Biomedical subjects

Jie Liang

Publications and source records attributed to Jie Liang.

At least 37 records · Page 2Linked to original sources

PubMed2005

Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction.

beta-Barrel membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Little is known about how residues in membrane beta-barrels interact preferentially with other residues on adjacent strands. We have developed probabilistic models to quantify propensities of residues for different spatial locations and for interstrand pairwise contact interactions involving strong H-bonds, side-chain interactions, and weak H-bonds. Using the reference state of exhaustive permutation of residues within the same beta-strand, the propensity values and p-values measuring statistical significance are calculated exactly by analytical formulae we have developed. Our findings show that there are characteristic preferences of residues for different membrane locations. Contrary to the "positive-inside" rule for helical membrane proteins, beta-barrel membrane proteins follow a significant albeit weaker "positive-outside" rule, in that the basic residues Arg and Lys are disproportionately favored in the extracellular cap region and disfavored in the periplasmic cap region. We find that different residue pairs prefer strong backbone H-bonded interstrand pairings (e.g. Gly-aromatic) or non-H-bonded pairings (e.g. aromatic-aromatic). In addition, we find that Tyr and Phe participate in aromatic rescue by shielding Gly from polar environments. We also show that these propensities can be used to predict the registration of strand pairs, an important task for the structure prediction of beta-barrel membrane proteins. Our accuracy of 44% is considerably better than random (7%). It also significantly outperforms a comparable registration prediction for soluble beta-sheets under similar conditions. Our results imply several experiments that can help to elucidate the mechanisms of in vitro and in vivo folding of beta-barrel membrane proteins. The propensity scales developed in this study will also be useful for computational structure prediction and for folding simulations.

Amino Acids, Aromatic↗

PubMed2005

Dual-specificity phosphatase DUSP1 protects overactivation of hypoxia-inducible factor 1 through inactivating ERK MAPK.

Hypoxia-inducible factor 1 (HIF-1) plays a critical role in controlling oxygen delivery and metabolic adaptation to hypoxic conditions in hypoxic tumor cells. HIF-1 activation is initiated by several factors including mitogen-activated protein kinase (MAPK) superfamily. We have previously reported that mitogen-activated protein kinase phosphatase DUSP1 (MKP-1) was implicated in the negative regulation of HIF-1alpha subunit phosphorylation and HIF-1 activity. However, the molecular basis by which MKP-1 influences HIF-1 activity is not clarified. In this paper, we show that hypoxia transcriptionally induces MKP-1 expression in a time-dependent manner. Meanwhile, hypoxia also activates extracellular signal-regulated kinase (ERK) whose activity is enhanced or reduced by MKP-1 suppression or MKP-1 overexpression, respectively. We also show that suppression of MKP-1 expression facilitates the interaction between HIF-1alpha subunit and p300, a co-activator of HIF-1. Moreover, MKP-1 suppression leads to enhanced HIF-1 activity, which can be counteracted by PD98059, an ERK kinase inhibitor. Taken together, the results presented here suggest that hypoxia-induced MKP-1 protects overactivation of HIF-1 activation through inhibiting ERK kinase activity.

Cell Cycle Proteins↗

PubMed2005

[Inhibition of the in vitro interaction between hypoxia inducible factor 1alpha and p300 by mitogen-activated protein kinase phosphatase 1].

OBJECTIVE: To investigate the effects of mitogen-activated protein kinase phosphatase-1 (MKP-1) on the interaction between hypoxia-inducible factor (HIF)-1alpha and coactivator p300. METHODS: Prokaryotic expression vector PGEX-4T1 was constructed based on DNA recombination technology. GST fusion proteins were purified by glutathione-agarose beads and transfected into Escherichia coli BL-21. Effects of MKP-1 or PD98059 on in vitro interaction between HIF-1alpha and p300 was determined by Pull-down assay coupled with Western bloting. Effects of MKP-1 on the p300 expression level was detected using Western bloting. RESULTS: (1) GST fusion proteins were expressed in BL-21 Escherichia coli and purified proteins were obtained. (2) Less amount of p300 was pulled down by GST fusion protein from SGC7901-MKP-1 cells than from control cells after 12 hours of exposure to hypoxia. (3) 12 hours after hypoxia, Less amount of p300 was pulled down by GST fusion protein from PD98059 treated cells than from DMSO treated cells or SGC7901 cells. (4) There were no significant differences in p300 expression levels between recombinant MKP-1 transfected cells and control cells after 12 hours of exposure to hypoxia. CONCLUSION: MKP-1 inhibits the in vitro interaction between HIF-1alpha and p300.

