[Minimal residual disease assessment and progress in multiple myeloma]

With the rapid iteration of multiple myeloma therapeutics over the last two decades, as well as increasing remission rates and depth of remission in patients, traditional methods for monitoring disease response are insufficient to meet the clinical needs of new drugs. Minimal residual disease (MRD) is a more sensitive test for determining the depth of response, and data from multiple clinical trials and meta-analyses show that a negative MRD correlates with a better prognosis than a traditional complete response. MM is at the forefront of MRD evaluation and treatment. MRD detection methods have been continuously updated. The current MRD assessment has three dimensions: bone marrow-based MRD testing, MRD testing based on images of residual metabolic of focal lesions, and peripheral blood-based MRD testing. The various MRD assessment methods complement one another. The goal of this article is to discuss the currently used MRD assays, the progress, and challenges of MRD in MM, and to provide a reference for clinicians to better use the techniques.

[Prognostic value of the Second Revision of the International Staging System in patients with newly diagnosed transplant-eligible multiple myeloma]

Objective: To verify the predictive value of the Second Revision of the International Staging System (R2-ISS) in newly diagnosed patients with multiple myeloma (MM) who underwent first-line autologous hematopoietic stem cell transplantation (ASCT) in a new drug era in China. Methods: This multicenter retrospective cohort study enrolled patients with newly diagnosed MM from three centers in China (Beijing Chao-Yang Hospital, Capital Medical University; the First Affiliated Hospital, Sun Yat-Sen University, and the Second Affiliated Hospital of Naval Medical University) from June 2008 to June 2018. A total of 401 newly diagnosed patients with MM who were candidates for ASCT were enrolled in this cohort, all received proteasome inhibitor and/or immunomodulator-based induction chemotherapy followed by ASCT. Baseline and follow-up data were collected. The patients were regrouped using R2-ISS. Progression-free survival (PFS) and overall survival (OS) were analyzed. The Kaplan-Meier method was used to analyze the survival curve and two survival curves were compared using the log-rank test. Cox regression analysis were performed to analyze the relationship between risk factors and survival. Results: The median age of the patients was 53 years (range 25-69 years) and 59.5% (240 cases) were men. Newly diagnosed patients with renal impairment accounted for 11.5% (46 cases). According to Revised-International Staging System (R-ISS), 74 patients (18.5 %) were diagnosed with stage Ⅰ, 259 patients (64.6%) with stage Ⅱ, and 68 patients (17.0%) with stage Ⅲ. According to the R2-ISS, the distribution of patients in each group was as follows: 50 patients (12.5%) in stage Ⅰ, 95 patients (23.7%) in stage Ⅱ, 206 patients (51.4%) in stage Ⅲ, and 50 patients (12.5%) in stage Ⅳ. The median follow-up time was 35.9 months (range, 6-119 months). According to the R2-ISS stage, the median PFS in each group was: 75.3 months for stage Ⅰ; 62.0 months for stage Ⅱ, 39.2 months for stage Ⅲ, and 30.3 months for stage Ⅳ; and the median OS was not reached, 86.6 months, 71.6 months, and 38.5 months, respectively. There were statistically significant differences in PFS and OS between different groups (both P<0.001). Multivariate Cox regression analysis showed that stages Ⅲ and Ⅳ of the R2-ISS were independent prognostic factors for PFS (HR=2.37, 95%CI 1.30-4.30; HR=4.50, 95%CI 2.35-9.01) and OS (HR=4.20, 95%CI 1.50-11.80; HR=9.53, 95%CI 3.21-28.29). Conclusions: The R2-ISS has significant predictive value for PFS and OS for transplant-eligible patients with MM in the new drug era. However, the universality of the R2-ISS still needs to be further verified in different populations.

Construction and validation of a personalized prediction model for postpartum anxiety in pregnant women with preeclampsia

BACKGROUND

Preeclampsia is a pregnancy-specific multi-system disease with multi-factor and multi-mechanism characteristics. The cure for preeclampsia is to terminate the pregnancy and deliver the placenta. However, it will reduce the perinatal survival rate, prolong the pregnancy cycle, and increase the incidence of maternal complications. With relaxation of the birth policy, the number of elderly pregnant women has increased significantly, and the prevalence rate of preeclampsia has increased. Inappropriate treatment can seriously affect the normal postpartum life of pregnant women. Studies have shown that postpartum anxiety in women with preeclampsia can affect physical and mental health, as well as infant growth and development.

AIM

To analyze the factors influencing preeclampsia in pregnant women complicated with postpartum anxiety, and to construct a personalized predictive model.

METHODS

We retrospectively studied 528 pregnant women with preeclampsia who delivered in Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine between January 2018 and December 2021. Their basic data were collected, and various physiological and biochemical indicators were obtained by laboratory examination. The self-rating anxiety scale was used to determine whether the women had postpartum anxiety 42 d after delivery. The independent factors influencing postpartum anxiety in early pregnant women with eclampsia were analyzed with multifactor logistic regression and a predictive model was constructed. The Hosmer-Lemeshow test and receiver operating characteristic (ROC) curve were used to evaluate the calibration and discrimination of the predictive model. Eighty pregnant women with preeclampsia admitted to our hospital from January 2022 to May 2022 were retrospectively selected to verify the prediction model.

RESULTS

We excluded 46 of the 528 pregnant women with preeclampsia because of loss to follow-up and adverse outcomes. A total of 482 cases completed the assessment of postpartum anxiety 42 d after delivery, and 126 (26.14%) had postpartum anxiety. Bad marital relationship, gender discrimination in family members, hematocrit (Hct), estradiol (E2) hormone and interleukin (IL)-6 were independent risk factors for postpartum anxiety in pregnant women with preeclampsia (P < 0.05). Prediction model: Logit (P) = 0.880 × marital relationship + 0.870 × gender discrimination of family members + 0.130 × Hct - 0.044 × E2 + 0.286 × IL-6 - 21.420. The area under the ROC curve of the model was 0.943 (95% confidence interval: 0.919-0.966). The threshold of the model was -1.507 according to the maximum Youden index (0.757), the corresponding sensitivity was 84.90%, and the specificity was 90.70%. Hosmer-Lemeshow χ2 = 5.900, P = 0.658. The sensitivity, specificity and accuracy of the model were 81.82%, 84.48% and 83.75%, respectively.

CONCLUSION

Poor marital relationship, family gender discrimination, Hct, IL-6 and E2 are the influencing factors of postpartum anxiety in preeclampsia women. The constructed prediction model has high sensitivity and specificity.

[Clinical features and related factors of invasive pulmonary aspergillosis in patients with acute exacerbation of chronic obstructive pulmonary disease]

