[Association of urinary cadmium levels with peripheral leukocyte classification counts among middle-aged and older adults aged 40-89 in selected areas of China].

Objective: To investigate the association of urinary cadmium levels with peripheral leukocyte classification counts among middle-aged and older adults aged 40 to 89 years in selected areas of China. Methods: The research was based on the survey of the impact of soil quality of agricultural land on human health in typical areas conducted in 2019-2020. A total of 5 600 middle-aged and older adults aged 40 to 89 years were included by using a multi-stage stratified random sampling method. Baseline characteristics of the subjects were collected and physical examinations were performed. Random midstream urine was collected to measure urinary cadmium and urinary creatinine and fasting venous blood was collected to measure the leukocyte count, neutrophil count, lymphocyte count, monocyte count and eosinophil count. The linear mixed effect model was used to analyse the association of urinary cadmium levels with leukocyte classification counts, and the dose-response relationship between them was analyzed by using the restricted cubic spline (RCS) function. Results: The age of the subjects was (63.17±12.02) years; 2 851 (50.91%) were males; and the M (Q1, Q3) of urinary creatinine-corrected urinary cadmium levels was 2.69 (1.52, 4.69) µg/g·creatinine. After adjusting for confounding factors, the results of linear mixed effects model analysis showed that for each 1-unit increase in urinary creatinine-corrected urinary cadmium level, the percentage change [% (95%CI)] of leukocyte count and lymphocyte count was -1.70% (-2.61%, -0.79%) and -1.57% (-2.86%, -0.26%), respectively. RCS function showed a negative linear relationship between urinary creatinine-corrected urinary cadmium levels and leukocyte counts and lymphocyte counts, respectively (all Pnon-linear>0.05). Conclusion: Urinary cadmium levels are negatively associated with leukocyte count and lymphocyte count among middle-aged and older adults aged 40 to 89 years in selected areas of China.

Paeonol impacts ovarian cancer cell proliferation, migration, invasion and apoptosis via modulating the transforming growth factor beta/smad3 signaling pathway.

Paeonol (2-hydroxy-4-methoxyphenylacetophenone) is a natural phenolic component isolated from the root bark of peony with multiple pharmacological activities and has been proven to have anti-cancer effects. The objective of this study is to investigate the influence mechanism of paeonol on the proliferatory and apoptotic activities of ovarian cancer (OC) cells by modulating the transforming growth factor beta (TGF-ß)/Smad3 pathway. The SKOV3 cells were pretreated with various concentrations of paeonol (0, 25, 50, 100, 200, 400 µg/mL) for 48 hours to determine the optimal experimental concentration of paeonol. Following this, the TGF-ß overexpression vector was constructed and transfected into the SKOV3 cells. The assessment of cell proliferation, invasion, and migration was conducted through MTT, colony formation, flow cytometry, transwell, and wound-healing experiments. The detection of TGF-ß/Smad3 pathway-related proteins and apoptosis-related proteins (B-cell lymphoma (Bcl-2) Bcl-2-associated X protein (Bax)) was performed using Western blot analysis. Paeonol exhibited a significant inhibitory effect on SKOV3 cell viability when administered at concentrations ranging from 50-400 µg/mL, with an IC50 value of 200 µg/mL. Within the concentration range of 50 to 200 µg/mL, paeonol exhibited a dose-dependent effect on the progression of SKOV3 cells, including a reduction in the anti-apoptotic protein Bcl-2, an increase in the pro-apoptotic protein Bax (P<0.05), inhibition of cell migration and invasion (P<0.05), and promotion of cell apoptosis (P<0.05), particularly at a concentration of 200 µg/mL. These effects were found to be more pronounced. The aforementioned effects of paeonol can be ascribed to its inhibition of the TGFß/Smad3 pathway, according to a mechanistic viewpoint. It is noteworthy that the inhibitory impact of paeonol on SKOV3 cell progression is counteracted by the elevation of TGF-ß levels following overexpression. We conclude that paeonol exerts regulatory effects on the TGF-ß/Smad3 pathway, leading to the inhibition of proliferation, migration, and invasion of OC cells, thereby attenuating malignant behavior of cancer cells.

