血清RBP4、NGAL、Klotho蛋白在慢性肾脏病病情监测及预后评估中的价值

目的:探讨血清视黄醇结合蛋白4(retinol binding protein 4,RBP4)、中性粒细胞明胶酶相关脂质运载蛋白(neutrophil gelatinase-associated lipocalin,NGAL)、Klotho蛋白在慢性肾脏病病情监测及预后评估中的价值。方法:收集我院2017年5月～2019年2月收治的297例慢性肾脏病患者为研究对象,依据肾小球滤过率(GFR)分为1期24例、2期46例、3期128例、4期66例、5期33例,并依据临床转归情况分为肾功能稳定组104例和肾功能恶化组193例;同期选择门诊健康体检者251例作为对照组。比较各组血清RBP4、NGAL、Klotho蛋白表达情况,并分析慢性肾脏病患者血清RBP4、NGAL、Klotho蛋白和GFR的相关性。结果:慢性肾脏病组血清RBP4、NGAL水平高于对照组,Klotho蛋白低于慢性肾脏病组(P0.05)。慢性肾脏病5期者血清RBP4、NGAL水平高于4期、3期、2期及1期者,Klotho蛋白低于4期、3期、2期及1期者,差异有统计学意义(P0.05)。慢性肾脏病患者血清RBP4、NGAL和GFR呈负相关,Klotho蛋白和GFR呈正相关(P0.05)。肾功能恶化组血清RBP4、NGAL水平高于肾功能稳定组,Klotho蛋白低于肾功能稳定组,差异有统计学意义(P0.05)。结论:血清RBP4、NGAL及Klotho蛋白表达水平的变化对了解慢性肾脏病患者病情程度及预后评估中有重要的参考价值,建议临床予以重视。     

妊娠期糖尿病患者血清NRG4、FGF-23、PGRN水平及其临床意义

摘要 目的：探讨妊娠期糖尿病患者血清神经调节蛋白4(NRG4)、成纤维细胞生长因子-23(FGF-23)、前颗粒体蛋白(PGRN)水平及其临床意义。方法：选择2018年4月至2019年11月我院诊治的90例妊娠期糖尿病患者作为糖尿病组,选择同期在我院进行健康体检的90名健康孕妇作为对照组。检测两组血清NRG4、FGF-23、PGRN水平,血脂指标[高密度脂蛋白（HDL）、总胆固醇（TC）、甘油三酯（TG）和低密度脂蛋白（LDL）]水平,肝功能指标[谷草转氨酶（AST）、谷丙转氨酶(ALT)]水平,血糖和胰岛素指标[空腹血糖（FPG）、空腹胰岛素(FINS)]水平,并计算抗胰岛素抵抗指数(HOMA-IR)、胰岛素敏感性指数（ISI）和胰岛?茁细胞功能指数(HOMA-β)。分析各临床指标间的关系。结果：与对照组相比,糖尿病组体质量指数（BMI）、TG、TC、FPG、FINS、HOMA-IR、NRG4、FGF-23、PGRN明显升高（P<0.05）,ISI和HOMA-β明显下降（P<0.05）。血清NRG4、FGF-23、PGRN与ISI和HOMA-β均呈负相关（P<0.05）,与BMI、TG、TC、FPG、FINS、HOMA-IR均呈正相关（P<0.05）。TG与NRG4表达联系密切（β=0.007,P<0.05）,ISI和HOMA-IR与FGF-23表达联系密切（β=-6.674、0.048,P<0.05）,FPG和TC与PGRN表达联系密切（β=22.308、0.507,P<0.05）。结论：妊娠期糖尿病患者血清NRG4、FGF-23、PGRN水平异常升高,并参与妊娠期糖尿病患者的糖脂代谢和胰岛素抵抗,检测其水平有助于评估妊娠期糖尿病的糖脂代谢异常情况。     