Cell Hypoxia↗

PubMed2005

Geometric cooperativity and anticooperativity of three-body interactions in native proteins.

Characterizing multibody interactions of hydrophobic, polar, and ionizable residues in protein is important for understanding the stability of protein structures. We introduce a geometric model for quantifying 3-body interactions in native proteins. With this model, empirical propensity values for many types of 3-body interactions can be reliably estimated from a database of native protein structures, despite the overwhelming presence of pairwise contacts. In addition, we define a nonadditive coefficient that characterizes cooperativity and anticooperativity of residue interactions in native proteins by measuring the deviation of 3-body interactions from 3 independent pairwise interactions. It compares the 3-body propensity value from what would be expected if only pairwise interactions were considered, and highlights the distinction of propensity and cooperativity of 3-body interaction. Based on the geometric model, and what can be inferred from statistical analysis of such a model, we find that hydrophobic interactions and hydrogen-bonding interactions make nonadditive contributions to protein stability, but the nonadditive nature depends on whether such interactions are located in the protein interior or on the protein surface. When located in the interior, many hydrophobic interactions such as those involving alkyl residues are anticooperative. Salt-bridge and regular hydrogen-bonding interactions, such as those involving ionizable residues and polar residues, are cooperative. When located on the protein surface, these salt-bridge and regular hydrogen-bonding interactions are anticooperative, and hydrophobic interactions involving alkyl residues become cooperative. We show with examples that incorporating 3-body interactions improves discrimination of protein native structures against decoy conformations. In addition, analysis of cooperative 3-body interaction may reveal spatial motifs that can suggest specific protein functions.

Computer Simulation↗

PubMed2005

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins.

Characterizing the interactions between amino acid residues and lipid molecules is important for understanding the assembly of transmembrane helices and for studying membrane protein folding. In this study we develop TMLIP (TransMembrane helix-LIPid), an empirically derived propensity of individual residue types to face lipid membrane based on statistical analysis of high-resolution structures of membrane proteins. Lipid accessibilities of amino acid residues within the transmembrane (TM) region of 29 structures of helical membrane proteins are studied with a spherical probe of radius of 1.9 A. Our results show that there are characteristic preferences for residues to face the headgroup region and the hydrocarbon core region of lipid membrane. Amino acid residues Lys, Arg, Trp, Phe, and Leu are often found exposed at the headgroup regions of the membrane, where they have high propensity to face phospholipid headgroups and glycerol backbones. In the hydrocarbon core region, the strongest preference for interacting with lipids is observed for Ile, Leu, Phe and Val. Small and polar amino acid residues are usually buried inside helical bundles and are strongly lipophobic. There is a strong correlation between various hydrophobicity scales and the propensity of a given residue to face the lipids in the hydrocarbon region of the bilayer. Our data suggest a possibly significant contribution of the lipophobic effect to the folding of membrane proteins. This study shows that membrane proteins have exceedingly apolar exteriors rather than highly polar interiors. Prediction of lipid-facing surfaces of boundary helices using TMLIP1 results in a 54% accuracy, which is significantly better than random (25% accuracy). We also compare performance of TMLIP with another lipid propensity scale, kPROT, and with several hydrophobicity scales using hydrophobic moment analysis.

Amino Acids↗

PubMed2005

ZNRD1 gene suppresses cell proliferation through cell cycle arrest in G1 phase.