Prognostic nutritional index as a prognostic factor in lung cancer patients receiving chemotherapy: a systematic review and meta-analysis.

OBJECTIVE: Lung cancer is one of the leading causes of morbidity and mortality in the world. In the past decade, numerous studies focus on the prognostic nutritional index (i.e., a measure of serum albumin and lymphocyte in peripheral circulation) as a possible biomarker to predict the survival outcomes in cancer patients undergoing chemotherapy. Prognostic nutritional index can reliably predict the survivability outcomes by effectively quantifying the nutritional and immunological status of cancer patients. To date, only one review has attempted to evaluate the impact of the prognostic nutritional index on the survival outcomes in lung cancer patients with certain limitations. The goal of the present systematic review and meta-analysis is to bridge the gap in the literature and evaluate the capacity of the prognostic nutritional index for predicting the survivability outcomes in lung cancer patients undergoing chemotherapy. The aim of the study is to evaluate the impact of prognostic nutritional index scoring on survival outcomes in lung cancer patients undergoing chemotherapy. MATERIALS AND METHODS:  A systematic academic literature search was performed based on the PRISMA guidelines across Web of Science, EMBASE, CENTRAL, Scopus, and MEDLINE databases. A random-effect meta-analysis was performed to evaluate the impact of prognostic nutritional index scoring (i.e., high/low) on survival outcomes (i.e., progression-free survival, overall survival) in lung cancer patients undergoing chemotherapy. RESULTS:  From 963 studies, 16 eligible studies with 4250 lung cancer patients (62.32 ± 5.08 years) undergoing chemotherapy were included. Our meta-analysis revealed worse mortality outcomes in terms of progression-free survival (HR: 1.31) and overall survival (1.21) for the group with a low prognostic nutritional index score as compared to the group with a high prognostic nutritional index score in lung cancer patients undergoing chemotherapy. Subsequent subgroup analyses further demonstrated markedly worse outcomes for progression-free survival (1.32) and overall survival (1.52) in non-small lung cancer patients with lower prognostic nutritional index scores. CONCLUSIONS:  We provide preliminary evidence suggesting that lower prognostic nutrition index scores are associated with worse survivability outcomes (progression-free survival and overall survival) in lung cancer patients undergoing chemotherapy. We also show that lower prognostic nutrition index scores correlate with even worse survival outcomes in patients with non-small lung cancer histological subtype of lung cancer. These findings should help clinicians to stratify the risks associated with the chemotherapeutic management of lung cancer patients.

Crown ether-based anion exchange membranes with highly efficient dual ion conducting pathways.

Anion exchange membranes (AEMs) are a crucial constituent for alkaline fuel cells. As the core component of fuel cells, the low performance AEMs restrict the development and application of the fuel cells. Herein, the trade-off between the OH- conductivity and dimensional stability was solved by constructing AEMs with adequate OH- conductivity and satisfactory alkali resistance using Tröger's base (TB) poly (crown ether)s (PCEs) as the main chain, the embedded quaternary ammonium (QA) and Na+-functionalized crown ether units as the cationic group. Crown ether is an electron donator, and can capture Na+ to form Na+-functionalized crown ether units to conveniently transfer OH- and significantly promote the alkaline stability of the AEMs. The influence of the Na+-functionalized crown ether units on the performance of AEMs was studied in detail. The PCEs based AEMs show an obvious hydrophobic-hydrophilic microphase separation. These features make them ideal platforms for the OH- conduction applications. As expected, the as-prepared PCEs-QA-100% (100% is the degree of cross-linking) AEM with an ionic exchange capacity (IEC) of 2.07 meq g-1 has a high OH- conductivity of 159 mS cm-1 at 80 °C. Furthermore, the membrane electrode assemblies fabricated using the PCEs-QA-100% AEM possess a maximum power density of 291 mW cm-2 under the current density of 500 mA cm-2.