尿神经突起导向因子1、肾损伤分子-1、视黄醇结合蛋白水平与妊娠期高血压疾病早期肾损伤的关系研究

摘要 目的：研究尿神经突起导向因子1（Netrin-1）、肾损伤分子-1（Kim-1）、视黄醇结合蛋白（RBP）水平与妊娠期高血压疾病（HDCP）早期肾损伤的关系。方法：将我院从2017年2月～2020年2月收治的HDCP患者80例纳入研究,按照HDCP严重程度分作妊娠期高血压组22例、轻度子痫前期组32例、重度子痫前期组26例,另随机选取同期于我院接受规律孕产检以及分娩正常妊娠孕妇40例作为正常妊娠组,检测并比较各组尿Netrin-1、Kim-1、RBP水平。此外,将HDCP患者按照是否出现早期肾损伤分作肾功能损伤组42例和肾功能正常组38例,比较两组尿Netrin-1、Kim-1、RBP以及肾功能指标水平,并进行相关性分析,通过Logistic回归分析HDCP早期肾损伤的影响因素。结果：正常妊娠组、妊娠期高血压组、轻度子痫前期组、重度子痫前期组尿Netrin-1水平呈逐渐降低趋势,而尿Kim-1、RBP水平均呈逐渐升高趋势,多组数据间两两对比差异均有统计学意义（均P＜0.05）。肾功能损伤组尿Netrin-1水平低于肾功能正常组,而尿Kim-1、RBP以及血尿素氮、血肌酐、24 h尿白蛋白排出量（UAE）水平均明显高于肾功能正常组（均P＜0.05）。经Pearson相关性分析可得：HDCP早期肾损伤患者尿Netrin-1水平和血尿素氮、血肌酐、UAE均呈负相关关系,而Kim-1、RBP水平和血尿素氮、血肌酐、UAE均呈正相关关系（均P＜0.05）。经Logistic回归分析发现：尿Netrin-1是HDCP早期肾损伤的保护因素,而尿Kim-1、RBP是HDCP早期肾损伤的危险因素（均P＜0.05）。结论：随着尿Netrin-1水平的降低以及Kim-1、RBP水平的升高,HDCP早期肾损伤风险越高,检测尿Netrin-1、Kim-1、RBP水平可能有助于评估HDCP的病情严重程度和肾功能损伤。     

铜蓝蛋白、鳞状细胞癌相关抗原与慢性肾功能衰竭的关系及对病情进展的预测价值研究

摘要 目的：分析铜蓝蛋白（CER）、鳞状细胞癌相关抗原（SCCA）与慢性肾功能衰竭的关系及对病情进展的预测价值。方法：选择我院自2019年4月至2021年4月接诊的169例慢性肾功能衰竭患者作为研究对象,根据24 h尿白蛋白定量分为微量白蛋白尿组（＜200 mg/24 h,102例）和大量白蛋白尿组（＞200 mg/24 h,67例）。比较两组各项实验室指标及血清CER、SCCA水平,分析CER、SCCA与慢性肾功能衰竭患者肾功能指标的关系。随访12个月,观察病情进展,使用受试者工作特征曲线（ROC）评价血清CER联合SCCA对病情进展的预测效能。结果：大量白蛋白尿组血清肌酐（Scr）、血尿素氮（BUN）水平均明显高于微量白蛋白尿组,肾小球滤过率（GFR）低于微量白蛋白尿组（P＜0.05）;大量白蛋白尿组血清CER、SCCA水平均高于微量白蛋白尿组（P＜0.05）;经Pearson相关性分析,慢性肾功能衰竭患者血清CER、SCCA水平均与Scr、BUN呈正相关,与GFR呈负相关（P＜0.05）;经多因素Logistic回归分析,GFR、CER、SCCA均是慢性肾功能衰竭患者病情进展的独立预测因素（P＜0.05）;经ROC曲线分析,血清CER联合SCCA预测慢性肾功能衰竭患者病情进展的AUC为0.925,明显大于GFR的0.620（P＜0.05）。结论：血清CER、SCCA水平与慢性肾功能衰竭患者肾功能呈负相关,联合预测病情进展效能较好,值得临床予以重视应用。     

