Bacteriophages: Foes or Friends?

Ramin Mazaheri Nezhad Fard

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-2 (e1)

•Bacteriophages are known for their roles in rapid development of the bacterial evolution and transfer of various genes.
•Safety issues have always been a great concern since primary uses of bacteriophages in medicine.
•Comprehensive studies are necessary to ensure safe uses of bacteriophages in medicine.

Some Clues on the Conformational Stability of Globular Proteins

Giuseppe Graziano

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-7 (e2)

The native structure of the glycine-rich antifreeze protein from snow flea, sfAFP, its conformational stability and cooperative folding-unfolding transitions represent a challenge for the current understanding and rationalization of protein folding and stability. The hydrophobic effect, the main stabilizing factor of folded structures, is redefined in terms of the solvent-excluded volume associated with the insertion of a given structure in water to arrive at a different molecular mechanism. The need to minimize the solvent-excluded volume in order to maximize the translational entropy gain of water molecules drives protein folding and determines the globular shape of folded structures. The burial of nonpolar side chains from water contact, as emphasized by the sfAFP folded structure, is not a necessary condition. In fact, a large fraction of nonpolar surface is water-accessible in the folded structures of globular proteins. The significant reduction in water accessible surface area upon chain folding is the necessary and fundamental condition, and rationalizes the conformational stability and cooperativity of sfAFP native structure.


•The stability and folding characteristics of antifreeze protein from snow flea, sfAFP, are challenging.
•The globular shape of sfAFP is not dictated by nonpolar side chains - water contact.
•The balance between the translational entropy of water molecules and the conformational entropy of the chain is important in protein folding.
•The balance between the formation of intramolecular peptide-peptide H-bonds and the breaking of intermolecular peptide-water H-bonds is important in protein folding.

Milk Fat Globule Membrane (MFGM): An Ingredient of Dairy Products as Nutraceutical

Jayanti Tokas, Himani Punia

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-9 (e3)

Over the recent couple of years, milk fat globule membrane perceived a considerable attention due to its complexity in structure and health beneficial properties. This chapter describes the complex structure of the milk fat globule membrane as potential ingredient of dairy products as nutraceutical. The structure and function of milk fat globule membrane proteins are significant markers of the dietary nature of milk which might be ensnared in an assortment of medical advantages. Utilization of MFGM as nutraceutical depends upon its chemical composition, modifications introduced during processing and individual specific prepared food products. The MFGM and its associated proteins are involved in energy production, signal transduction, metabolic process regulation, cell to cell communication, and boost up immune system. This cross examination gives more bits of knowledge into the dynamic organization of human MFGM proteins, which thus will improve our comprehension of the physiological noteworthiness of MFGM proteins. We present the summary of the advances of research and functions of membrane and its associated proteins that are relevant to health and wellness. Milk fat globule membrane (MFGM) has attained a greater consideration as a potential source of nutraceutical with regards to its lipid-soluble vitamins, phospholipids and essential fatty acids.

•Milk fat globule membrane is a complex biological membrane of lipid-protein, surrounded by the minute fat globules.
•MFGM holds a great potential as nutraceutical with health beneficial properties.
•Functionally important bioactivities associated with milk fat globule membrane protein include immune-stimulating, antimicrobial and antiviral properties.
•MFGM proteins plays a role in a protection against colon cancer and gastrointestinal stress.

Studies of Molecular Energy Changes in AQP5 in the Presence and Absence of Water Using Computational Method

Ahmad Alaei, Mehdi Pooladi, Soheila Karani, Saba Abolhasan Dust

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-7 (e4)

Aquaporins (AQPs) are water channel proteins. Up to now, 13 AQPs have been known in mammals. AQPs play a key role in water osmotic flow in various cells. the members of aquaporin protein family have been identified as H2O transposters across organelle and plasma membranes. AQPs of the aquaammoniaporin type are highly permeable for water and ammonia. In this study, we have evaluated the structure of AQP5 using two computational methods. We investigated the potential and kinetic energy, as well as maximum and minimum difference of atomic charge for AQP5. The atomic study of AQP5 protein showed that the minimum and maximum value of atomic charge in the presence and absence of water were related to sections (1-15). The water effect is generally considered to be the major driving force in the folding of AQP5. different sections of AQP5 behaved different in the presence or absence of water, and have different functionalities. Also, the absolute value of atomic charge difference for AQP5 sections was proven as an important feature in protein structural changes.