[Clinical characteristics and death risk factors of severe COVID-19].

Objective: To analyze the clinical features and death-related risk factors of COVID-19. Methods: We enrolled 891 COVID-19 patients admitted to the Affiliated Hospital of Jianghan University from December 2019 to February 2020, including 427 men and 464 women. Of the 891 cases, 582 were severe or critical, including 423(73%)severe and 159 (27%) critical cases. We compared the demographics, laboratory findings, clinical characteristics, treatments and prognosis data of the 582 severe patients. Univariate and multivariate logistic regression analysis was conducted to explore the risk factors associated with death in COVID-19 patients. Results: The 582 severe patients included 293 males and 289 females, with a median age of 64(range 24 to 106). Sixty-three patients died, including 45 males and 18 females, with a median age of 71(range 37 to 90). The average onset time of the 582 patients was 8 days, of whom 461 (79%) had fever, 358 (62%) dry cough, 274 (47%) fatigue. There were 206 cases with shortness of breath (35%), 155 cases with expectoration (27%), 83 cases with muscle pain or joint pain (14%), 71 cases with diarrhea (12%), and 29 cases with headache (4%). Underlying diseases were present in 267 (46%) patients, most commonly hypertension (194, 33%), followed by diabetes (69, 12%), coronary atherosclerotic heart disease (37, 6%), tumor (18, 3%), and chronic obstructive pulmonary disease (5, 1%). Chest CT showed bilateral lung involvement in 505 patients (87%). Upon admission, the median lymphocyte count of the 582 patients was 0.8(IQR, 0.6-1.1)×10(9)/L, the median D-dimer was 0.5 (IQR, 0.4- 0.8) mg/L, the median N-terminal brain natriuretic peptide precursor (NT-proBNP) was 433 (IQR, 141- 806) pg/L, and the median creatinine was 70.3 (IQR, 56.9-87.9) µmol/L. The death group had a median lymphocyte count of 0.5 (0.4-0.8)×10(9)/L, D-dimer 1.1 (0.7-10.0)mg/L, N-terminal brain natriuretic peptide precursor 1479(893-5 087) pg/ml, and creatinine 89.9(67.1-125.3) µmol/L. Multivariate logistic analysis showed that increased D-dimer (OR: 1.095, 95% CI: 1.045-1.148, P<0.001), increased NT-proBNP (OR: 4.759, 95% CI: 2.437-9.291, P<0.001), and decreased lymphocyte count (OR: 0.180, 95% CI: 0.059-0.550, P=0.003) were the risk factors of death in COVID-19 patients. Conclusions: The average onset time of severe COVID-19 was 8 days, and the most common symptoms were fever, dry cough and fatigue. Comorbidities such as hypertension were common and mostly accompanied by impaired organ functions on admission. Higher D-dimer, higher NT-proBNP, and lower lymphocyte count were the independent risk factors of death in COVID-19 patients.

Reducing postsurgical exudate in breast cancer patients by using San Huang decoction to ameliorate inflammatory status: a prospective clinical trial.