利妥昔单抗治疗肾病综合征患者效果观察及对视黄醇结合蛋白、微循环状态的影响分析

摘要 目的：探讨与分析利妥昔单抗（RTX）治疗肾病综合征患者效果观察及对视黄醇结合蛋白（RBP）、微循环状态的影响。方法：2018年9月到2021年11月选择在本院诊治的肾病综合征患者66例作为研究对象,所有患者按入院先后顺序编号,依据治疗方法分为利妥昔单抗组和对照组各33例,对照组给予糖皮质激素治疗,利妥昔单抗组在对照组治疗的基础上给予利妥昔单抗治疗,治疗观察3个月,观察与检测血清RBP、微循环状态变化情况。结果：治疗后利妥昔单抗组的总有效率为97.0 %,明显高于对照组的81.8 %（P<0.05）。两组治疗后的尿蛋白定量、尿蛋白定性水平低于治疗前,利妥昔单抗组明显低于对照组,而血浆白蛋白较治疗前高,且利妥昔单抗组高于对照组（P<0.05）。两组治疗后的甲襞微循环管绊形态、流态评分明显低于治疗前,利妥昔单抗组明显低于对照组（P<0.05）。两组治疗后的血清RBP含量低于治疗前,利妥昔单抗组明显低于对照组（P<0.05）。两组治疗期间不良反应对比无明显差异（P>0.05）。结论：利妥昔单抗治疗肾病综合征患者能有效改善微循环状态,抑制血清RBP的表达,能提高治疗效果,还可促进改善肾功能,具有安全性。     

血清Klotho蛋白、视锥蛋白样蛋白-1、高迁移率族蛋白1与阿尔茨海默病患者认知功能和预后不良的关系

摘要 目的：探讨阿尔兹海默病（AD）患者血清Klotho蛋白、视锥蛋白样蛋白-1（VILIP-1）、高迁移率族蛋白1（HMGB1）与认知功能及预后的关系。方法：选取2019年4月-2021年5月在我院接受治疗的136例AD患者作为AD组,另选取150例同时期在我院进行体检的健康志愿者作为对照组,应用酶联免疫吸附法检测两组血清Klotho蛋白、VILIP-1、HMGB1表达水平,采用简易精神状态检查量表（MMSE）评估两组认知功能,采用Pearson相关性分析以上三指标与MMSE评分之间的关系;AD患者根据治疗1年后的预后情况分为预后良好组（n=74）与预后不良组（n=62）,应用单因素、多因素Logistic回归分析引发AD患者预后不良的危险因素;采用受试者工作特征（ROC）曲线评估血清Klotho蛋白、VILIP-1、HMGB1联合检测对AD患者预后的预测效能。结果：AD组的MMSE评分、血清Klotho蛋白水平显著低于对照组,而血清VILIP-1及HMGB1水平显著高于对照组（均P＜0.05）;Pearson相关性结果显示血清Klotho蛋白水平与MMSE评分之间呈显著正相关（P＜0.05）,而血清VILIP-1、HMGB1水平与MMSE评分之间呈显著负相关（均P＜0.05）;多因素Logistic回归分析显示血清VILIP-1、HMGB1水平升高是引发AD患者预后不良的独立危险因素,而血清Klotho蛋白水平升高是其保护因素（P＜0.05）;ROC曲线显示 Klotho蛋白、VILIP-1、HMGB1联合检测AD患者曲线下面积为0.839,敏感度为80.65%,特异度为83.78%。结论：血清Klotho蛋白、VILIP-1、HMGB1表达水平与AD患者认知功能和预后均具有较强的关联性,临床可以通过联合检测以上三指标辅助评估AD患者的预后。     