Objective: To study the clinical features and related factors of invasive pulmonary aspergillosis (IPA) in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Methods: This retrospective study enrolled patients hospitalized for AECOPD in ten tertiary hospitals of China from September 2017 to July 2021. AECOPD patients with IPA were included as case group, AECOPD patients without IPA were randomly selected as control group from the same hospitals and same hospitalization period as the patients with IPA using the random function in the software of Microsoft Excel 2003, at a ratio of 2∶1. The clinical characteristics, treatment and outcome were compared between the two groups. Binary logistic regression model was used to analyze the factors associated with IPA in AECOPD patients. Results: A total of 14 007 inpatients with AECOPD were included in this study, and 300 patients were confirmed to have IPA, with an incidence rate of 2.14%. According to the above matching method, 600 AECOPD patients without aspergillus infection were enrolled as the control group. The age of the case group and the control group were (72.5±9.7) and (73.5±10.3) years old, with 78.0%(n=234) male and 76.8%(n=461) male, respectively. There were no significant differences in age and gender composition between the two groups (all P>0.05). The prognosis of case group was significantly worse than that of the control group, with longer hospital stay [M(Q₁,Q₃)], [14 (10-20) d vs 11 (8-15) d, P<0.001], higher ICU admission rate [16.3% (49 case) vs 10.0% (60 case), P=0.006], higher in-hospital mortality [4.0% (12 cases) vs 1.3% (8 cases), P=0.011], and higher hospitalization costs (28 000 ¥ vs 13 700 ¥, P<0.001). The smoking index of the case group and proportions of patients with diabetes mellitus, chronic pulmonary heart disease in the case group were significantly higher than those in control group (all P<0.05). In terms of clinical features, the proportions of patients with cough, expectoration, purulent sputum, hemoptysis and fever in the case group were higher than those in the control group, the serum albumin was significantly lower than that in the control group, and the proportions of patients with bronchiectasis and pulmonary bullae on imaging were significantly higher than those in the control group (all P<0.05). Diabetes (OR=1.559, 95%CI: 1.084-2.243), chronic pulmonary heart disease (OR=1.476, 95%CI: 1.075-2.028), bronchiectasis (OR=1.506, 95%CI: 1.092-2.078), pulmonary bullae (OR=1.988, 95%CI: 1.475-2.678) and serum albumin<35 g/L (OR=1.786, 95%CI: 1.325-2.406) were the related factors of IPA in patients with AECOPD. Conclusions: The incidence of IPA in AECOPD patients is relatively high and the prognosis of these patients is worse. Diabetes, chronic pulmonary heart disease, bronchiectasis, pulmonary bulla, hypoproteinemia are the related factors of IPA in patients with AECOPD.

[Study on related factors and characteristics of multimorbidity of overweight and obesity-related diseases in children in Hunan Province]

From January 2019 to December 2021, overweight and obese children who visited in health outpatient Center of Hunan Children's Hospital were studied to explore and analyze the rate, related factors and patterns of multimorbidity of overweight and obesity-related diseases in children in Hunan Province. Univariate and multivariate logistic regression models were used to analyze the multimorbidity-related factors of overweight and obesity-related diseases in children. Association rules (apriori algorithm) were used to explore the multimorbidity patterns of overweight and obesity-related diseases in children. A total of 725 overweight and obese children were included in this study. The multimorbidity rate of overweight and obesity-related diseases in children was 46.07% (334/725). Age, waist circumference, the frequency of food consumption such as hamburgers and fries and adding meals before bedtime were multimorbidity-related factors of overweight and obesity-related diseases in children. The multimorbidity associated with nonalcoholic fatty liver disease (NAFLD) was relatively common. The patterns with the top three support degrees were "NAFLD+dyslipidemia","NAFLD+hypertension" and "NAFLD+hyperuricemia". The patterns with the top three confidence and elevation degrees were "Hypertension+dyslipidemia => NAFLD","Hyperuricemia => NAFLD" and "NAFLD+hypertension => dyslipidemia".

[Clinical analysis of multiple myeloma with second primary malignancies and multiple myeloma secondary to malignancies]

Objective: To compare the clinical characteristics and survival outcomes of multiple myeloma (MM) with second primary malignancies (SPMs) and MM secondary to malignancies. Methods: The clinical data of MM patients diagnosed and treated in Beijing Chaoyang Hospital, Capital Medical University from January 2002 to January 2021 were included. The patients were divided into two groups: MM with SPMs group and MM secondary to malignancies group. The gender, age at first diagnosis, classification, stage, type of combined malignant tumor and the treatment were analyzed. The clinical characteristics and survival differences were compared between the two groups. Results: There were 20 patients in the MM with SPMs group, 9 males and 11 females, aged [M(Q₁,Q₃)] 61.5(56.8, 68.0)years, and the overall survival (OS) was 49.5(32, 58) months, while the time to death from secondary tumor was 12(4,21)months. There were 29 patients in the MM secondary to malignancies group, 13 males and 16 females, aged 64.0(57.0, 71.0)years, and the OS was 97(61, 171) months, while the time to death from secondary MM was 32(18, 47) months. The time from patients diagnosed with MM to SPMs was 37(18, 50) months, which was significantly earlier than that of MM secondary to malignancies [53(31,117) months](P=0.016). The type of tumor was also different between the two groups (P<0.001). In the group of MM with SPMs, the most common type of SPMs was hematopoietic malignancies (12/20, 60.0%), whereas in the group of MM secondary to malignancies, MM was most often secondary to genitourinary malignancies (13/29, 44.8%) (P<0.001). Conclusions: Both MM with SPMs and MM secondary to malignancies can affect the survival of patients. Secondary hematological malignancies account for a high proportion of the second tumors in MM patients, while genitourinary malignancies account for a high proportion of malignant tumors associated with MM.

[Analysis of the relationship between syncope and poor prognosis in patients with acute pulmonary embolism and related factors]

Objective: To explore the association between syncope and poor prognosis and related factors of syncope in patients with acute pulmonary embolism (APE). Methods: A total of 740 patients with first diagnosed APE treated in West China Hospital of Sichuan University from September 1, 2016 to December 30, 2019 were enrolled. The basic information and clinical information (including clinical manifestations, complications, auxiliary examination, treatment and prognosis, etc.) of the patients were obtained from inpatient medical records. The patients were divided into the syncope group and the non-syncope group according to whether they had syncope or not. The basic and clinical conditions of the two groups were compared, and the factors related to syncope in APE patients were analyzed by multiple logistic regression model. Results: The proportion of APE patients with syncope was 12.6% (93/740). Age was (59±16) years in the syncope group (93 cases) and (59±17) years in the non-syncope group (647 cases), with 57.0% (53/93) and 60.4% (391/647) males, respectively. The body mass index, in-hospital mortality, proportions with high risk APE and mechanical ventilation of the syncope group were higher than those of the non-syncope group [(24.5±4.0) kg/m² vs (23.3±3.8) kg/m², 16.1% vs 7.7%, 4.4% vs 1.3% and 9.7% vs 2.5%, respectively]. The length of hospital stay [M (Q₁, Q₃)] of the syncope group was longer than that of the non-syncope group [15 (10, 22) d vs 14 (9, 22) d], and the proportions with chest pain and hemoptysis were lower than those of the non-syncope group (19.4% vs 36.8% and 14.0% vs 27.2%, respectively) (all P values<0.05). Multivariate logistic regression analysis showed that enlargement of the right heart [OR (95%CI): 2.46 (1.07, 5.64)] was a factor associated with syncope in APE patients. Conclusion: The proportion of APE patients with syncope is relatively high and is associated with poor prognosis, while enlargement of the right heart is associated with syncope in APE patients.

[The prognostic relationship between CD56 expression and newly diagnosed multiple myeloma]

Objective: To evaluate the prognostic value of CD56 expression in newly diagnosed MM (NDMM). Methods: A total of 332 NDMM patients were enrolled in Beijing Chaoyang Hospital, Capital Medical University from January 1, 2011 to January 1, 2021, with a median age of 60 years and a male to female ratio of 1.2∶1. CD56 expression on myeloma cells was detected by flow cytometry before induction therapy. Overall survival (OS) and progression-free survival (PFS) data were collected. In order to reduce the confounding factors, the propensity score matching technique was used to match CD56 positive versus negative patients at a ratio of 1∶1. Results: Among 332 patients, CD56 positivity rate was 65.1% (216/332). Patients with CD56 expression had significantly longer median OS (58.4 vs. 43.1 months, P=0.024) and PFS (28.7 vs. 24.1 months, P=0.013) than those with negative CD56. Univariate Cox proportional hazards regression analyses showed that CD56 expression was positively correlated with OS (HR=0.644, 95%CI 0.438-0.947, P=0.025) and a favorable prognostic factor for PFS (HR=0.646, 95%CI 0.457-0.913,P=0.013). The favorable effect of CD56 expression on PFS was confirmed in multivariate analysis (HR=0.705, 95%CI 0.497-0.998, P=0.049), but OS was not affected (P>0.05).In the propensity score matching analysis, 194 patients with 97 in each group were identified. CD56 positivity consistently predicted longer PFS (34.2 vs.25.1 months, P=0.047), but not OS (63.4 vs.43.1 months, P=0.056). Conclusion: These results demonstrate that CD56 expression is a favorable prognostic factor for PFS of newly diagnosed MM patients.