Background: Reducing inflammatory factors in wound exudate is a promising treatment approach for healing wounds in postsurgical breast cancer patients. Traditional Chinese Medicine (tcm) treatments have been shown to be beneficial and safe for optimal regulation of oxidative stress during the postoperative period. In the present clinical trial, we evaluated the effectiveness of a promising Chinese herbal formula, San Huang decoction [shd (Radix astragali, Radix et rhizoma rhei, and Rhizoma curcuma longa, 3:1:1; supplemental Table 1)], on wound inflammatory response after mastectomy. Methods: The study randomized 30 patients with breast cancer who fulfilled the inclusion and exclusion criteria to either a treatment (n = 15) or a control group (n = 15). Patients in the treatment group received liquid shd, taken twice daily with or without food. Treatment was given for 1 day before surgery and for 7 days postoperatively. Participants in the control group received a placebo on the same schedule as the treatment group. Outcomes measured in every subject included clinical tcm and wound inflammation symptom scores, daily and total amounts of drainage fluid, and levels of inflammatory factors in the exudate [tumour necrosis factor α (tnf-α), interleukins 6 (il-6), 8 (il-8), and 2R (il-2R), human C-reactive protein (crp)] at 2 hours and on days 1, 3, and 7 postoperatively. Results: The total amount of drainage fluid over 7 days was significantly lower in the treatment group (572.20 ± 93.95 mL) than in the control group (700.40 ± 107.38 mL). The tcm symptom score was also lower in treatment group (day 7: 1.87 ± 0.83 vs. 4.80 ± 3.61, p = 0.049), as was the inflammatory symptom score (day 7: 0.67 ± 0.72 vs. 3.67 ± 2.50, p = 0.001). Levels of tnf-α, il-6, il-8, il-2R, and crp in drainage fluid were significantly lower with shd treatment. Conclusions: Perioperative treatment with shd effectively lessened postoperative exudate and ameliorated inflammatory symptoms in patients who underwent surgery for breast cancer.

[Research advances in the role of mesenchymal stem cells and their exosomes in treatment of liver diseases].

At present, liver transplantation remains the most effective treatment for acute liver failure and advanced cirrhosis, but its use and promotion are limited by insufficient organ donors, financial consideration, and requirements for lifelong immunosuppression. In recent years, stem cell transplantation has been recommended as an effective substitutive therapy for liver disease. Mesenchymal stem cells, also known as pluripotent interstitial stromal cells, are self-renewing cells that can be found in almost all postnatal organs and tissues, including the liver. Their potential to differentiate into hepatocytes and immunomodulatory properties provide new insights into the use of mesenchymal stem cells in the treatment of acute and chronic liver diseases. This article reviews the characteristics of mesenchymal stem cells, their mechanisms in the treatment of acute and chronic liver diseases, and related risks.

Clinical observation of umbilical cord mesenchymal stem cell treatment of severe systolic heart failure.

The aim of this study was to evaluate the effectiveness of umbilical cord mesenchymal stem cells (MSCs) in the treatment of chronic systolic heart failure. Fifty-nine hospitalized patients with heart failure were randomly divided into a treatment group (30 patients) and a control group (29 patients). The treatment group received treatment with medication as well as intracoronary transplantation of umbilical cord MSCs, and the control group, only medication. The cardiac structure, function change, and rehospitalization and mortality rates of the 2 groups were observed before and 1 and 6 months after treatment. One month after the transplantation of umbilical cord MSCs, the incidence of fatigue, chest tightness, and dyspnea was high in the treatment group. The 6-min walking distance of the treatment group was found to be significantly higher than that of the control group (P < 0.05); in addition, the NT-proBNP level, left ventricular ejection fraction, and mortality rate of the treatment group were statistically lower than those of the control group (P < 0.05). Readmission rates showed a downward trend, but the difference was not statistically significant (P > 0.05). Using umbilical cord MSCs in the treatment of congestive heart failure can help improve cardiac remodeling and cardiac function and reduce the mortality rate.

MKL1-184C>T gene polymorphism is associated with coronary artery disease in the Chinese Han population.

We investigated genetic susceptibility to coronary artery disease (CAD) by studying the association of MKL1 gene polymorphisms with CAD in the Chinese Han population. We performed a case-control study with 476 unrelated CAD patients and 325 non-CAD controls. All SNPs were genotyped with a TaqMan SNP genotyping assay. The distribution of MKL1-184C>T gene polymorphism in each group was in Hardy-Weinberg equilibrium. The frequency of the MKL1 T allele in the CAD group was significantly higher than in the control group (38.6 vs 30.8%). After logistic regression models adjusted for CAD risk factors, the risk of CAD among CT genotypes was 1.765 times higher than among the CC genotypes [odds ration (OR) = 1.765, 95% confidence interval (CI) = 1.246-2.5], and for TT genotypes it was 1.806 times higher than for the CC genotypes (OR = 1.806, 95%CI = 1.203-2.71). In summary, genotypes with at least one T allele (CT or TT genotypes) had a significantly increased CAD risk than the CC genotypes, with a ratio of 1.78 to 1 (OR = 1.780, 95%CI = 1.311-2.418). There was a close association between -184 T allele and 3VD (OR = 1.614, 95%CI = 1.259-2.07, P < 0.05). We conclude that the -184C>T of MKL1 is an important susceptibility factor for CAD in the Han Chinese in Henan Province. Homozygosity for the T allele is not only associated with an increased risk for CAD, it is also correlated with severity of stenosis in the Chinese Han population.