冠心病患者血清IMA、cathepsin S、RBP4水平与炎性因子及心肌缺血程度的相关性研究

摘要 目的：探讨血清缺血修饰白蛋白（IMA）、组织蛋白酶S（cathepsin S）、视黄醇结合蛋白4（RBP4）水平与冠心病患者炎性因子、心肌缺血程度的相关性。方法：选择2017年2月至2019年10月我院收治的100例冠心病患者,根据心肌缺血程度分为稳定型心绞痛组（34例）、不稳定型心绞痛组（42例）、急性心肌梗死组（24例）。检测并比较患者血清IMA、cathepsin S、RBP4、炎性因子[白介素-6（IL-6）、C反应蛋白（CRP）、肿瘤坏死因子-α（TNF-α）]水平,分析IMA、cathepsin S、RBP4与炎性因子、SYNTAX积分的相关性,采用多元有序Logistic回归分析影响冠心病患者心肌缺血程度的因素。结果：冠心病患者心肌缺血程度越严重,血清IMA、cathepsin S、RBP4及炎性因子水平越高（P＜0.05）。Pearson相关性分析结果显示,血清IMA、cathepsin S、RBP4水平与炎性因子、SYNTAX积分均呈正相关（P＜0.05）。多元有序Logistic回归分析结果显示,高CRP、IMA、cathepsin S、RBP4水平是冠心病心肌缺血程度的影响因素（OR=1.702、1.183、1.881、2.003,P＜0.05）。结论：血清IMA、cathepsin S、RBP4水平与冠心病患者心肌缺血程度及炎性因子有关,IMA、cathepsin S、RBP4可能与炎症反应共同作用参与冠心病发病过程。     

新诊断2型糖尿病患者血清Pannexin-1、Apelin、RBP4、VEGF水平与糖脂代谢和胰岛素抵抗的关系研究

摘要 目的：探讨新诊断2型糖尿病患者血清缝隙连接蛋白-1(Pannexin-1)、爱帕琳肽（Apelin）、视黄醇结合蛋白4(RBP4)、血管内皮生长因子（VEGF）水平与糖脂代谢和胰岛素抵抗的关系。方法：选择2018年2月至2020年2月我院诊治的120例新诊断2型糖尿病患者作为糖尿病组,选择同期在我院进行体检的120例健康者作为对照组。检测所有受试者甘油三酯（TG）、总胆固醇（TC）、谷草转氨酶（AST）、谷丙转氨酶(ALT)、高密度脂蛋白（HDL）和低密度脂蛋白（LDL）水平、空腹血糖（FPG）、空腹胰岛素(FINS)、Pannexin-1、Apelin、RBP4、VEGF水平,计算胰岛素抵抗指数(HOMA-IR)、胰岛素敏感性指数（ISI）和胰岛?茁细胞功能指数(HOMA-β)。分析Pannexin-1、Apelin、RBP4、VEGF水平与糖脂代谢和胰岛素抵抗相关指标的关系,分析影响上述指标表达的相关因素。结果：与对照组相比,糖尿病组体质量指数（BMI）、TG、TC、FPG、FINS、Pannexin-1、Apelin、RBP4、VEGF水平,HOMA-IR明显升高（P<0.05）,ISI和HOMA-β明显下降（P<0.05）。新诊断2型糖尿病患者血清Pannexin-1、Apelin、RBP4、VEGF水平与ISI和HOMA-β均呈负相关（P<0.05）,与BMI、TG、TC、FPG、FINS、HOMA-IR均呈正相关（P<0.05）。TG与Pannexin-1表达联系密切（β=0.006,P<0.05）,ISI和HOMA-IR与Apelin表达联系密切（β=-6.673、0.049,P<0.05）,FPG和TC与RBP4表达联系密切（β=22.309、0.506,P<0.05）,HOMA-IR与VEGF表达联系密切（β=0.574,P<0.05）。结论：新诊断2型糖尿病患者血清Pannexin-1、Apelin、RBP4、VEGF水平异常升高,并参与新诊断2型糖尿病患者的糖脂代谢和胰岛素抵抗,在2型糖尿病的诊断和预防中有一定临床价值。     

尿毒症血液透析患者血清Lp-PLA2、FGF-23与自体动静脉内瘘成熟不良的关系研究

摘要 目的：探讨尿毒症血液透析患者血清脂蛋白相关磷脂酶A2（Lp-PLA2）、成纤维细胞生长因子-23（FGF-23）与自体动静脉内瘘（AVF）成熟不良的关系。方法：选取2021年2月～2022年12月联勤保障部队第908医院肾内科收治的170例接受血液透析的尿毒症患者,根据AVF成熟情况分为成熟不良组57例和成熟组113例。采用酶联免疫吸附法检测血清Lp-PLA2、FGF-23水平。通过多因素Logistic回归分析尿毒症血液透析患者AVF成熟不良的影响因素,受试者工作特征（ROC）曲线分析血清Lp-PLA2、FGF-23水平对尿毒症血液透析患者AVF成熟不良的预测效能。结果：成熟不良组血清Lp-PLA2、FGF-23水平高于成熟组（P＜0.05）。多因素Logistic回归分析显示,血磷、低密度脂蛋白胆固醇（LDL-C）、Lp-PLA2、FGF-23升高为尿毒症血液透析患者AVF成熟不良的独立危险因素（P＜0.05）。ROC曲线分析显示,血清Lp-PLA2、FGF-23水平单独和联合预测尿毒症血液透析患者AVF成熟不良的曲线下面积（AUC）分别为0.725、0.763、0.822,血清Lp-PLA2、FGF-23水平联合预测的AUC最大。结论：尿毒症血液透析患者血清Lp-PLA2、FGF-23水平升高与AVF成熟不良独立相关,血清Lp-PLA2、FGF-23水平联合对AVF成熟不良的预测效能良好。     