•AQP5’s function and structure are dependent on the presence and absence of water.
•The presence of water molecules around AQP5 protein causes changes in dynamic properties.
•The optimum functions of AQP5 are arisen at low energy levels and the presence of water.
•kinetic energy for AQP5 protein in mode of no water has the lowest fluctuations but in presence of water considerable fluctuations are seen.

The Effect of Radio Frequency (RF) on Proteomics Pattern of Brain Tissue in male Wister Rats

Maryam Sadat Heidari Tekyeh, Minoo Shahani, Hessam Sepasi Tehrani, Azadeh Hekmat

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-8 (e5)

Radiated waves from mobile phones are in the Radio Frequency (RF) range, so those are unable to cause ionization and electron excitation. RF that are produced and emitted from sender antenna on the surface of mobile phone systems, ranges from 30 up to 300 GHz in electromagnetic wave spectrum. There is no complete information about the effects of RF on protein changes. For this purpose, we have examined the effects of RF waves on the changes in protein expression pattern of the brain. In this study, 10 heads of male Wistar rats, weighing between 200-250 g, were exposed to transmission antenna in 100-180 meter distance. Then, proteome of RF900 GHz exposed group and control group were extracted. Two-dimensional gel electrophoresis evaluation and proteomics analysis was performed. Results showed altered proteome pattern due to radiation. Tissue exposed to nonstandard waves showed similar pattern of changes in the expression of some proteins, which have key roles in the induction of apoptosis. The expressions of key proteins including Bcl-2-A1, Bid, Neurofilament and Cytochrome Oxidase were decreased. Expression or suppression of apoptosis related proteins such as BCL-2 in rat brain proteome exposed to standard RF900 MHz (at 180m and beyond), can serve as a biomarker of brain activity, memory and sleep. RF radiated from transmission antenna in urban and standard spaces may not be carcinogenic, but, individuals exposed in nonstandard distances to those antennas (less than 180meter) may be at risk.

•Radio Frequency (RF) waves can affect the protein expression profile of the cell.
•Exposure to nonstandard RF waves changed the expression profile of apoptosis key proteins.
•Changes in the expression of Bcl-2-A1, Bid, Neurofilament and Cytochrome Oxidase under the RF was evident.

Methylglyoxal Binding to Bovine Liver Catalase Results in Loss of Activity and Heme Dislocation

Subramanian Sivakami, Sejal A Shah, George Suji, Vikrant M Bhor, Ahmad Ali

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-8 (e6)

Glycation, the non-enzymatic attachment of glucose to protein, is one of the important events in the pathophysiology of diabetes mellitus, Alzheimer’s, Parkinson’s and other diseases. Methylglyoxal (MG), a dicarbonyl compound formed during glycation, monosaccharide autoxidation, and metabolism is elevated during diabetes mellitus. Among other antioxidant enzymes, catalase is important for the defense against oxidative damage. However, antioxidant enzymes including catalase can themselves become targets of non-enzymatic modification by methylglyoxal. In this study, catalase was incubated with increasing concentrations of MG for different time intervals. Structural and functional alterations to catalase were monitored by a variety of approaches, namely, assay of enzyme activity, staining of gels for activity as well as heme, measurement of protein carbonyls and Arg pyrimidine, which is a specific MG modification product. A progressive increase in electrophoretic mobility and detachment of heme from the monomer were observed with increasing concentrations of methylglyoxal. The MG-modified enzyme showed reduced affinity towards the substrate hydrogen peroxide. Molecular modeling studies revealed that MG can access the heme and arginine residues close to it. Thus, the decrease in activity of methylglyoxal-modified catalase may be important in aggravating the severity of secondary complications seen in diabetes mellitus.

•Increase in concentration of methylglyoxal caused a progressive increase in electrophoretic mobility and detachment of heme from the monomer.
•MG-modified enzyme showed reduced affinity towards the substrate hydrogen peroxide.
•Molecular modeling studies showed that MG can access the heme and arginine residues close to it.