Impact of changes in postnatal nutrition on puberty onset and the expression of hypothalamic GnRH and ghrelin.

OBJECTIVES: Ghrelin is an octanoylated peptide hormone with multiple and diverse physiologic functions including an important role in energy homeostasis and reproduction. In this study, the adjustment effects of different postnatal nutritional status on puberty onset and the expression of hypothalamic ghrelin and gonadotrophin-releasing hormone (GnRH) were examined in 1 day-old female Sprague-Dawley rats. MATERIALS AND METHODS: Animals were randomly assigned into four groups: overnutrition group (Group O), normal group (Group N, control group), and undernutrition groups (Group U and U2). Western blot analysis and immunohistochemistry were used to analyze the expression of hypothalamic ghrelin and GnRH. RESULTS: With a low level expression of hypothalamic ghrelin, the appearance of puberty onset and secretion peak of GnRH in Group O was earlier than the other groups. CONCLUSIONS: Undernutrition delayed puberty onset and the GnRH peak, at the same time, promoted the expression of hypothalamic ghrelin.While, the expression of hypothalamic ghrelin was suppressed at puberty onset.

Association of CYP1B1 gene polymorphisms and the positive expression of estrogen alpha and estrogen beta with endometrial cancer risk.

To investigate the relationship between the CYP1B1 L432V polymorphism, ERalpha and ERbeta positivities and the incidence of endometrial cancer. The relationship between CYP1B1 L432V polymorphism, ERalpha and ERbeta positivities and endometrial cancer was investigated using the allele-specific polymerase chain reaction method to analyze gene polymorphism in exon 3 codon 432 (C-G) of CYP1B1. Our results are as follows: in endometrial cancer cases the prevalence rates of CYP1B1 L432V genotypes C/C, C/G, and G/G were 47.2%, 36.1%, and 16.7%, respectively, and 68.8%, 23.8% and 7.5% in the control group, respectively. The frequencies of CYP1B1 C and G alleles were 65.3% and 34.7% in endometrial cancer patients and 80.6% and 19.4% in the control group. A significant difference was found in the genotype distributions or allele frequencies of CYP1B1 L432V polymorphism between the two groups (p < 0.05). Compared with wild-type C/C, the susceptibility of endometrial cancer with homozygotic mutation G/G and heterozygotic mutation C/G increased by 3.235 (95%CI 1.111-9.425) and 2.214 (95% CI 1.067-4.593). Moveover, the positive expression of ERalpha in genotypes G/G and C/G was higher than in the wild genotype C/C (p < 0.05). In conclusion, allelic polymorphism of CYP1B1 L432V increases the risk of endometrial cancer and has a positive correlation with ERalpha expression.

Chinese medicinal formula Guan-Xin-Er-Hao protects the heart against oxidative stress induced by acute ischemic myocardial injury in rats.

