Estimating false discovery rates for peptide and protein identification using randomized databases

MS‐based proteomics characterizes protein contents of biological samples. The most common approach is to first match observed MS/MS peptide spectra against theoretical spectra from a protein sequence database and then to score these matches. The false discovery rate (FDR) can be estimated as a function of the score by searching together the protein sequence database and its randomized version and comparing the score distributions of the randomized versus nonrandomized matches. This work introduces a straightforward isotonic regression‐based method to estimate the cumulative FDRs and local FDRs (LFDRs) of peptide identification. Our isotonic method not only performed as well as other methods used for comparison, but also has the advantages of being: (i) monotonic in the score, (ii) computationally simple, and (iii) not dependent on assumptions about score distributions. We demonstrate the flexibility of our approach by using it to estimate FDRs and LFDRs for protein identification using summaries of the peptide spectra scores. We reconfirmed that several of these methods were superior to a two‐peptide rule. Finally, by estimating both the FDRs and LFDRs, we showed for both peptide and protein identification, moderate FDR values (5%) corresponded to large LFDR values (53 and 60%).     

Substitution of norleucine for methionine residues in a crustacean pigment-dispersing hormone

In order to evaluate the structural/functional roles of Met residues in an octadecapeptide pigment-dispersing hormone (PDH: Asn-Ser-Gly-Met-Ile-Asn-Ser-Ile-Leu-Gly-Ile-Pro-Arg-Val-Met-Thr-Glu-Ala- NH2), first described as light-adapting distal retinal pigment hormone (DRPH) from Pandalus, three analogs were synthesized: Nle4-PDH, Nle15-PDH, and Nle4,15-PDH. When tested for melanophore pigment-dispersing activity in destalked Uca, all three Nle-analogs were more potent than unsubstituted PDH. Performic acid oxidation caused a marked loss of potency of PDH, Nle4-PDH, and Nle15-PDH. The analog Nle4,15-PDH was resistant to oxidation and displayed 6-fold higher potency than PDH. Thus Met4 and Met15 are not essential for the PDH activity. The oxidation-induced loss of activity of unsubstituted PDH may result from introduction of oxygen (in methionine sulfone) and a consequent conformational change in the octadecapeptide.     

Ribulose-1,5-bisphosphate carboxylase as a nuclear and chloroplast marker

Summary The data on the primary structure of ribulose-1,5-bisphosphate carboxylase/oxygenase are reviewed. Examples of their use as markers and in the elucidation of the evolution, adaptation and function of this key enzyme are given.     

Estrogen Stimulates Degradation of ��-Amyloid Peptide by Up-regulating Neprilysin

Postmenopausal estrogen depletion is a characterized risk factor for Alzheimer disease (AD), a human disorder linked to high levels of β-amyloid peptide (Aβ) in brain tissue. Previous studies suggest that estrogen negatively regulates the level of Aβ in the brain, but the molecular mechanism is unknown. Here, we provide evidence that estrogen promotes Aβ degradation mainly through a principal Aβ degrading enzyme, neprilysin, in neuroblastoma SH-SY5Y cells. We also demonstrate that up-regulation of neprilysin by estrogen is dependent on both estrogen receptor α and β (ERα and ERβ), and ligand-activated ER regulates expression of neprilysin through physical interactions between ER and estrogen response elements (EREs) identified in the neprilysin gene. These results were confirmed by in vitro gel shift and in vivo chromatin immunoprecipitation analyses, which demonstrate specific binding of ERα and ERβ to two putative EREs in the neprilysin gene. The EREs also enhance ERα- and ERβ-dependent reporter gene expression in a yeast model system. Therefore, the study described here provides a putative mechanism by which estrogen positively regulates expression of neprilysin to promote degradation of Aβ, reducing risk for AD. These results may lead to novel approaches to prevent or treat AD.     

PEGylation of therapeutic proteins

Since the first PEGylated product was approved by the Food and Drug Administration in 1990, PEGylation has been widely used as a post-production modification methodology for improving biomedical efficacy and physicochemical properties of therapeutic proteins. Applicability and safety of this technology have been proven by use of various PEGylated pharmaceuticals for many years. It is expected that PEGylation, as the most established technology for extension of drug residence in the body, will play an important role in the next generation therapeutics, such as peptides, protein nanobodies and scaffolds, which due to their diminished molecular size need half-life extension. This review focuses on several factors important in the production of PEGylated biopharmaceuticals enabling efficient preparation of highly purified PEG-protein conjugates that have to meet stringent regulatory criteria for their use in human therapy. Areas addressed are PEG properties, the specificity of PEGylation reactions, separation and large-scale purification, the availability and analysis of PEG reagents, analysis of PEG-protein conjugates, the consistency of products and processes and approaches used for rapid screening of pharmacokinetic properties of PEG-protein conjugates.     