The Effect of Calcium Alginate Entrapment on the Stability of Novel Lipases from P. Reinekei and P. brenneri

Priyanka Priyanka, Gemma K. Kinsella, Gary T. Henehan, Barry J. Ryan

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-10 (e7)

The high cost of soluble enzymes can limit their use for commercial and industrial purposes. Immobilization can enhance enzyme reusability, thereby reducing product isolation costs and overcoming this economic barrier. In the current study, two novel, purified lipases from Pseudomonas sp. (Pseudomonas reinekei and Pseudomonas brenneri) were entrapped in a calcium alginate matrix, with the aim of simultaneously enhancing enzyme reusability and stability. Following entrapment, the retained activity of the enzyme-alginate composite was verified by an enzymatic hydrolysis reaction of a p-nitrophenol palmitate substrate. The effect of the enzyme-alginate entrapment against various physiochemical parameters such as pH, temperature, metal ions, and solvents were subsequently examined. The entrapment was found to have minimal beneficial stability gains. However, enhanced enzyme reusability (up to 3 cycles) and stability (up to 18 days at 4°C) of the calcium alginate entrapped lipase, as indicated by residual hydrolysis of p-nitrophenol palmitate, was observed, suggesting potential roles for calcium alginate entrapped lipases in cost efficient enzyme catalysis.

•Two novel lipases have been entrapped in calcium alginate for the first time.
•A statistically enhanced stability in 1M EDTA was observed following entrapment.
•The novel entrapped lipases display excellent storage stability and reusability.

Insulin-Like Growth Factor-1 (IGF-1) is a small peptide with 70 amino acids and 7.6 kDa molecular weight that acts as the major mediator of growth hormone. According to the previous studies, recombinant production of human IGF-1 (rhIGF-1) in E. coli has resulted in an inactive form of protein (inclusion body). There are several strategies to transform inclusion body to a soluble form. Production in the form of fusion proteins as a suitable strategy, helps researcher in recombinant production of proteins in the soluble and active form. In current study, NusA fusion protein was used to produce IGF-1 soluble form, instead of insoluble protein. In previous study, rhIGF-1 was optimally expressed in inclusion body with 1.2 g/L concentration. rhIGF1 -NusA construct was cloned and expressed in E. coli, then, cell lysate was analyze by SDS-PAGE and densitometry techniques, to assay soluble and insoluble form of rhIGF-1. Results showed that rhIGF-1 concentration in soluble phase was 0.14 g/L, indicating that about 12% of total expression of rhIGF-1 was in the soluble form through NusA-fusion protein strategy. These results confirmed that some fusion proteins like NusA could improve the solubility of recombinant proteins expressed in heterogeneous bacterial hosts.


  • Fusion proteins is a suitable strategy for recombinant production of proteins in e soluble form.
  • NusA fusion tag improves the solubility of recombinant proteins expressed in bacterial hosts.
  •  NusA fusion protein convert IGF-1 insoluble form to soluble form in E. coli.

In the recent years, the morbidity and death rates of diabetes have quickly increased. The enzyme inhibitors and antioxidants are very important as they can treat or reduce the complications of diabetes type II. The sea cucumbers are potential sources for finding bioactive compounds such as antioxidant and enzymatic-inhibitor compounds; hence, the present study was focused on the screening two species of sea cucumbers extracts included (Holothuria leucospilota, and Stichopus hermanni) from Persian Gulf on α-glucosidase inhibition and antioxidant activities using two methods of DPPH radical scavenging and reducing power. In enzymatic inhibition assay, the properties of the extracts are divided into three categories, included inhibitory, activatory properties and without any effects. More extracts had inhibitory properties, some of which were activator and some did not have any effects. In both sea cucumbers, the extract of respiration tree showed maximum inhibition of 34% and 40% for S. hermani and H. leucospilota, respectively, on α-glucosidase activity. The respiration tree extract showed the highest activity in both enzyme inhibition and antioxidant activity compared to methanol and dichloromethane extracts of other parts.


  • Most of extracts had inhibitory properties on α-glucosidase.
  • In both sea cucumbers, the extract of respiration tree showed maximum inhibition of α-glucosidase.
  • The respiration tree extract showed the highest activity in antioxidant activity compared to other extracts.