ZNRD1, a transcription-associated gene, was recently found in our laboratory significantly suppress the cell proliferation of stomach cancer cells in vitro and in vivo. In this study, we firstly characterized ZNRD1 expression in a wide spectrum of gastric diseases by immunohistochemistry and RT-PCR. We also investigated its antiproliferative effects and associated molecular alterations in human gastric cancer cell line AGS and mouse fibroblast cell line NIH3T3. Anti-ZNRD1 monoclonal antibody H6 was found to react with 38 (63%) of normal gastric tissues, and 51 (81%) of gastritis. In contrast, no positive expression was found in gastric adenocarcinomas. Thus, the expression of ZNRD1 in normal gastric tissues was significantly higher than that in gastric adenocarcinomas. Compared with the control clones, ZNRD1-transfected cells exhibited significant inhibition of cell growth with G1 cell cycle arrest mediated by the suppression of cyclin D1 expression. These results showed that ZNRD1 may play an important role in the regulation of gastric carcinogenesis and could be used as a new target in treatment of stomach cancer.

Adenocarcinoma↗

PubMed2005

The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect.

Membrane proteins have important roles in many cellular processes. Computational analysis of their sequences and structures has provided much insight into the organizing principles of transmembrane helices. In a recent study, the membrane-water interface region was examined in detail for the first time. The results have revealed that this interface region has an important role in constraining protein secondary structure. This study raises new questions and opens up new directions for studying membrane proteins.

Cell Membrane↗

PubMed2005

Optimal block boundary pre/postfiltering for wavelet-based image and video compression.

This paper presents a pre/postfiltering framework to reduce the reconstruction errors near block boundaries in wavelet-based image and video compression. Two algorithms are developed to obtain the optimal filter, based on boundary filter bank and polyphase structure, respectively. A low-complexity structure is employed to approximate the optimal solution. Performances of the proposed method in the removal of JPEG 2000 tiling artifact and the jittering artifact of three-dimensional wavelet video coding are reported. Comparisons with other methods demonstrate the advantages of our pre/postfiltering framework.

Algorithms↗

PubMed2005

Protein surface analysis for function annotation in high-throughput structural genomics pipeline.

Structural genomics (SG) initiatives are expanding the universe of protein fold space by rapidly determining structures of proteins that were intentionally selected on the basis of low sequence similarity to proteins of known structure. Often these proteins have no associated biochemical or cellular functions. The SG success has resulted in an accelerated deposition of novel structures. In some cases the structural bioinformatics analysis applied to these novel structures has provided specific functional assignment. However, this approach has also uncovered limitations in the functional analysis of uncharacterized proteins using traditional sequence and backbone structure methodologies. A novel method, named pvSOAR (pocket and void Surface of Amino Acid Residues), of comparing the protein surfaces of geometrically defined pockets and voids was developed. pvSOAR was able to detect previously unrecognized and novel functional relationships between surface features of proteins. In this study, pvSOAR is applied to several structural genomics proteins. We examined the surfaces of YecM, BioH, and RpiB from Escherichia coli as well as the CBS domains from inosine-5'-monosphate dehydrogenase from Streptococcus pyogenes, conserved hypothetical protein Ta549 from Thermoplasm acidophilum, and CBS domain protein mt1622 from Methanobacterium thermoautotrophicum with the goal to infer information about their biochemical function.

Adenine Nucleotides↗

PubMed2005

Computational design of combinatorial peptide library for modulating protein-protein interactions.