Guan-Xin-Er-Hao (GXEH) is a Chinese medicine formula for treating ischemic heart diseases (IHD) and has a favorable effect. Our aim was to examine whether or not acute oral GXEH could protect the heart against myocardial infarction and apoptosis in acute myocardial ischemic rats. If so, we would explain the antioxidative mechanism involved. The left anterior descending coronary artery was occluded to induce myocardial ischemia in hearts of Sprague-Dawley rats. At the end of the 3h ischemic period (or 24h for infarct size), we measured the myocardial infarct size, myocardial apoptosis and the activities of antioxidative enzymes. GXEH reduced infarct size, myocardial apoptosis and the serum level of malondialdehyde (MDA), increased the activities of total antioxidant capacity (T-AOC), superoxide dismutase (SOD) and GSH-peroxidase (GPX) activities and the serum level of glutathione (GSH). GXEH exerts significant cardioprotective effects against acute ischemic myocardial injury in rats, likely through its antioxidation and antilipid peroxidative properties, and thus may be used as a promising agent for both prophylaxis and treatment of IHD.

A novel mutation in the NADH-cytochrome b5 reductase gene of a Chinese patient with recessive congenital methemoglobinemia.

Recessive congenital methemoglobinemia due to nicotinamide adenine dinucleotide (NADH)-cytochrome b5 reductase (b5R) deficiency is classified into 2 clinical types: type 1 (erythrocyte type) and type 2 (generalized type). We found a Chinese family with type 1 recessive congenital methemoglobinemia, the patients from which were diagnosed according to clinical symptoms and b5R enzyme activity in the blood cells. To learn the molecular basis of type 1 recessive congenital methemoglobinemia in this Chinese family, we isolated total RNA from the peripheral leukocytes of the propositus and b5R complementary DNA (cDNA) by reverse transcription- polymerase chain reaction (RT-PCR). The coding region of the b5R cDNA was analyzed by sequencing the cloned PCR products. The results showed that the propositus was homozygous for a G-->A transition at codon 203 in exon 7, changing a cysteine to a tyrosine (Cys203Tyr). To characterize the mutant enzyme, both glutathione S-transferase (GST)-fused wild-type b5R and GST-fused mutant Cys203Tyr b5R were expressed in Escherichia coli and affinity purified. The results showed that the catalytic activity of the enzyme was not much affected by this amino acid substitution, but the mutant enzyme exhibited decreased heat stability and increased susceptibility to trypsin. These properties of the mutant enzyme would account for the restricted b5R deficiency and mild clinical manifestations of these type 1 patients. The finding of this novel mutation makes codon 203 the only position within the b5R gene at which more than 1 mutation has been found.

PSMA mimotope isolated from phage displayed peptide library can induce PSMA specific immune response.

Prostate-specific membrane antigen (PSMA) is a cell surface glycoprotein expressed predominantly in prostate secretory acinar epithelium and prostate cancer cells as well as in several extraprostatic tissues. Mouse monoclonal antibody 4G5 specific to the extracellular domain of PSMA was used to screen two phage displayed peptide libraries (9aa linear and 9aa cys library). Three 4G5-reactive phagotopes were identified. Sequence analysis of isolated clones demonstrated that the interaction motif "VDPA/SK" has high homology to 719-725aa on PSMA. Immunohistochemical staining of the prostate cancer sample with the PSMA-mimic phagotope (mimotope) immunized serum antibodies demonstrate that the mimotope isolated from the phage displayed peptide libraries can induce PSMA specific immune response in vivo.

Extended metal environments of cytochrome c oxidase structures.

The metals of the cytochrome c oxidase structures of the bovine heart mitochondrion (PDB code 1occ) and of the soil bacterium Paracoccus denitrificans (1arl) include a dicopper center (CuA), magnesium, two proximal hemes, a copper (CuB) atom, and a calcium. The mitochondrial structure also possesses a bound distant zinc ion. The extended environments of the metal sites are analyzed emphasizing residues of the second shell in terms of polarity, hydrophobicity, secondary structure, solvent accessibility, and H-bonding networks. A significant difference in the CuA metal environments concerns D-51 I in 1occ, absent from 1arl. The D-51 I appears to play an important role in the proton pumping pathway. Our analysis uncovers several statistically significant residue clusters, including a cysteine-histidine-tyrosine cluster overlapping the CuA-Mg complex; a histidine-acidic cluster enveloping the environment of Mg, the two hemes, and CuB; and on the protein surface a mixed charge cluster, which may help stabilize the quaternary structure and/or mediate docking to cytochrome c. These clusters may constitute possible pathways for electron transfer, for O2 diffusion, and for H2O movement. Many hydrogen bonding relations along the interface of subunits I and II demarcate this surface as a potential participant in proton pumping.