[Autologous stem cell transplantation improve the survival of newly diagnosed multiple myeloma patients]

目的

评估自体造血干细胞移植（auto-HSCT）对初治多发性骨髓瘤（MM）疗效及生存的影响。

方法

回顾性分析2008年10月1日至2019年10月1日243例65岁以下接受auto-HSCT的初治MM患者，同时以同期176例≤65岁适合移植但未进行auto-HSCT的初治MM患者作为对照，评估auto-HSCT对患者疗效及生存的影响。为平衡auto-HSCT和非auto-HSCT患者之间各因素的分布，利用倾向性评分匹配技术按照1∶1比例匹配以减少组间的偏差。

结果

通过倾向性评分匹配分析，共筛选出128例患者（每组64例）。64例患者诱导治疗后接受auto-HSCT，24例（37.5％）获得严格意义的完全缓解（sCR），16例（25.0％）获得完全缓解（CR），15例（23.4％）获得非常好的部分缓解（VGPR），9例（14.1％）获得部分缓解（PR），auto-HSCT组疗效明显优于非auto-HSCT组（P＝0.032）。与非auto-HSCT组相比，auto-HSCT组总生存（OS）和无进展生存（PFS）期明显延长［OS：87.6（95％ CI 57.3～117.9）个月对53.9（95％ CI 36.1～71.7）个月，P＝0.011；PFS：42.2（95％ CI 29.9～54.5）个月对22.4（95％ CI 17.1～27.7）个月，P＝0.007］。多因素分析显示auto-HSCT是OS（HR＝0.448，95％CI 0.260～0.771，P＝0.004）和PFS（HR＝0.446，95％CI 0.280～0.778，P＝0.003）的独立保护因素。

结论

auto-HSCT可改善适合移植初治MM患者的OS和PFS。

[Risk factors associated with mortality in patient with non-high-risk pulmonary embolism and cancer and the prognostic value of Charlson comorbidity index]

Objective: To investigate the risk factors associated with mortality and the prognostic value of Charlson comorbidity index (CCI) for mortality in patients with non-high-risk pulmonary embolism complicated by caner. Methods: Patients diagnosed with non-high-risk pulmonary embolism and caner from the medical departments of West China Hospital of Sichuan University from May, 2015 to April, 2018 were included in this study. The patients were classified into death group and survival group according to whether they died during hospitalization. Clinical information was collected and univariate along with multivariate analysis were performed in order to identify the independent risk factor related to short-term mortality in these patients. Besides, all the patients were assessed the comorbidity burden using CCI score and thereby to evaluate the prognostic value of CCI for short-time mortality. Results: A total of 195 patients were included in this study, including 115 males and 80 females. In all, 32 patients died during hospitalization and the mortality rate was 16.4%. Univariate analysis showed that male (P=0.044), age ≥65y (P=0.008), staying in bed (P=0.001), chronic pulmonary diseases (P=0.030), central venous catheterization (P=0.015), stroke history within 1 month (P=0.015), pneumonia (P=0.017), respiratory failure (P=0.017), diabetes mellitus (P=0.005) and anemia (P=0.035) were related to short term mortality of these patients. As for laboratory examination results, levels of hemoglobin and sodium in death group were significantly lower than survival group (P<0.05). Multivariate logistic regression showed that age ≥65y (OR=3.01, 95%CI: 1.05-8.68, P=0.041), staying in bed (OR=4.15, 95%CI: 1.37-12.54, P=0.012), central venous catheterization (OR=16.10, 95%CI: 2.09-124.08, P=0.008), stroke history within 1 month (OR=6.56, 95%CI: 1.05-40.95, P=0.044) and hyponatremia (OR=2.75, 95%CI: 1.06-7.15, P=0.038) were independent risk factors of short term mortality in these patients. Besides, CCI score in death group was significantly higher than that in survival group (5.66±2.96 vs 4.13±2.74, P=0.005). Pulmonary embolism patients with CCI≥4 were associated with 4.25-fold increased risk of mortality compared with patients with CCI<4 (OR=4.25, 95%CI: 1.83-9.89, P=0.001), and the per additional 1-score increase of CCI after 4 was associated with 4.89-fold increased risk of mortality (OR=4.89, 95%CI: 2.07-11.55, P<0.001). Survival analysis showed that patients with CCI≥4 had lower survival rate than the patients with CCI<4 during hospitalization (P<0.001). Conclusions: Age ≥65y, staying in bed, central venous catheterization, stroke history within 1 month and hyponatremia are independent risk factor of short-term mortality in patients with non-high-risk pulmonary embolism and caner. CCI score has prognostic value of short term mortality in these patients, and the risk increases with the increase of comorbidities patients have.

[Comparison of minimal residual disease in multiple myeloma patients detected by 8-color panels and next generation flow cytometry]

Objective: To compare the sensitivity of 8-color panels and next generation flow cytometry (NGF) for detecting minimal residual disease of multiple myeloma patients. Methods: 8-color-membrane antigens (8C-Mem) panel was built including CD45, CD38, CD138, CD19, CD56, CD81, CD27 and CD117 to identify the plasma cells, while 8-color-cytoplasmic antigens (8C-Cyto) panel was built including CD45, CD38, CD138, CD19, CD56, CD81, cKappa (cK) and cLambda (cλ) , and 8-color-two-tubes (8C-2tubes) panel were built including 8C-Mem and 8C-Cyto panels, the data of three groups was analyzed by Diva software. NGF uses Infinicyt software to fuse 8C-2tubes data to further analyze the expression of plasma antigens. Bone marrow aspiration obtained from 20 controls and 76 multiple myeloma patients who achieved complete remission were measured and analyzed. Results: Positive MRD samples were discriminated in 88.2% of the specimen evaluated through either abnormal plasma cells (aPCs) or clonal plasma cells (cPCs) by NGF antigens panel, Among of them, consistency was 94.7%. The median percentage of cPCs was 0.3530%, The lowest sensitivity of NGF was 0.0003%. In 8-color panels, the positive MRD rates of 8C-Mem, 8C-Cyto and 8C-2tubes panels were 84.2%, 85.5% and 86.8%, respectively, which lower than that of NGF (P<0.001) . The positive MRD rate of 8C-Mem and 8C-Cyto panels were lower than that of 8C-2tubes panel (P<0.001) , and the positive MRD rate of 8C-Mem panel was lower than that of 8C-Cyto panel (P<0.001) . Sensitivity and specificity of NGF was higher than that of 8-color panels. 8C-2tubes panel has the best sensitivity, accuracy, negative predicted value, positive predicted value and specificity than other 8-color panels. However, huge data and low efficiency for analysis is the disadvantage. 8C-Cyto panel was the second choice, and 8C-Mem panel was the last. Conclusions: Membrane and cytoplasmic light chain is a better method for multiple myeloma-MRD detection and NGF panel is an ideal approach. 8C-Cyto panel is recommended in 8-MFC groups.

