo simulation method based on the bond fluctuation model. We investigate the chain size and shape of adsorbed chains, such as mean-square radius of gyration S2, mean-square bond length b2, shape factors sf(i) and delta*, and the orientation of chain segments P2 , to illuminate how the shape of polymer chains changes during the process of tensile elongation. There are some special behaviors of the chain size and shape at the beginning of elongation, especially for strong attraction interaction. For example, mean fraction of adsorbed segments decreases abruptly in the region of small elongation ratio and then decreases slowly with increasing elongation ratio. In fact, the chain size and shape also changes abruptly for small elongation ratio with strong attraction interaction. Some thermodynamics properties are also investigated here. Average Helmholtz free energy increases fast for elongation ratio lambda<1.15, especially with strong attraction, and increases slowly for lambda>1.15. Similar behaviors are obtained for average energy per bond. Elastic force (f ) and energy contribution to force (f(U)) are also studied, and we find that elastic force decreases abruptly for lambda<1.15, and there is a minimum of elastic force for strong attraction interaction, then increases very slowly with increasing elongation ratio. However, there are different behaviors for weak attraction interaction. For energy contribution to force (f(U)), there is a maximum value for strong attraction interaction in the region of lambda<1.15. Some comparisons with the atomic force microscopy experiments are also made. These investigations may provide some insights into the elastic behaviors of adsorbed polymer chains.

Journal Article↗

PubMed2004

Elastic behavior of short compact polymers.

In this paper, we investigate the elastic behaviors of short compact polymers using the enumeration calculation method and the HP model on a two-dimensional square lattice. Both the mean-square end-to-end distance R(2) and the ratio of R(2)/S(2) increase with lambda. However, when the elongation ratio becomes larger, the curves of R(2)/S(2) become smooth and they are close to the limit of 10.50 for different compact polymers. We also investigate the changes of interior conformations in the process of tensile elongation through calculating the probabilities of three bond angles (i.e., 90 degrees, 180 degrees, and 270 degrees). The average energy and Helmholtz free energy per bond are both negative and increase with elongation ratio lambda. In the meantime, the elastic force per bond (f ) also increases with elongation ratio lambda, and the energy contribution to the elastic force (f(U)) increases first and then drops, and there exists the maximum of f(U) in the region of lambda=1.40-1.80 for different sequences. The entropy contribution to force (f(S)) is close to zero at a small elongation ratio lambda and then increases with lambda. Some comparisons with different sequences (including nonfolding and folding sequences) are also made.

Journal Article↗

PubMed2003

Predicting protein structure from long-range contacts.

Short-range and long-range contacts are important in forming protein structure. The proteins can be grouped into four different structural classes according to the content and topology of alpha-helices and beta-strands, and there are all-alpha, all-beta, alpha/beta and alpha+beta proteins. However, there is much difference in statistical property for those classes of proteins. In this paper, we will discuss protein structure in the view of the relative number of long-range (short-range) contacts for each residue. We find the percentage of residues having a large number of long-range contacts in protein is small in all-alpha class of proteins, and large in all-beta class of proteins. However, the percentage of residues is almost the same in alpha/beta and alpha+beta classes of proteins. We calculate the percentage of residues having the number of long-range contacts greater than or equal to (>/=) N(L)=5, and 7 for 428 proteins. The average percentage is 13.3%, 54.8%, 41.4% and 37.0% for all-alpha, all-beta, alpha/beta and alpha+beta classes of proteins with N(L)=5, respectively. With N(L) increasing, the percentage decreases, especially for all-alpha class of proteins. In the meantime, the percentage of residues having the number of short-range contacts greater than or equal to N(S) (>/=N(S)) in protein samples is large for all-alpha class of proteins, and small for all-beta class of proteins, especially for large N(S). We also investigate the ability of amino residues in forming a large number of long-range and short-range contacts. Cys, Val, Ile, Tyr, Trp and Phe can form a large number of long-range contacts easily, and Glu, Lys, Asp, Gln, Arg and Asn can form a large number of long-range contacts, but with difficulty. We also discuss the relative ability in forming short-range contacts for 20 amino residues. Comparison with Fauchere-Pliska hydrophobicity scale and the percentage of residues having large number of long-range contacts is also made. This investigation can provide some insights into the protein structure.

Amino Acids↗

PubMed2002

[Quantitive detection of multi-gene expressions and DNA content in the precancerous cells of esophageal carcinoma].