Effects of Cultivation Conditions on the Expression Level of Recombinant scFv Antibody against EpEX in Escherichia coli

Seyyed ali Mohammadi Vadoud, Atieh Hashemi, Malihe keramati, Farideh Rasouli Kery Bozorg

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-6 (e10)

The EpCAM (epithelial cell adhesion molecule) is a cell surface antigen over expressed in many types of epithelial cell cancers including colon, stomach, pancreas, lung, ovarian, and breast. So, it can be an attractive target for active and passive immunotherapy of cancers. ScFv (single chain fragment variable) fragment is a class of engineered antibodies in which the genes coding for the heavy (VH) and light chains (VL) of an immunoglobulin have been linked with a short flexible peptide linker. Inexpensive media, rapid growth rates, and relatively minimal laboratory set up make Escherichia coli (E. coli) a suitable host for expression of a large variety of recombinant proteins. Here, we assessed the effect of cultivation conditions on the level of expressed scFv against extracellular domain of EpCAM (EpEX) in E. coli. pET22b-antiEpEX-scFv was transformed into prepared E. coli Rosetta™(DE3) competent cells. To evaluate the effect of cultivation conditions on protein expression level, three factors of incubation temperature (25, 30, 37°C), the IPTG (isopropyl-β-D-thiogalactoside) concentration (0.1, 0.25, 0.5, 1 mM), and induction duration (3, 5, 7, 18 h) were considered. SDS-PAGE and western blot analysis demonstrated an estimated 30 kDa-size protein band which was related to the recombinant scFv expressed in E. coli Rosetta™(DE3) strain. At optimal condition (5 h after induction with 0.5 mM IPTG at 25 °C), the final production yield of the antiEpEX-scFv was 403.29 ± 87.50 μg/mL. Our results provide a foundation for the development of scFv-based drugs’ production as effective therapeutic agents in cancers with epithelial origin.



  • The antiEpEX-scFv was successfully expressed in E. coli Rosetta™(DE3) strain.
  • The highest concentration of protein was obtained with 0.5 mM IPTG at 30°C.
  • The final yield of recombinant antiEpEX-scFv was approximately 403.29 ± 87.50 mg/L.

Measurement of Heat and Pressure Induced Denaturation of Whey Protein Isolate Using Reversed-Phase HPLC and FTIR-Spectroscopy

Md. Amdadul Haque, M. Manjurul Haque, M. Sazzat Hossain Sarker, Benu Adhikari

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-6 (e11)

The protein molecules experience various external stresses leading to denaturation of protein during the process of transforming original whey to the concentrated whey proteins or while the concentrated proteins are used in the protein-enriched food formulation. This study was designed for a comparative assessment of the denaturation of whey protein isolate (WPI) under an important thermal stress, isothermal heat treatment (IHT), and high hydrostatic pressure treatment (HPT). The type and extent of denaturation were determined using reversed-phase HPLC and FTIR spectroscopy. The HPLC results demonstrated that the isothermal heat treatment caused higher denaturation of protein due to IHT at 80oC for 600s (88.38%) than that of HPT (58.5%). However, the infra-red spectroscopic analyses suggested that the HPT caused severe destruction of the structural conformation of WPI. The state of protein has a great impact on food formation; hence, the findings of this study would alert the concentrate protein producers and protein-enriched food manufacturers to prepare more active functional foods.


  •  Heat (IHT) and pressure (HPT) stresses caused 88% and 58% WPI to denature, respectively.
  •  Reversed phase-HPLC determined the denatured protein through aggregation.
  • FTIR together with HPLC is required for better characterization of denatured protein.

Author Package, TPPS, Vol. 4 (2019)

Maryam Tabarzad

Trends in Peptide and Protein Sciences, Vol. 4 (2019), 1 January 2019, Page 1-12

The Trends in Peptide and Protein Sciences is a peer-reviewed, online-only (previously print-online), scientific journal owned by Protein Technology Research Center, Shahid Beheshti University of Medical Sciences and documents in all important aspects of the research in peptides and proteins focusing on analytics and impurities, bioinformatics, biopharmaceuticals and vaccines, biotechnology, chemical synthesis, conformational analysis, design and  development of protein therapeutics, determination of structure, enzymology, folding and sequencing,  formulation and stability, function, genetics,  immunology, kinetics, modeling, molecular biology, pharmacokinetics and pharmacodynamics of therapeutic proteins and antibodies, pharmacology,  protein engineering and development, protein-protein interaction, proteomics, purification/expression/production, simulation, thermodynamics and  hydrodynamics and protein biomarkers. The aim of this Journal is to publish high quality original research articles, reviews, short communications and letters and to provide a medium for scientists and researchers to share their findings from the area of peptides and proteins. The Trends in Peptide and Protein Sciences is published in collaboration with Iranian Association of Pharmaceutical Scientists. From volume 3 (2018) of TPPS, articles are continuously published online only, as soon as the review process is completed.