高通量血液透析联合肾衰宁颗粒对尿毒症患者钙磷代谢、炎症反应以及营养状况的影响

摘要 目的：探讨高通量血液透析（HFHD）联合肾衰宁颗粒对尿毒症患者钙磷代谢、炎症反应以及营养状况的影响。方法：选取2017年1月~2019年10月在我院接受血液透析治疗的尿毒症患者114例作为研究对象,按随机数字表法分成对照组和观察组,每组各57例,对照组给予HFHD,观察组在对照组基础上口服肾衰宁颗粒。两组均治疗3个月。比较两组患者治疗前后肾功能指标,包括尿素氮（BUN）、血肌酐（Scr）、肾小球滤过率（GFR）;钙磷代谢相关指标血清钙、血清磷、甲状旁腺激素（PTH）;炎症反应指标,包括降钙素原（PCT）、C反应蛋白（CRP）、白细胞介素-6（IL-6）;营养状况指标,包括白蛋白（ALB）、血红蛋白（Hb）、血清总蛋白（TP）。结果：治疗后两组患者BUN、Scr、GFR、血清磷、PTH、PCT、CRP、IL-6较治疗前降低,血清钙、ALB、Hb、TP较治疗前升高,观察组患者BUN、Scr、GFR、血清磷、PTH、PCT、CRP、IL-6低于对照组,血清钙、ALB、Hb、TP高于对照组,差异均有统计学意义（P<0.05）。结论：HFHD联合肾衰宁颗粒治疗尿毒症,可有效改善患者的钙磷代谢和肾功能,改善机体炎症状态及营养状况。     

Protein misfolding, aggregation, and degradation in disease

Pathologies associated with protein misfolding have been observed in neurodegenerative diseases such as Alzheimer’s disease, metabolic diseases like phenylketonuria, and diseases affecting structural proteins like collagen or keratin. Misfolding of mutant proteins in these and many other diseases may result in premature degradation, formation of toxic aggregates, or incorporation of toxic conformations into structures. We review common traits of these diverse diseases under the unifying view of protein misfolding. The molecular pathogenesis is discussed in the context of protein quality control systems consisting of molecular chaperones and intracellular proteases that assist the folding and supervise the maintenance of the folded structure. Furthermore, genetic and environmental factors that may modify the severity of these diseases are underscored. The present article represents a partly revised and updated version of chapter 1 published earlier in volume 232 of the series Methods in Molecular Biology (Walker, J. M., ed., Humana Press, Totowa, NJ), Protein Misfolding and Disease: Principles and Protocols (Bross, P. & Gregersen, N., eds.), pp. 3–16 (2003).     

Core glycan in the yeast multicopper ferroxidase, Fet3p: A case study of N-linked glycosylation, protein maturation, and stability