OBJECTIVE: To explore the molecular events and mechanism in the carcinogenesis of esophageal epithelium in the high incidence area of esophageal carcinoma. METHODS: Epithelial cells collected from the high incidence area of esophageal carcinoma were used to detect DNA content and ploidy by propidium iodide(PI) stain. The expressions of p53, p16 and cyclin D1 were stained by indirect immunofluorescence of fluorescein isothiocyanate(FTTC), which were detected by flow cytometry (FCM). RESULTS: During the process of carcinogenesis, DNA content increased significantly. The diploid cells decreased while heteroploid cells increased sharply, with a heteroploidy rate of 84.2%. At the same time, the p53 protein accumulated and p16 was deleted. The positive rates of p53 and oncogene cyclin D1 were both 100%(5/5, 6/6) in the cancer group. CONCLUSION: In the early carcinogenesis of esophageal epithelium, DNA content and heteroploidy rates increase with tumor suppressor gene p16 deletion and p53 protein accumulation while oncogene cyclin D1 is overexpressed. Multiple molecular events have already occurred when esophageal carcinoma develops.

Cyclin D1↗

PubMed2002

[Effects of conditioned medium derived from different keratinocytes on proliferation and collagen synthesis of hypertrophic scar fibroblasts].

OBJECTIVE: To observe the effects of supernatants of normal skin keratinocytes(NK) and scar keratinocytes(SK) on proliferation and collagen synthesis of hypertrophic scar fibroblasts(HSFB). METHODS: The supernatant, collected from cultured NK and SK, was added to the cultivated HSFB. The MTT-method, 3H-proline incorporation and radioimmunoassay were employed to measure the cell proliferation, collagen synthesis and secretion. RESULTS: NK supernatant could inhibit HSFB proliferation and increase the collagen synthesis, but inhibit collagen secretion, as compared with the control group. On the contrary, SK supernatant could increase collagen synthesis and secretion, which had little effects on HSFB proliferation. CONCLUSION: Keratinocytes derived from normal skin and hypertrophic scar show different effects on hypertrophic scar fibroblasts.

Cell Division↗

PubMed2002

[The influence of Matrine on apoptosis of fibroblasts and the expression of apoptotic modulation related protein in hypertrophic scar of rabbit ear].

OBJECTIVE: To investigate the effects of Matrine on apoptosis of fibroblasts and the expression of apoptotic modulation related protein in the hypertrophic scar. METHODS: Hypertrophic scar was produced on the ear of 24 New Zealand white rabbits, which were employed as the model, and were randomly and equally divided into control (CC) and Matrine (M) groups (12 in each group). Matrine (50 g/L) was injected into the ear scar in M group and with normal saline in C group once every four days. At 2, 4, 6, 8 and 12 weeks after the injection, the apoptotic fibroblast count in the scar was determined by TUNEL method, and the expressions of apoptosis related modulation proteins p53, bcl-2, bax were detected by immunohistochemistry method. RESULTS: The apoptotic fibroblast count was much larger in M group than that in C group at all test time points (P < 0.05). Furthermore, the bax expression was increased and that of p53 and bcl-2 was decreased significantly in M group. In adding, the scar became flat in M group. CONCLUSION: Matrine might obviously enhance the fibroblast apoptosis in rabbit ear hypertrophic scar, and up-regulate the expression of apoptosis related modulation protein bax and down-regulate the expression of p53 and Bcl-2.

Alkaloids↗

PubMed2002

[The expanded distant skin flap and its application].

OBJECTIVE: To summarize and present the experiences and results of the expanded distant skin flaps used in plastic and reconstructive operations. METHODS: 102 patients who had undergone expanded distant skin flap transfer were reviewed and followed up. RESULTS: Good results were obtained. Especially when there was no sufficient normal skin close to the lesion or defect, the distant skin flaps were employed. The expanded distant skin flap can be directly transferred as a pedicle skin flap or an island skin flap. It can be indirectly transferred with an intermediary carrier or as a free skin flap. CONCLUSION: The expanded distant skin flaps have many advantages, indications, worthy of recommendation.

Humans↗

PubMed2002

[Influence of endothelial cells on the proliferation of scar-derived fibroblast in hypertropic scar tissue].

OBJECTIVE: To investigate the influence of the endothelial cells on the scar-derived fibroblasts in the hypertropic scar tissue. METHODS: The endothelial cell from the human umbilical vein was cultured and its supernatant was then collected. Thereafter, it was mixed with the pre-cultured scar-derived fibroblasts from the hypertropic scar tissue. The fibroblasts were analyzed with a flow cytometer in a MTT-assay method to evaluate the cell proliferation and its division cycle. RESULTS: The endothelial cells were significantly increasing the scar-derived fibroblast proliferation (P < 0.05), compared with the control. The proportion of the fibroblasts in the S-stage of cell cycle was also quite high. CONCLUSION: The endothelial cells may secrete some active products, which may enhance the proliferation of the scar-derived fibroblasts and stimulate the fibroblasts into the S-stage of cell generation cycle.

Cell Cycle↗