Screening phage-displayed combinatorial peptide library is an effective approach for discovery of peptide modulators for protein-protein interactions. However, as peptide length increases, the chance of finding active peptides in a finite size library diminishes. To increase the likelihood of finding peptides that bind to a protein, we develop statistical potential for computational construction of biased combinatorial antibody-like peptide libraries. Based on the alpha shapes of antibody-antigen complexes, we developed an empirical pair potential for antigen-antibody interactions that depends on local packing. We validate this potential and show that it can successfully discriminate the native interface peptides from a simulated library of 10,000 random peptides for 34 antigen-antibody complexes. In addition, we show that it can successfully recognize the native binding surface patch among all possible surface patches taken from either the antibody or the antigen for seven antibody-antigen protein complexes contained in the CAPRI (Critical Assessment of Predicted Interactions) dataset. We then develop a Weighted Amino Acid Residue sequence Generator (WAARG) for design of biased peptide library. When compared with a random peptide library, WAARG libraries contain more native-like binding peptides at a significantly smaller size. Our method can be used to construct peptide library for screening of antibody variants with improved specificity and affinity to a target antigen. It can also be used for screening of antibody-like antagonist peptides modulating other protein-protein interactions.

Amino Acid Sequence↗

PubMed2005

[Chromosomal aberration in human keloid analyzed by comparative genomic hybridization].

OBJECTIVE: To identify the genetic alteration in human keloid. METHODS: Comparative genomic hybridization was applied in 6 cases of keloid to investigate the genomic imbalance (the gain or loss of genetic material). RESULTS: The study showed that the loss of chromosome DNA copies included chromosome, 1,7,9,13,16,17,18,19,20,22. Among them, the frequently detected chromosome loss was chromosome 1 p(66.7%), 16 (83.3%), 20 (83.3%) and 22 (83.3%). The minimum overlapping regions were 1 pter-32.2,16p13.2p11.l,20q11.1-q13.2 and 16p13.2-p11.1. Frequent gain of DNA copy numbers was not found in the special regions. CONCLUSIONS: The mapping of DNA copy variation frequency in keloid showed that there may be inhibitory genes in chromosomes 1p,16,20,22. The loss of these genes may be involved in the development and progress of keloid.

Adult↗

PubMed2005

[The function of basic fibroblastic growth factor on revascularization of pearl fat graft transplantation].

OBJECTIVE: To investigate the function of basic fibroblastic growth factor on the survival of fat transplantation. METHODS: Basic fibroblastic growth factor was used in pearl fat graft transplantation on experimental animal models. Microvessels densities both on experimental sides and control sides were quantitatively researched in various periods. The growth course of vessels was observed. RESULTS: Microvessels can be observed clearly. The Microvessels densities both on experimental sides and control sides raised gradually. The density reached highest in 14 days on experimental side and in 28 days on control side, and fell down slightly later. The densities on every experimental sides were higher than that on control sides. CONCLUSIONS: Basic fibroblastic growth factor can effectually accelerate the growth of blood vessels in pearl fat graft.

Adipose Tissue↗

PubMed2005

[Repair of upper lip defects with an island flap based on the inferior labial arterial arch].

OBJECTIVE: To investigate one-stage repairing upper lip defects with an island flap based on the inferior labial arterial arch. METHODS: An island flap pedicled with the inferior labial arterial arch was used to repair upper lip defects. The size of the wedge-shaped flap ranged from 1.5 cm x 1.5 cm to 1.5 cm x 2.0 cm. Since 1993, fifteen patients with upper lip defects have been treated with this method. RESULTS: All the flaps survived with satisfactory function and appearance. CONCLUSIONS: The island flap of the inferior labial arterial arch is effective and applicable in repairing severe secondary deformities of congenital bilateral cleft lips.

Adolescent↗

PubMed2004

Membrane-associated and secreted genes in breast cancer.