Glycosylation is essential to the maintenance of protein quality in the vesicular protein trafficking pathway in eukaryotic cells. Using the yeast multicopper oxidase, Fet3p, the hypothesis is tested that core glycosylation suppresses Fet3p nascent chain aggregation during synthesis into the endoplasmic reticulum (ER). Fet3p has 11 crystallographically mapped N‐linked core glycan units. Assembly of four of these units is specifically required for localization of Fet3p to the plasma membrane (PM). Fet3 protein lacking any one of these glycan units is found in an intracellular high‐molecular mass species resolvable by blue native gel electrophoresis. Individually, the remaining glycan moieties are not required for ER exit; however, serial deletion of these by N → A substitution correlates with these desglycan species failure to exit the ER. Desglycan Fet3 proteins that localize to the PM are wild type in function indicating that the missing carbohydrate is not required for native structure and biologic activity. This native function includes the interaction with the iron permease, Ftr1p, and wild type high‐affinity iron uptake activity. The four essential sequons are found within relatively nonpolar regions located in surface recesses and are strongly conserved among fungal Fet3 proteins. The remaining N‐linked sites are found in more surface exposed, less nonpolar environments, and their conservation is weak or absent. The data indicate that in Fet3p the N‐linked glycan has little effect on the enzyme's molecular activity but is critical to its cellular activity by maximizing the protein's exit from the ER and assembly into a functional iron uptake complex.     

Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.

What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded β-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Fingerclasp, a dimer of interdigitating β–β–α units, the simplest variant of the “handshake” structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather—a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.     

Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function

Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Three complexes that have previously been partially characterized include (a) the Golgi transport complex (GTC), identified in an in vitro membrane transport assay, (b) the ldlCp complex, identified in analyses of CHO cell mutants with defects in Golgi-associated glycosylation reactions, and (c) the mammalian Sec34 complex, identified by homology to yeast Sec34p, implicated in vesicular transport. We show that these three complexes are identical and rename them the conserved oligomeric Golgi (COG) complex. The COG complex comprises four previously characterized proteins (Cog1/ldlBp, Cog2/ldlCp, Cog3/Sec34, and Cog5/GTC-90), three homologues of yeast Sec34/35 complex subunits (Cog4, -6, and -8), and a previously unidentified Golgi-associated protein (Cog7). EM of ldlB and ldlC mutants established that COG is required for normal Golgi morphology. "Deep etch" EM of purified COG revealed an approximately 37-nm-long structure comprised of two similarly sized globular domains connected by smaller extensions. Consideration of biochemical and genetic data for mammalian COG and its yeast homologue suggests a model for the subunit distribution within this complex, which plays critical roles in Golgi structure and function.     

A 3-disulfide mutant of mouse prion protein expression, oxidative folding, reductive unfolding, conformational stability, aggregation and isomerization

The structure of wild-type mouse prion protein mPrP(23-231) consists of two distinctive segments with approximately equal size, a disordered and flexible N-terminal domain encompassing residues 23-124 and a largely structured C-terminal domain containing about 40% of helical structure and stabilized by one disulfide bond (Cys(178)-Cys(213)). We have expressed a mPrP mutant with 4 Ala/Ser-->Cys replacements, two each at the N-(Cys(36), Cys(112)) and C-(Cys(134), Cys(169)) domains. Our specific aims are to study the interaction between N- and C-domains of mPrP during the oxidative folding and to produce stabilized isomers of mPrP for further analysis. Oxidative folding of fully reduced mutant, mPrP(6C), generates one predominant 3-disulfide isomer, designated as N-mPrP(3SS), which comprises the native disulfide (Cys(178)-Cys(213)) and two non-native disulfide bonds (Cys(36)-Cys(134) and Cys(112)-Cys(169)) that covalently connect the N- and C-domains. In comparison to wild-type mPrP(23-231), N-mPrP(3SS) exhibits an indistinguishable CD spectra, a similar conformational stability in the absence of thiol and a reduced ability to aggregate. In the presence of thiol catalyst and denaturant, N-mPrP(3SS) unfolds and generates diverse isomers that are amenable to further isolation, structural and functional analysis.     

NHERFs, NEP, MAGUKs, and more: interactions that regulate PTEN

This year marks the 10th anniversary of the discovery of the PTEN/MMAC1/TEP1 tumor suppressor gene (hereafter referred to as PTEN), one of the most commonly mutated genes in cancer. PTEN encodes a lipid phosphatase that dephosphorylates phosphoinositide-3,4,5-triphosphate (PIP(3)), thereby counteracting mitogenic signaling pathways driven by phosphoinositol-3-kinases (PI3K). By opposing PI3K signaling, PTEN inhibits the activation of the critical PI3K effector proteins Akt1-3 (also known as protein kinase B or PKB). Given its central role in antagonizing PI3K signaling, one might expect that like PI3K, the activity of the PTEN protein would be highly regulated by numerous protein/protein interactions. However, surprisingly little is known about such interactions. This fact, combined with the generally accepted notion that phosphatases are less exquisitely regulated than kinases, has led to the idea that PTEN may function in a relatively unregulated fashion. Here we review the identities and proposed functions of known PTEN-interacting proteins, and point out avenues of investigation that we hope may be fruitful in identifying important new mechanisms of PTEN regulation in mammalian cells.     