[Comparison of risk factors and short-term and long-term prognosis of pulmonary embolism between the Tibetan and Han people]

Objective: To compare the differences of risk factors and prognosis of pulmonary embolism (PE) between the Tibetans and the Hans. Methods: Patients over 18 years old with confirmed PE and complete clinical data from West China Hospital of Sichuan University from January 2010 to January 2016 were prospectively enrolled and divided into Tibetan group and Han group. Clinical data were collected to compare risk factors and short-term prognosis between Han group and Tibetan group. In addition, a 2-year follow-up was conducted among patients after discharge to investigate the long-term prognosis. Results: A total of 90 patients in Tibetan group and 626 patients in Han group were finally included in this study. Patients in Tibetan group were younger than Han group [(52.2±15.8) vs (59.8±16.6) years old, P<0.001], and the proportion of elderly patients (age ≥70 years) in Tibetan group was significantly lower than that of Han group (15.6% vs 33.7%, P=0.001). The hemoglobin, hematocrit, platelet counts and fibrinogen in Tibetan group were higher than those in Han group [(134.0±32.0) vs (122.2±25.7) g/L, (41.2±9.2)% vs (37.6±7.3)% and (222.2±97.5)×10(9)/L vs (187.5±87.2)×10(9)/L, 3.71(2.51, 4.89) vs 3.31(2.44, 4.42) g/L; P<0.001, <0.001 and P=0.001, 0.048, respectively]. Malignancy and chronic obstructive pulmonary disease were more common in Han group (P=0.011, 0.001), while prior venous thromboembolism history, pregnancy or a history delivery within 1 month were more common in Tibetan group (P=0.041, 0.001). Both short-term and long-term mortality in Tibetan group were significantly lower than that in Han group (2.2% vs 11.5%, 13.6% vs 24.9%; P=0.005, 0.020). Conclusions: Hypercoagulable state plays an important role in the pathogenesis of PE in Tibetan patients. Both short-term and long-term prognosis of PE in Tibetan patients are better than that in Han patients.

[Risk factors of pulmonary embolism in senile and non-senile inpatients and the predictive value of Caprini risk assessment model in these two populations]

Objective: To investigate the risk factors of pulmonary embolism (PE) in senile and non-senile inpatients, and evaluate the predictive value of Caprini risk assessment model in these two populations. Methods: Case control study design was used in this study. All the PE patients diagnosed in West China Hospital of Sichuan University between January 2012 and December 2014 was included and divided into senile PE group (age ≥65 years old) and non-senile PE group (age <65 years old). Age matched controls (senile control group and non-senile control group) were selected from the patients admitted into the same departments during the same time period as PE patients, at a ratio of 2∶1. The risk factors of PE for senile and non-senile inpatients were investigated through comparing senile or non-senile PE patients with corresponding controls. All the subjects were retrospectively evaluated by Caprini risk assessment model, and the associations between risk stratifications and PE risk were analyzed. Results: A total of 135 senile PE patients and 212 non-senile PE patients were finally included in this study, with average age of (73.58±6.66) years old and (45.60±13.11) years old, respectively. And 233 age-matched senile controls and 418 non-senile controls were also included. The multivariate analysis showed diabetes (OR=4.08, 95%CI: 1.58-10.51, P=0.004) , heart failure (OR=3.67, 95%CI: 1.10-12.20, P=0.034) , swollen legs (OR=10.50, 95%CI: 5.57-19.79, P<0.001) , severe lung disease (OR=2.05, 95%CI: 1.08-3.90, P=0.028) , patient confined to bed (>72 h) (OR=58.33, 95%CI: 7.46-456.17, P<0.001) were independent risk factors of PE in senile patients, while obesity[body mass index (BMI)≥25 kg/m(2)](OR=2.72, 95%CI: 1.42-5.24, P=0.003), history of deep venous thrombosis (DVT)/PE (OR=17.54, 95%CI: 2.74-112.19, P=0.002) , hip, pelvis, or leg fracture (OR=18.31, 95%CI: 1.97-170.11, P=0.011) , swollen legs (OR=18.53, 95%CI: 11.29-30.40, P<0.001) , severe lung disease ( OR=4.11, 95%CI: 2.41-7.00, P<0.001) , patient confined to bed (>72 h) (OR=4.04, 95%CI: 2.03-8.04, P<0.001) were independent risk factors of PE in non-senile patients. Among the senile patients, the risk of PE increased with the increase of Caprini risk levels; compared with Caprini moderate risk, classifications of high risk and highest risk were associated with 4.64-fold (95%CI: 1.05-20.44, P=0.043) and 10.74-fold (95%CI: 2.46-46.94, P=0.002) increased risk of PE, respectively; within the highest subgroup, the per 2-score increase of Caprini score was associated with 3.02-fold (95%CI: 1.76-5.19, P<0.001) increased risk of PE. Among those non-senile patients, the risk of PE for Caprini low risk and high risk patients was not significantly different, compared with Caprini moderate risk patients; however, the highest risk was still associated with 3.94-fold (95%CI: 2.39-6.51, P<0.001) increased risk of PE compared with moderate risk; within this subgroup, the per 2-score increase of Caprini score was associated with 2.13-fold (95%CI: 1.21-3.73, P=0.008) increased risk of PE. Conclusions: Swollen legs, severe lung disease, confined to bed (>72 h) are common PE risk factors among both senile and non-senile inpatients. Diabetes, heart failure are unique PE risk factors for senile inpatients, while obesity (BMI≥25 kg/m(2)), history of DVT/PE, hip, pelvis, or leg fracture are unique PE risk factors for non-senile inpatients. The Caprini risk assessment model has better predictive value in senile patients than non-senile patients, while Caprini highest risk classification is companied by significantly increased risk of PE in both populations.

Floral nectar of the obligate outcrossing Canavalia gladiata (Jacq.) DC. (Fabaceae) contains only one predominant protein, a class III acidic chitinase

Floral nectar can affect the fitness of insect-pollinated plants, through both attraction and manipulation of pollinators. Self-incompatible insect-pollinated plants receive more insect visits than their self-compatible relatives, and the nectar of such species might face increased risk of infestation by pathogens carried by pollinators than self-compatible plants. Proteins in nectar (nectarins) play an important role in protecting the nectar, but little is known regarding nectarins in self-incompatible species. The nectarins from a self-incompatible and insect-pollinated leguminous crop, Canavalia gladiata, were separated using two-dimensional electrophoresis and analysed using mass spectrometry. The predominant nectarin gene was cloned and the gene expression pattern investigated using quantitative real-time PCR. Chitinolytic activity in the nectar was tested with different substrates. The C. gladiata nectar proteome only has one predominant nectarin, an acidic class III chitinase (CaChi3). The full-length CaChi3 gene was cloned, coding for a protein of 298 amino acids with a predicted signal peptide. CaChi3 is very similar to members of the class III chitinase family, whose evolution is dominated by purifying selection. CaChi3 was expressed in both nectary and leaves. CaChi3 has thermostable chitinolytic activity according to glycol-chitin zymography or a fluorogenic substratem but has no lysozyme activity. Chitinase might be a critical protein component in nectar. The extremely simple nectar proteome in C. gladiata disproves the hypothesis that self-incompatible species always have more complex nectar proteomes. Accessibility of nectar might be a significant determinant of the evolutionary pressure to develop nectar defence mechanisms.