The extended environment of mononuclear metal centers in protein structures.

The objectives of this and the following paper are to identify commonalities and disparities of the extended environment of mononuclear metal sites centering on Cu, Fe, Mn, and Zn. The extended environment of a metal site within a protein embodies at least three layers: the metal core, the ligand group, and the second shell, which is defined here to consist of all residues distant less than 3.5 A from some ligand of the metal core. The ligands and second-shell residues can be characterized in terms of polarity, hydrophobicity, secondary structures, solvent accessibility, hydrogen-bonding interactions, and membership in statistically significant residue clusters of different kinds. Findings include the following: (i) Both histidine ligands of type I copper ions exclusively attach the Ndelta1 nitrogen of the histidine imidazole ring to the metal, whereas histidine ligands for all mononuclear iron ions and nearly all type II copper ions are ligated via the Nepsilon2 nitrogen. By contrast, multinuclear copper centers are coordinated predominantly by histidine Nepsilon2, whereas diiron histidine contacts are predominantly Ndelta1. Explanations in terms of steric differences between Ndelta1 and Nepsilon2 are considered. (ii) Except for blue copper (type I), the second-shell composition favors polar residues. (iii) For blue copper, the second shell generally contains multiple methionine residues, which are elements of a statistically significant histidine-cysteine-methionine cluster. Almost half of the second shell of blue copper consists of solvent-accessible residues, putatively facilitating electron transfer. (iv) Mononuclear copper atoms are never found with acidic carboxylate ligands, whereas single Mn2+ ion ligands are predominantly acidic and the second shell tends to be mostly buried. (v) The extended environment of mononuclear Fe sites often is associated with histidine-tyrosine or histidine-acidic clusters.

Characterizations of diverse residue clusters in protein three-dimensional structures.

We present new methods for identifying and analyzing statistically significant residue clusters that occur in three-dimensional (3D) protein structures. Residue clusters of different kinds occur in many contexts. They often feature the active site (e.g., in substrate binding), the interface between polypeptide units of protein complexes, regions of protein-protein and protein-nucleic acid interactions, or regions of metal ion coordination. The methods are illustrated with 3D clusters centering on four themes. (i) Acidic or histidine-acidic clusters associated with metal ions. (ii) Cysteine clusters including coordination of metals such as zinc or iron-sulfur structures, cysteine knots prominent in growth factors, multiple sets of buried disulfide pairings that putatively nucleate the hydrophobic core, or cysteine clusters of mostly exposed disulfide bridges. (iii) Iron-sulfur proteins and charge clusters. (iv) 3D environments of multiple histidine residues. Study of diverse 3D residue clusters offers a new perspective on protein structure and function. The algorithms can aid in rapid identification of distinctive sites, suggest correlations among protein structures, and serve as a tool in the analysis of new structures.

The use of amino acid patterns of classified helices and strands in secondary structure prediction.

Elements of secondary structure from known protein three-dimensional structures have been classified with respect to their environments in tertiary structures. The size of the solvent-inaccessible face of an alpha-helix and the accessibility patterns on the two sides of a beta-strand have been used to classify the secondary structures. For each class, we have derived a sequence template, giving the amino acid propensity at each position. A prediction is made by calculating the compatibility of segments of polypeptide sequence against templates for each type of secondary structure. This method predicts not only position of a secondary structure in a protein sequence but also the orientation of the secondary structure with respect to the core of the protein tertiary structure. A jack-knife test is applied to 78 proteins of known structure solved at better than 2 A resolution. It shows that this method predicts between 13% and 17% better than the methods of Lim, GOR and Chou and Fasman at the level of secondary structure. The orientations of inaccessible faces are predicted within 50 degrees of correct value for about two-thirds of alpha-helices.