Inhibition of Cancer Cell Adhesion,Migration and Proliferation by a Bispecific Antibody that Targets two Distinct Epitopes on αv Integrins

Members of the αv family of integrins regulate activation of transforming growth factor beta (TGFβ) and are directly involved in pro-tumorigenic phenotypes. Thus, αv integrins may be therapeutic targets for fibrosis and cancer, yet the isolation of selective inhibitors is currently a challenge. We generated synthetic antibodies selective for αv integrins by phage display selections on cell lines that displayed integrin heterodimers. We identified antibodies that targeted two distinct epitopes on cell-surface αv integrins and partially inhibited cell adhesion mediated by interactions between integrins and the latency-associated peptide, part of the pro-form of TGFβ. Using the isolated antibody paratope sequences we engineered a bispecific antibody capable of binding to both epitopes simultaneously; this antibody potently and completely inhibited cell adhesion mediated by integrins αvβ1, αvβ3 and αvβ5. In addition, the bispecific antibody inhibited proliferation and migration of lung carcinoma lines, where the highest and lowest potencies observed correlated with integrin-αv cell surface expression levels. Taken together, our results demonstrate that phage display selections with live cells can yield high quality anti-integrin antibodies, which we used as biparatopic building blocks to construct a bispecific antibody that strongly inhibited integrin function and may be a therapeutic candidate for cancer and fibrosis.     

The peptides of α-aminosuberic acid II. Synthesis of deamino-dicarba-eel-calcitonin sequence 1–9

Summary. The paper describes the synthesis of Asu⁶-octapeptide derivatives by condensing two alternative pentapeptide fragments with Asu-containing tripeptides. After partial deprotection these linear peptides compounds are subject to cyclization experiments aimed to give the N-terminal [1–9] sequence of deamino-dicarba-eel calcitonin. This is a key substance for the semi-synthesis of the respective analogues of eel calcitonin. Received November 27, 2000 Accepted December 8, 2000     

MALDI-TOF质谱技术研究多肽一级结构特性

海兔酸性多肽(Aplysiaacidicpeptide,AAP)和海兔胰岛素Cβ(AplysiaInsulinCβ,AICβ)的一级结构分别由27和15个氨基酸残基组成,其中前者含有6个亮氨酸残基(L),并组成3对LL键,后者仅有2个亮氨酸残基,组成1对LL键。选用基质辅助激光解吸离子化飞行时间(matrixassistedlaserdesorptionionizationtimeoffight,MALDITOF)质谱技术研究AAP,AICβ和它们分解产物的一级结构稳定性过程中,发现在弱酸性介质条件下,AAP和AICβ的LL酰氨键键能比LR键能(R表示除了L以外的氨基酸残基)更强,不易被分解。AICβ和猪血管紧张肽I(angiotensinI,AnI)样品中均含有单电荷的多聚肽。随着多肽聚合数递增,多肽质谱峰的相对强度剧减。AICβ在形成多聚肽过程中,发生释放H+的现象 。     

Biostable insect kinin analogs reduce blood meal and disrupt ecdysis in the blood-gorging Chagas’ disease vector,Rhodnius prolixus

Rhodnius prolixus is a blood-gorging hemipteran that takes blood meals that are approximately 10 times its body weight. This blood meal is crucial for growth and development and is needed to ensure a successful molt into the next instar. Kinins are a multifunctional family of neuropeptides which have been shown to play a role in the control of feeding in a variety of insects. In this study, two biostable Aib-containing kinin analogs were tested to see if they interfere with blood-feeding and subsequent development into the next instar. One of the analogs, 1729 (Ac-R[Aib]FF[Aib]WGa), had no effect on the size of the blood meal or on the subsequent molting of the insect into the next instar. This analog also did not interfere with either short-term or long-term diuresis. The second analog, 1728 ([Aib]FF[Aib]WGa), appeared to be an antifeedant. Insects feeding on blood containing this analog (15 μM) only consumed 60% of the blood meal taken by insects fed on blood without analog. Insects feeding on blood containing 1728 had a slower rate of rapid diuresis (diuresis in the first 3–5 h after feeding) leading to less urine being excreted by 5 days post feeding. The consequence of these effects was that insects fed on 1728 did not molt. This data indicates that the biostable Aib-containing analog 1728 disrupts normal growth and development in the blood-feeding insect, R. prolixus.     

Analysis of monoclonal antibody product heterogeneity resulting from alternate cleavage sites of signal peptide

Signal peptides used in biosynthesis of proteins are cleaved at a very specific site by signal peptidase during posttranslational translocation of cytoplasmic proteins across the membrane. In some cases, however, there can be cleavage at nonspecific sites, giving rise to heterogeneity in the mature protein, which manifests itself as either elongation or truncation of the N terminus of the mature protein. When used as biopharmaceutical therapeutics, such heterogeneities may be a cause for concern, depending on the nature of the heterogeneity. This article describes the determination of such heterogeneity by peptide mapping in both the heavy chain and the light chain (LC) of a Chinese hamster ovary (CHO) cell-expressed monoclonal antibody (mAb). The peptide map method described here was capable of detecting the extended N-terminal peptides at levels as low as 1% relative to the peak area of the intact N-terminal peptide. The LC of a mAb product was truncated at its N termini by two amino acid residues at approximately 3-4% levels, resulting from alternate signal peptide cleavage. This article describes the quantitation of this truncation by liquid chromatography-mass spectrometry (LC-MS) peptide mapping. Also described is analysis and characterization of LC truncation by reduced and denatured capillary electrophoresis in sodium dodecyl sulfate (CE-SDS). The truncated mAb, which was devoid of the two N-terminal amino acids, was engineered and shown to migrate as the “pre-LC” peak in reduced CE-SDS assay. The amount of the pre-LC peak recovered from the CE-SDS assay was shown to correlate with the amount of truncated peptide observed from the reduced and alkylated peptide map of the engineered mAb.