[A retrospective analysis of prognosis in favorable-risk acute myeloid leukemia patients with different consolidation regimens]

Objective: To explore the impact on prognosis in favorable-risk acute myeloid leukemia (AML) patients with different consolidation regimens after first complete remission (CR(1)). Methods: A total of 107 cases of non-refractory adult AML from January 2010 to June 2015 in single center were enrolled in the study. HD-Ara-C group (38 cases) as the control group, we explore the prognosis in three consolidation regimens, including micro-transplantation (16 cases) , autologous transplantation (auto-PBSCT, 14 cases) , allogeneic transplantation (allo-HSCT, 39 cases). Results: Of 107 patients (59 males and 48 females) , with a median age of 33 (16-59) years old and a median follow-up of 36.5 (5.3-79.1) months, the overall relapse rate was 20.6% (22/107) , and overall mortality rate was 18.7% (20/107). The 5 years cumulative relapse rate (CIR) of HD-Ara-C, micro-transplantation, auto-PBSCT and allo-HSCT group were 39.7%, 6.2%, 14.3% and 5.6%, respectively (P<0.001). The CIR of the observed group was lower than the HD-Ara-C group. The 5 years progression-free survival (PFS) rate of HD-Ara-C, micro-transplantation, auto-PBSCT and allo-HSCT group were 44.7%, 93.8%, 85.7% and 78.1%, respectively (P=0.011). The PFS of observed groups were similar, but superior to that in HD-Ara-C group. The 5-year overall survival (OS) in four groups was 54.9%, 100%, 92.9% and 77.4%, respectively (P>0.05). Multiple factors analysis showed that compared to HD-Ara-C regimen, allo-HSCT could improve PFS (HR=0.376, P=0.031) , but not OS (P>0.05) ; micro-transplantation and auto-PBSCT could not improve the PFS or OS (P>0.05). Conclusion: As compared with HD-Ara-C regimen, allo-HSCT could obviously decrease CIR, improve PFS, but treatment-related mortality is high. These results show that auto-PBSCT and micro-transplantation have similar outcomes, compared to HD-Ara-C regimen, so both can be used as a option of consolidation treatment for favorable-risk AML.

Selective deletion of Pten in theca-interstitial cells leads to androgen excess and ovarian dysfunction in mice

Theca cell-selective Pten mutation (tPtenMT) in mice resulted in increases in PDK1 and Akt phosphorylation, indicating an over-activation of PI3K signaling in the ovaries. These mice displayed elevated androgen levels, ovary enlargement, antral follicle accumulation, early fertility loss and increased expression of Lhcgr and genes that are crucial to androgenesis. These abnormalities were partially reversed by treatments of PI3K or Akt inhibitor. LH actions in Pten deficient theca cells were potentiated. The phosphorylation of Foxo1 was increased, while the binding of Foxo1 to forkhead response elements in the Lhcgr promoter was reduced in tPtenMT theca cells, implying a mechanism by which PI3K/Akt-induced upregulation of Lhcgr in theca cells might be mediated by reducing the inhibitory effect of Foxo1 on the Lhcgr promoter. The phenotype of tPtenMT females is reminiscent of human PCOS and suggests that dysregulated PI3K cascade in theca cells may be involved in certain types of PCOS pathogenesis.

[Risk factors of venous thromboembolism recurrence and the predictive value of simplified pulmonary embolism severity index in medical inpatients]

OBJECTIVE

To explore the risk factors of venous thromboembolism (VTE) recurrence and the predictive value of simplified pulmonary embolism severity index (sPESI) in medical inpatients.

METHODS

A total of 149 consecutive patients with first diagnosed VTE from the medical departments of West China Hospital of Sichuan University from January 2011 and December 2012 were enrolled and followed-up for 24 months. The VTE recurrence rate was calculated and univariate and multivariate cox proportional hazards regression analysis were performed to identify the risk factors associated with VTE recurrence. All the patients were evaluated by sPESI, and survival analysis was used to explore its value in predicting VTE recurrence in these medical patients.

RESULTS

Out of the included 149 patients, 23(15.4%) patients had VTE recurrence during the 2 years' follow-up and median recurrence time was 167 days. The univariate analysis showed bed rest, severe lung disease, nephrotic syndrome, inappropriate anticoagulant therapy, smoking, diabetes, and malignant neoplasm might be associated with VTE recurrence (P=0.043, 0.006, 0.009, 0.032, 0.098, 0.048, 0.021). Among these risk factors, the multivariate analysis revealed severe lung disease, nephrotic syndrome, and malignant neoplasm were the independent risk factors (HR=3.45, 5.67, 3.60; P=0.020, 0.020, 0.047); while for inappropriate anticoagulant therapy, the P value was marginal (HR=3.94, 95% CI: 0.99-15.63, P=0.051). The median sPESI scores of the patients with VTE recurrence was higher than that of the patients without VTE recurrence[1(1, 2) vs 0(0, 1), P=0.001], and patients with sPESI≥1 were associated with 5.57-fold increased risk of VTE recurrence compared with patients with sPESI=0 (95%CI: 1.79-17.30, P=0.001). Survival analysis also showed that the 2-year cumulative VTE recurrence rate of patients with sPESI≥1 was significant higher than that of patients with sPESI=0 (38.4% vs 5.7%, P=0.001).

CONCLUSIONS

The medical VTE patients have high VTE recurrence risk, and severe lung disease, nephrotic syndrome, malignant neoplasm and inappropriate anticoagulant therapy are important risk factors of VTE recurrence. The sPESI has predictive value for VTE recurrence in medical patients.

Association of XRCC5 polymorphisms with COPD and COPD-related phenotypes in the Han Chinese population: a case-control cohort study

Genome-wide association studies (GWAS) and integrative genomic approaches have demonstrated significant associations between chronic obstructive pulmonary disease (COPD) and polymorphisms of the X-ray repair cross-complementing protein 5 gene (XRCC5) in non-Asian populations. We investigated whether XRCC5 polymorphisms might be associated with COPD susceptibility and COPD-related phenotypes in the Chinese Han population. Nine single nucleotide polymorphisms (SNPs) (rs3821104, rs12470053, rs207936, rs3770498, rs6704622, rs3770492, rs4674066, rs7573191, and rs207906) in the XRCC5 gene were genotyped in a case-control study including 680 COPD patients and 687 controls. To estimate the strength of association, odds ratios (ORs) were calculated and the effects of potentially confounding variables were tested by logistic regression analysis. The association between haplotypes and COPD outcome was also assessed. Our data identified that the SNP rs207936 was associated with COPD with an adjusted P value of 0.038, which was also found when analyzing only data of current smokers (P=0.046). No significant associations were found between any of the SNPs and pulmonary function. Eight SNPs (rs3821104, rs12470053, rs207936, rs3770498, rs6704622, rs3770492, rs4674066, and rs7573191) showed strong linkage disequilibrium (R2≥0.9). Two major haplotypes were observed and showed a significant difference between case and control groups (P=0.0054 and 0.0081, respectively). The present study showed that the XRCC5 locus might be a contributor to COPD susceptibility in the Chinese Han population.

Immune modulation of co-transplantation mesenchymal stem cells with islet on T and dendritic cells

Allogeneic pancreatic islet transplantation theoretically represents a cure for type 1 diabetes. However, current immune suppressive therapies are often associated with undesired side effects. Given this problem, and the shortage of human islet donors, the majority of type 1 diabetes patients cannot currently be offered an islet transplant. However, it has been found that mesenchymal stem cells (MSCs) could exert unique immunosuppressive effects both in vitro and in vivo. Herein we transplanted allogeneic 200 islets alone or in combination with MSCs (3 x 10(6) cells) under the kidney capsules of diabetic C57LB/6 mouse. We found that the ratios of T helper type 1 (Th1) to Th2 and Tc1 to Tc2 were reduced, and the numbers of naive and memory T cells were down-regulated in peripheral blood after transplantation. In addition, the maturation, endocytosis and interleukin-12 secretion of dendritic cell (DCs)-derived bone marrow cells (BMCs) from receptor mice were suppressed. Rejection reaction was alleviated by MSCs which exerted suppressive effects through T lymphocyte subsets and DCs.