The identification of membrane-associated and secreted genes that are differentially expressed is a useful step in defining new targets for the diagnosis and treatment of cancer. Extracting information on the subcellular localization of genes represented on DNA microarrays is difficult and is limited by the incomplete sequence and annotation that is available in existing databases. Here we combine a biochemical and bioinformatic approach to identify membrane-associated and secreted genes expressed in the MCF-7 breast cancer cell line. Our approach is based on the analysis of differential hybridization levels of RNAs that have been physically separated by virtue of their association with polysomes on the endoplasmic reticulum. This approach is specifically applicable to oligonucleotide microarrays such as Affymetrix, which use single-color hybridization instead of dual-color competitive hybridizations. Assignment to membrane-associated and secreted class membership is based on both the differential hybridization levels and an expression threshold, which are calculated empirically from data collected on a reference set of known cytoplasmic and membrane proteins. This method enabled the identification of 755 membrane-associated and secreted probe sets expressed in MCF-7 cells for which this annotation did not previously exist. The data were used to filter a previously reported expression dataset to identify membrane-associated and secreted genes which are associated with poor prognosis in breast cancer and represent potential targets for diagnosis and treatment. The approach reported here should provide a useful tool for the analysis of gene expression patterns, identifying membrane-associated or secreted genes with biological relevance that have the potential for clinical applications in diagnosis or treatment.

Breast Neoplasms↗

PubMed2004

Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.

Energetic hot spots account for a significant portion of the total binding free energy and correlate with structurally conserved interface residues. Here, we map experimentally determined hot spots and structurally conserved residues to investigate their geometrical organization. Unfilled pockets are pockets that remain unfilled after protein-protein complexation, while complemented pockets are pockets that disappear upon binding, representing tightly fit regions. We find that structurally conserved residues and energetic hot spots are strongly favored to be located in complemented pockets, and are disfavored in unfilled pockets. For the three available protein-protein complexes with complemented pockets where both members of the complex were alanine-scanned, 62% of all hot spots (DeltaDeltaG>2kcal/mol) are within these pockets, and 60% of the residues in the complemented pockets are hot spots. 93% of all red-hot residues (DeltaDeltaG>/=4kcal/mol) either protrude into or are located in complemented pockets. The occurrence of hot spots and conserved residues in complemented pockets highlights the role of local tight packing in protein associations, and rationalizes their energetic contribution and conservation. Complemented pockets and their corresponding protruding residues emerge among the most important geometric features in protein-protein interactions. By screening the solvent, this organization shields backbone hydrogen bonds and charge-charge interactions. Complemented pockets often pre-exist binding. For 18 protein-protein complexes with complemented pockets whose unbound structures are available, in 16 the pockets are identified to pre-exist in the unbound structures. The root-mean-squared deviations of the atoms lining the pockets between the bound and unbound states is as small as 0.9A, suggesting that such pockets constitute features of the populated native state that may be used in docking.

Models, Molecular↗

PubMed2004

Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models.

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.

Computer Simulation↗

PubMed2004

pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino acid Residues) provides an online resource to identify similar protein surface regions. pvSOAR can take a structure either uploaded by a user or obtained from the Protein Data Bank, and identifies similar surface patterns based on geometrically defined pockets and voids. It provides several search modes to compare protein surfaces by similarity in local sequence, local shape and local orientation. Statistically significant search results are reported for visualization and interactive exploration. pvSOAR can be used to predict biological functions of proteins with known three-dimensional structures but unknown biological roles. It can also be used to study functional relationship between proteins and for exploration of the evolutionary origins of structural elements important for protein function. We present an example using pvSOAR to explore the biological roles of a protein whose structure was solved by the structural genomics project. The pvSOAR web server is available at http://pvsoar.bioengr.uic.edu/.

Amino Acids↗

PubMed2004

Developing optimal non-linear scoring function for protein design.

UNLABELLED: Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitness landscape of many proteins simultaneously. RESULTS: To find optimal design scoring functions, we introduce two geometric views and propose a formulation using a mixture of non-linear Gaussian kernel functions. We aim to solve a simplified protein sequence design problem. Our goal is to distinguish each native sequence for a major portion of representative protein structures from a large number of alternative decoy sequences, each a fragment from proteins of different folds. Our scoring function discriminates perfectly a set of 440 native proteins from 14 million sequence decoys. We show that no linear scoring function can succeed in this task. In a blind test of unrelated proteins, our scoring function misclassfies only 13 native proteins out of 194. This compares favorably with about three-four times more misclassifications when optimal linear functions reported in the literature are used. We also discuss how to develop protein folding scoring function.

Algorithms↗