Structures, basins, and energies: a deconstruction of the Protein Coil Library

Globular proteins adopt complex folds, composed of organized assemblies of alpha-helix and beta-sheet together with irregular regions that interconnect these scaffold elements. Here, we seek to parse the irregular regions into their structural constituents and to rationalize their formative energetics. Toward this end, we dissected the Protein Coil Library, a structural database of protein segments that are neither alpha-helix nor beta-strand, extracted from high-resolution protein structures. The backbone dihedral angles of residues from coil library segments are distributed indiscriminately across the phi,psi map, but when contoured, seven distinct basins emerge clearly. The structures and energetics associated with the two least-studied basins are the primary focus of this article. Specifically, the structural motifs associated with these basins were characterized in detail and then assessed in simple simulations designed to capture their energetic determinants. It is found that conformational constraints imposed by excluded volume and hydrogen bonding are sufficient to reproduce the observed ,psi distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with alpha-helices, strands of beta-sheet, canonical beta-turns, and polyproline II conformers comprise approximately 90% of all protein structure.     

qNABpredict: Quick,accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids

Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since they must predict every amino acid in the input sequence and rely on multiple sequence alignments. We propose an alternative approach that predicts content (fraction) of the NA-binding residues, offering more information than the protein-level prediction and much shorter runtime than the residue-level tools. Our first-of-its-kind content predictor, qNABpredict, relies on a small, rationally designed and fast-to-compute feature set that represents relevant characteristics extracted from the input sequence and a well-parametrized support vector regression model. We provide two versions of qNABpredict, a taxonomy-agnostic model that can be used for proteins of unknown taxonomic origin and more accurate taxonomy-aware models that are tailored to specific taxonomic kingdoms: archaea, bacteria, eukaryota, and viruses. Empirical tests on a low-similarity test dataset show that qNABpredict is 100 times faster and generates statistically more accurate content predictions when compared to the content extracted from results produced by the residue-level predictors. We also show that qNABpredict's content predictions can be used to improve results generated by the residue-level predictors. We release qNABpredict as a convenient webserver and source code at http://biomine.cs.vcu.edu/servers/qNABpredict/ . This new tool should be particularly useful to predict details of protein–NA interactions for large protein families and proteomes.     

Symmetric primary and tertiary structure mutations within a symmetric superfold: a solution, not a constraint, to achieve a foldable polypeptide

In previous studies designed to increase the primary structure symmetry within the hydrophobic core of human acidic fibroblast growth factor (FGF-1) a combination of five mutations were accommodated, resulting in structure, stability and folding kinetic properties similar to wild-type (despite the symmetric constraint upon the set of core residues). A sixth mutation in the core, involving a highly conserved Met residue at position 67, appeared intolerant to substitution. Structural analysis suggested that the local packing environment of position 67 involved two regions of apparent insertions that distorted the tertiary structure symmetry inherent in the beta-trefoil architecture. It was postulated that a symmetric constraint upon the primary structure within the core could only be achieved after these insertions had been deleted (concomitantly increasing the tertiary structure symmetry). The deletion of these insertions is now shown to permit mutation of position 67, thereby increasing the primary structure symmetry relationship within the core. Furthermore, despite the imposed symmetric constraint upon both the primary and tertiary structure, the resulting mutant form of FGF-1 is substantially more stable. The apparent inserted regions are shown to be associated with heparin-binding functionality; however, despite a marked reduction in heparin-binding affinity the mutant form of FGF-1 is surprisingly approximately 70 times more potent in 3T3 fibroblast mitogenic assays. The results support the hypothesis that primary structure symmetry within a symmetric protein superfold represents a possible solution, rather than a constraint, to achieving a foldable polypeptide.