Clinical value of tumour specific growth factor (TSGF) and carbohydrate antigen-125 (CA-125) in carcinoma of the endometrium

This study estimated the clinical value of tumour specific growth factor (TSGF) and carbohydrate antigen-125 (CA-125) in the diagnosis of endometrial carcinoma. Blood was collected from the peripheral and uterine veins of endometrial cancer patients, and serum TSGF and CA-125 levels were compared with those in uterine myoma patients (non-tumour controls) and normal women. Significantly higher levels of TSGF and TGSF-positive rates were observed in endometrial cancer patients versus non-tumour and normal controls. The sensitivity and specificity for detecting TGSF-positive rates in the endometrial carcinoma group were 64.9% and 62.5%, respectively. The TSGF levels in uterine blood were significantly higher than in peripheral blood and the TSGF-positive rate was also higher. The TSGF levels gradually increased with progression through the clinical stages and pathological grades of endometrial carcinoma. The sensitivity and specificity of combined TSGF and CA-125 for detecting endometrial cancer were 75.7% and 56.3%, respectively. It is concluded that there is an important correlation between serum levels of TSGF, CA-125 and endometrial cancer and that measurement of both TSGF and CA-125 combined would be of value in the diagnosis of endometrial carcinoma.

Biotype status and distribution of Bemisia tabaci (Hemiptera: Aleyrodidae) in Shandong province of China based on mitochondrial DNA markers

Bemisia tabaci has caused significant crop losses in China during the last decade. Recent research has shown that two potentially invasive variants, biotypes B and Q, have been found in several regions of China. Our objective was to determine the biotype status and the distribution of B. tabaci in Shandong province, an important agricultural region of China. Based on mitochondrial DNA markers, both biotypes B and Q were detected, with B being the predominant biotype. The results indicate that the more recently introduced biotype Q has not only been located in China but also has established and spread in some regions.

Predicted structures of two proteins involved in human diseases

Structures of 79 proteins involved in human diseases were predicted by sequence alignments with structural templates. The predicted structures for ALDP and CSA, proteins responsible for adrenoleukodystrophy and the Cockayne syndrome, respectively, were analyzed to elucidate the molecular basis of disease mutations. In particular we positioned residue P484 of ALDP in the homodimer interface. This positioning is consistent with a recent experimental finding that the mutation P484R significantly decreases the self-interaction of ALDP and suggests that the disease mechanism of this mutation lies in the impaired ALDP dimerization. We identified two new WD repeats in CSA and suggest that one of these forms part of the interaction surface with other proteins.

The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins

Recently many attempts have been made to design high-affinity DNA-binding proteins by linking two domains. Here a theory for guiding these designs is presented. Flexible linkers may play three types of roles: (a) linking domains which by themselves are unfolded and bind to DNA only as a folded dimer (as in a designed single-chain Arc repressor), (b) connecting domains which can separately bind to DNA (as in the Oct-1 POU domain), and (c) linking a DNA-binding domain with a dimerization domain (as in the lambda repressor). In (a), the linker keeps the protein as a folded dimer so that it is always DNA-binding-competent. In (b), the linker is predicted to enhance DNA-binding affinity over those of the individual domains (with dissociation constants K(A) and K(B)) by p(d(0))/K(B) or p(d(0))/K(A), where p(d(0)) = (3/4pil(p)bL)(3/2) exp(-3d(0)(2)/4l(p)bL)(1 - 5l(p)/4bL +...) is the probability density for the end-to-end vector of the linker with L residues to have a distance d(0). In (c), the linker is predicted to enhance the binding affinity by K(d)(C)/p(d(0)), where K(d)(C) is the dimer dissociation constant for the dimerization domain. The predicted affinity enhancements are found to be actually reached by the Oct-1 POU domain and lambda repressor. However, there is room for improvement in many of the recently designed proteins. The theoretical limits presented should provide a useful guide for current efforts of designing DNA-binding proteins.

A unified picture of protein hydration: prediction of hydrodynamic properties from known structures

Hydration is essential for the structural and functional integrity of globular proteins. How much hydration water is required for that integrity? A number of techniques such as X-ray diffraction, nuclear magnetic resonance (NMR) spectroscopy, calorimetry, infrared spectroscopy, and molecular dynamics (MD) simulations indicate that the hydration level is 0.3-0.5 g of water per gram of protein for medium sized proteins. Hydrodynamic properties, when accounted for by modeling proteins as ellipsoids, appear to give a wide range of hydration levels. In this paper we describe an alternative numerical technique for hydrodynamic calculations that takes account of the detailed protein structures. This is made possible by relating hydrodynamic properties (translational and rotational diffusion constants and intrinsic viscosity) to electrostatic properties (capacitance and polarizability). We show that the use of detailed protein structures in predicting hydrodynamic properties leads to hydration levels in agreement with other techniques. A unified picture of protein hydration emerges. There are preferred hydration sites around a protein surface. These sites are occupied nearly all the time, but by different water molecules at different times. Thus, though a given water molecule may have a very short residence time (approximately 100-500 ps from NMR spectroscopy and MD simulations) in a particular site, the site appears fully occupied in experiments in which time-averaged properties are measured.

Disparate ionic-strength dependencies of on and off rates in protein-protein association

Electrostatic interactions have been observed to play important roles in the kinetics of protein-protein association. Ionic strength, by its ability to modulate the magnitude of electrostatic interactions, has often been conveniently used to test their presence. From experiments on a wide range of associating proteins, a common feature has emerged: the on rates show strong dependence on ionic strength whereas the off rates are relatively insensitive. Here this feature is explained by an explicit description of a transition state for the association process and the suggestion that this transition is near the final bound state of two proteins. The molecular basis of the transition state in the bimolecular process lies in the fact that the bound state is characterized by local specific (e.g., van der Waals, hydrophobic, and electrostatic) interactions, whereas the unbound state is characterized by translational and rotational freedom. In the transition state the protein-protein pair encounters a free-energy maximum since its translational-rotational entropy is reduced while the specific interactions are not yet attained. In this formalism of the protein-protein association process, the enhancement of on rates by long-range electrostatic interactions can be written (analogous to an ordinary transition-state theory) in the form k(on) = k(0)(on)exp(-G(el)/k(B)T), where G(el) is the electrostatic free energy of the transition state.

Stabilization of proteins in confined spaces

We present theory showing that confining a protein to a small inert space (a "cage") should stabilize the protein against reversible unfolding. Examples of such spaces might include the pores within chromatography columns, the Anfinsen cage in chaperonins, the interiors of ribosomes, or regions of steric occlusion inside cells. Confinement eliminates some expanded configurations of the unfolded chain, shifting the equilibrium from the unfolded state toward the native state. The partition coefficient for a protein in a confined space is predicted to decrease significantly when the solvent is changed from native to denaturing conditions. Small cages are predicted to increase the stability of the native state by as much as 15 kcal/mol. Confinement may also increase the rates of protein or RNA folding.

Prediction of protein interaction sites from sequence profile and residue neighbor list

Protein-protein interaction sites are predicted from a neural network with sequence profiles of neighboring residues and solvent exposure as input. The network was trained on 615 pairs of nonhomologous complex-forming proteins. Tested on a different set of 129 pairs of nonhomologous complex-forming proteins, 70% of the 11,004 predicted interface residues are actually located in the interfaces. These 7732 correctly predicted residues account for 65% of the 11,805 residues making up the 129 interfaces. The main strength of the network predictor lies in the fact that neighbor lists and solvent exposure are relatively insensitive to structural changes accompanying complex formation. As such, it performs equally well with bound or unbound structures of the proteins. For a set of 35 test proteins, when the input was calculated from the bound and unbound structures, the correct fractions of the predicted interface residues were 69 and 70%, respectively.

Cystic echinococcosis in semi-nomadic pastoral communities in north-west China

In order to determine the prevalence of human cystic echinococcosis (CE) in semi-nomadic traditional pastoralist groups in north-west China, 2 large community studies were undertaken in Altai and Tacheng Prefectures in 1990/91 and 1995/96, respectively. The Kekergash community (Altai) comprised mainly ethnic Kazakhs, whereas the Narenhebuke community (Tacheng) comprised mainly Mongolians. Populations were screened for CE by abdominal ultrasound scan (US) and serological tests. The total prevalence of confirmed human CE was higher in Narenhebuke (2.7%, 49/1844) than in Kekergash (0.9%, 17/1861; P < 0.01). Within each community there was no significant difference of CE prevalence between the Kazakh and Mongolian groups, although Han Chinese exhibited twice the rate of CE (4.9%) in Narenhebuke compared to the dominant Mongolian population. For each community, human CE prevalence increased with age and there was a greater risk associated with the practice of home slaughter of livestock. Dogs were screened for Echinococcus granulosus infection and re-infection levels using a highly specific coproantigen test. The proportion of dogs with positive coproantigen tests was significantly higher in Narenhebuke (36.0%, 50/139) compared to Kekergash (17.8%, 16/90). In Narenhebuke the re-infection levels of dogs, as determined by coproantigen positivity, were higher in the winter quarters (49.4%, 39/79) compared to the summer quarters (18.3%, 11/60; P < 0.01). Furthermore, coproantigen re-test positivity was 25% at 3 months and 29.2% at 7 months. Highest dog coproantigen positivity was obtained over the winter period.

Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading

A homology-based structure prediction method ideally gives both a correct fold assignment and an accurate query-template alignment. In this article we show that the combination of two existing methods, PSI-BLAST and threading, leads to significant enhancement in the success rate of fold recognition. The combined approach, termed COBLATH, also yields much higher alignment accuracy than found in previous studies. It consists of two-way searches both by PSI-BLAST and by threading. In the PSI-BLAST portion, a query is used to search for hits in a library of potential templates and, conversely, each potential template is used to search for hits in a library of queries. In the threading portion, the scoring function is the sum of a sequence profile and a 6x6 substitution matrix between predicted query and known template secondary structure and solvent exposure. "Two-way" in threading means that the query's sequence profile is used to match the sequences of all potential templates and the sequence profiles of all potential templates are used to match the query's sequence. When tested on a set of 533 nonhomologous proteins, COBLATH was able to assign folds for 390 (73%). Among these 390 queries, 265 (68%) had root-mean-square deviations (RMSDs) of less than 8 A between predicted and actual structures. Such high success rate and accuracy make COBLATH an ideal tool for structural genomics.

Epidemiology of alveolar echinococcosis in Xinjiang Uygur autonomous region, China: a preliminary analysis

The Xinjiang Uygur autonomous region (XUAR) in north-western China is known to be endemic for Echinococcosis multilocularis, the causative agent of human alveolar echinococcosis (HAE). Despite regular reports of HAE cases in their region, very little is known about the local epidemiology of the disease or the transmission of E. multilocularis. The epidemiology of HAE in Xinjiang has now been investigated by the analysis of data collected from the medical records of 157 clinical cases who had attended the four main hospitals in the region. These data indicate that the disease is relatively common in the Altai, western Junggar, and Tianshan mountain ranges, whereas the Tarim and Junggar basins are likely to be of low endemicity. The prevalence of the disease in the Kunlun mountains is not clear. Semi-nomadic groups, especially those of Kazakh or Mongol origin, have a higher risk of infection than other ethnic groups. Prevalence of the disease in humans appears to be correlated with aspects of the local climate, such as annual precipitation and temperature. Red foxes, Microtinae, Ochotona spp. and Marmota spp. may be important hosts of E. multilocularis in the XUAR, sustaining the transmission cycles of the parasite.

Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities

A survey of 322 proteins showed that the short polar (SP) side chains of four residues, Thr, Ser, Asp, and Asn, have a very strong tendency to form hydrogen bonds with neighboring backbone amides. Specifically, 32% of Thr, 29% of Ser, 26% of Asp, and 19% of Asn engage in such hydrogen bonds. When an SP residue caps the N terminal of a helix, the contribution to helix stability by a hydrogen bond with the amide of the N3 or N2 residue is well established. When an SP residue is in the middle of a helix, the side chain is unlikely to form hydrogen bonds with neighboring backbone amides for steric and geometric reasons. In essence the SP side chain competes with the backbone carbonyl for the same hydrogen-bonding partner (i.e., the backbone amide) and thus SP residues tend to break backbone carbonyl-amide hydrogen bonds. The proposition that this is the origin for the low propensities of SP residues in the middle of alpha helices (relative to those of nonpolar residues) was tested. The combined effects of restricting side-chain rotamer conformations (documented by Creamer and Rose, Proc Acad Sci USA, 1992;89:5937-5941; Proteins, 1994;19:85-97) and excluding side- chain to backbone hydrogen bonds by the helix were quantitatively analyzed. These were found to correlate strongly with four experimentally determined scales of helix-forming propensities. The correlation coefficients ranged from 0.72 to 0.87, which are comparable to those found for nonpolar residues (for which only the loss of side-chain conformational entropy needs to be considered).

Conformation gating as a mechanism for enzyme specificity

Acetylcholinesterase, with an active site located at the bottom of a narrow and deep gorge, provides a striking example of enzymes with buried active sites. Recent molecular dynamics simulations showed that reorientation of five aromatic rings leads to rapid opening and closing of the gate to the active site. In the present study the molecular dynamics trajectory is used to quantitatively analyze the effect of the gate on the substrate binding rate constant. For a 2. 4-A probe modeling acetylcholine, the gate is open only 2.4% of the time, but the quantitative analysis reveals that the substrate binding rate is slowed by merely a factor of 2. We rationalize this result by noting that the substrate, by virtue of Brownian motion, will make repeated attempts to enter the gate each time it is near the gate. If the gate is rapidly switching between the open and closed states, one of these attempts will coincide with an open state, and then the substrate succeeds in entering the gate. However, there is a limit on the extent to which rapid gating dynamics can compensate for the small equilibrium probability of the open state. Thus the gate is effective in reducing the binding rate for a ligand 0.4 A bulkier by three orders of magnitude. This relationship suggests a mechanism for achieving enzyme specificity without sacrificing efficiency.

Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar

The electrostatic enhancement of the association rate of barnase and barstar is calculated using a transition-state theory like expression and atomic-detail modeling of the protein molecules. This expression predicts that the rate enhancement is simply the average Boltzmann factor in the region of configurational space where association occurs instantaneously in the diffusion-controlled limit. Based on experimental evidence, this "transition state" is defined by configurations in which, relative to the stereospecifically bound complex, the two proteins are shifted apart by approximately 8 A (so a layer of water can be accommodated in the interface) and the two binding surfaces are rotated away by 0 degrees to 3 degrees. The values of the average Boltzmann factor, calculated by solving the Poisson-Boltzmann equation, for the wild-type complex and 16 complexes with single mutations are found to correlate well with experimental results for the electrostatic rate enhancement. The predicted rate enhancement is found to be somewhat insensitive to the precise definition of the transition state, due to the long-range nature of electrostatic interactions. The experimental ionic strength dependence of the rate enhancement is also reasonably reproduced.

Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site

The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., < 5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate.

Design of fast enzymes by optimizing interaction potential in active site

The diffusional encounter between substrate and enzyme, and hence catalytic efficiency, can be enhanced by mutating charged residues on the surface of the enzyme. In this paper we present a simple method for screening such mutations. This is based on our earlier result that electrostatic enhancement of the enzyme-substrate binding rate constant can be accounted for just by the interaction potential within the active site. Assuming that catalytic and structural integrity is maintained, the catalytic efficiency can be optimized by surface charge mutations which lead to stronger interaction potential within the active site. Application of the screening method on superoxide dismutase shows that only charge mutations close to the active site will have practical effect on the catalytic efficiency. This rationalizes a large number of findings obtained in previous simulation and experimental studies.

Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor

Electrostatic interactions are known experimentally to enhance the rate of protein-protein association by three to four orders of magnitude. However, theoretical efforts to quantitatively account for such rate enhancement have been hampered by the need to consider a large number of relative configurations of two associating proteins sampled during their diffusional encounter. Our recent work indicates that a good estimate of the rate enhancement is given by the average Boltzmann factor in the region of configurational space where association can effectively take place. This estimate is tested on a model system consisting of two spherical proteins, each with a "reactive patch." Three different forms of interaction potential are considered. Comparison with exact results for the association rate constant demonstrates that predictions based on the local Boltzmann factor are accurate to within approximately 50% for realistic sizes of the reactive region and amplitudes of the interaction potential.

Modeling of protein conformational fluctuations in pKa predictions

A method is presented to account for conformational fluctuations of a protein in predicting the pK(a) values of its titrating groups. Conformations of the protein are generated by conventional molecular dynamics or Monte Carlo simulations, in which the protonations of the titrating groups are fixed. For each protein conformation, the electrostatic free energies required to add a proton charge to a titrating group while other groups are either unprotonated or protonated are calculated within a dielectric continuum model. These are used to determine the mean protonations of the titrating groups in the conformation at a series of pH values. The mean protonations are then used to determine the relative weight of the particular conformation with the titrating groups having all possible protonations. A conformationally averaged mean protonation for each titrating group is finally obtained by the weighted sum of the group's mean protonations in all the conformations. This method is applied to yeast iso-1-ferricytochrome c. The predicted pK(a) values are in general agreement with experimental results.

Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions

A general formalism is developed for calculating the time-dependent rate coefficient k(t) of an irreversible diffusion-influenced reaction. This formalism allows one to treat most factors that affect k(t), including rotational Brownian motion and conformational gating of reactant molecules and orientation constraint for product formation. At long times k(t) is shown to have the asymptotic expansion k(infinity)[1 + k(infinity) (pie Dt)-1/2 /4 pie D + ...], where D is the relative translational diffusion constant. An approximate analytical method for calculating k(t) is presented. This is based on the approximation that the probability density of the reactant pair in the reactive region keeps the equilibrium distribution but with a decreasing amplitude. The rate coefficient then is determined by the Green function in the absence of chemical reaction. Within the framework of this approximation, two general relations are obtained. The first relation allows the rate coefficient for an arbitrary amplitude of the reactivity to be found if the rate coefficient for one amplitude of the reactivity is known. The second relation allows the rate coefficient in the presence of conformational gating to be found from that in the absence of conformational gating. The ratio k(t)/k(0) is shown to be the survival probability of the reactant pair at time t starting from an initial distribution that is localized in the reactive region. This relation forms the basis of the calculation of k(t) through Brownian dynamics simulations. Two simulation procedures involving the propagation of nonreactive trajectories initiated only from the reactive region are described and illustrated on a model system. Both analytical and simulation results demonstrate the accuracy of the equilibrium-distribution approximation method.

In vitro evolution of thermodynamically stable turns

To determine the role of primary structure in specifying turns, random sequences (guests) were substituted for the native turn sequences in a series of proteins (hosts) of differing thermodynamic stabilities.The fraction of inserts that result in active proteins is measured as a function of the stability of the host and temperature. With a highly stable host, more than half of the inserts give functional proteins. However, a smaller fraction of sequences supports folding as the stability of the host decreases, and the temperature increases. The sequences of many of the selected inserts resemble the wild-type turn, and those that diverge match other established turn preferences. Thermodynamic measurements show that turn sequences selected under stringent conditions result in the most stable proteins. Thus, beta-turns appear to be under evolutionary pressure favouring thermodynamically stable structures.

Calculation of translational friction and intrinsic viscosity. I. General formulation for arbitrarily shaped particles

A general method for calculating translational friction and intrinsic viscosity is developed through exploiting relations between hydrodynamics and electrostatics. An approximate relation xi = 6 pi eta 0C between the translational friction coefficient xi of a particle (eta 0: solvent viscosity) and its capacitance C was derived previously. This involved orientationally preaveraging the Oseen tensor, but the result was found to be very accurate. Based on preaveraging, we find that the intrinsic viscosity [eta] of a particle can be estimated from its polarizability alpha through [eta] = 3/4 alpha + 1/4 Vp, where Vp is the volume of the particle. Both the capacitance and the polarizability can be obtained in a single calculation using the boundary-element technique. An efficient approach is thus found for estimating [eta], a quantity that is very useful in practice because of its sensitivity to particle shape but is notoriously difficult to calculate. Illustrative calculations on ellipsoids, cylinders, and dumbbells demonstrate both the accuracy of the approximate relations and the efficiency of the present method.

Protein design: a hierarchic approach

The de novo design of peptides and proteins has recently emerged as an approach for investigating protein structure and function. Designed, helical peptides provide model systems for dissecting and quantifying the multiple interactions that stabilize secondary structure formation. De novo design is also useful for exploring the features that specify the stoichiometry and stability of alpha-helical coiled coils and for defining the requirements for folding into structures that resemble native, functional proteins. The design process often occurs in a series of discrete steps. Such steps reflect the hierarchy of forces required for stabilizing tertiary structures, beginning with hydrophobic forces and adding more specific interactions as required to achieve a unique, functional protein.

Structural analysis of the N- and C-termini in a peptide with consensus sequence

We present a structural analysis of a peptide, the sequence of which includes amino acids that show preferences for specific positions near the N- and C-termini in protein helices. This peptide has the sequence ac-YMSEDELKAAEAAFKRHGVP-amide, which includes a strong version of an N-terminal Harper-Rose capping box structure as well as a Gly located close to the C-terminus designed to elucidate its role in C-terminal capping. The sequence of five residues at the middle is inserted to separate effects at the two ends via a helix-stabilizing linker. Application of a simulated annealing procedure using interproton distance constraints derived from 1H NOESY experiments in water reveals the presence of a C-terminal structure in this model. The C-terminus forms a folded back structure in a significant fraction of structures generated by the annealing, in most of which Gly assumes an alpha L conformation. This structure occurs within a highly flexible region of the molecule and hence is occupied only a fraction of the time.

Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR

The presence and location of water of hydration (that is, bound water) in the solution structure of human interleukin-1 beta (hIL-1 beta) was investigated with water-selective two-dimensional heteronuclear magnetic resonance spectroscopy. It is shown here that in addition to water at the surface of the protein and ordered internal water molecules involved in bridging hydrogen bonds, positionally disordered water is present within a large, naturally occurring hydrophobic cavity located at the center of the molecule. These water molecules of hydration have residency times in the range of 1 to 2 nanoseconds to 100 to 200 microseconds and can be readily detected by nuclear magnetic resonance (NMR). Thus, large hydrophobic cavities in proteins may not be truly empty, as analysis of crystal structures appears to show, but may contain mobile water molecules that are crystallographically invisible but detectable by NMR.

Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: evidence for an N terminal "capping box"

A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as "capping boxes," we have reexamined the side chain-main chain interactions in a variant sequence using 1H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved. Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant.(ABSTRACT TRUNCATED AT 250 WORDS)

Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin

We have begun to use molecular dynamics to simulate the kinetics of nitric oxide rebinding to myoglobin after photodissociation. Rebinding was simulated using a potential function that switches smoothly between a nonbinding potential and a binding potential as a function of the position and orientation of the ligand, with no barrier arising from the crossing of potential surfaces of different electron spin. In 96 of 100 trajectories, the ligand rebound in < 15 ps. The kinetic progress curve was obtained by determining the time in each trajectory at which the ligand rebound and then calculating the fraction of unbound ligands as a function of time. The curve can be well reproduced by a simple model based on the dynamics of a Langevin particle moving on a one-dimensional potential of mean force calculated from nonreactive protein trajectories. The rate of escape from the energy well adjacent to the heme is in good agreement with the value calculated from experimental data, suggesting that a multiple-well model provides a plausible explanation for the nonexponential rebinding kinetics. A transition-state analysis suggests that protein conformational relaxation coupled to the displacement of the iron from the heme plane is an unlikely cause for the nonexponential rebinding of nitric oxide.