Results from a study at The Scripps Research Institute (TSRI), the United States, have nearly tripled the number of proteins associated with the critical process of apoptosis, or programmed cell death, and have disproved a long-held idea about the life cycle of proteins. The research focused on proteolysis, the act of enzymes breaking down larger proteins into smaller components. The research team led by Dr. Benjamin Cravatt, chair of the Chemical Physiology Department at TSRI, wanted to begin filling in the many gaps in the understanding of proteolysis, including the full range of proteins broken down during specific cellular processes and what happens to the protein fragments.

The method developed, Protein Topography and Migration Analysis Platform (PROTOMAP), combines cutting-edge technologies in a powerful way. Dr. Cravatt and his colleagues processed samples of cells undergoing apoptosis, as well as control samples of intact cells, using electrophoresis. The scientists then sliced gels at set intervals and used mass spectrometry to identify the proteins found in each slice.

A key aspect of PROTOMAP is a new bioinformatics tool that the group devised to analyse mass spectroscopy data and presents it in a way that is readily interpretable and searchable. PROTOMAP enabled the scientists to access broad views of the entire landscape of proteins in the cells studied and to discern patterns that were completely unexpected.

Source: www.scripps.edu

Researchers from the University of Rochester Medical Centre (URMC), the United States, found a new protein produced excessively in malignant melanoma. The protein, IMP-3, is over-expressed in the most dangerous types of skin cancer and in thin melanomas, a subset of lesions that can be difficult to predict. “This protein may have a key role in helping us understand and distinguish between various types of melanocytic lesions,” said first author Dr. Jennifer G. Pryor, a third-year resident in the URMC Department of Pathology and Laboratory Medicine. IMP-3 is an insulin-like growth factor-II mRNA binding protein involved in cell proliferation and appears to play a role in tumour formation in a number of cancers.

The pilot study investigated 56 biopsied lesion samples from 48 adults. The lesions fell into the category of cutaneous melanocytic neoplasms, a diverse group that includes benign moles, Spitz nevi and malignant melanoma. Dr. Pryor and co-authors showed why IMP-3 might be an important tool for pathologists, as the protein is produced excessively in most melanomas, and overly expressed more often in metastatic melanomas. The protein is also over-expressed in rare cases of invasive thin melanomas. This is significant because while most thin melanomas have a good prognosis, some act more aggressively and at present there is no accurate way to distinguish between the types of thin lesions.

        
Source: www.endowmentmed.org

Scientists at the Virginia Bioinformatics Institute (VBI) at Virginia Tech, the United States, have identified the region of a large family of virulence proteins in oomycete plant pathogens that enables the proteins to enter the cells of their hosts. The protein region contains the amino acid sequence motifs RXLR and dEER and has the ability to carry the virulence proteins across the membrane surrounding plant cells without any other machinery from the pathogen. Once inside the plant cell, the proteins suppress the plant’s immune system, allowing the infection to progress. The work focused on the virulence protein Avr1b from the soybean plant pest Phytophthora sojae.

P. sojae infestation results in annual soybean losses estimated at US$1-2 billion worldwide. All oomycete species contain hundreds of genes that encode for virulence proteins that have the RXLR-dEER region. The virulence proteins enter the soybean host where they are capable of suppressing programmed cell death (apoptosis) in plants. By preventing this protective mechanism in the host, the virulence proteins ensure that the pathogen can establish an unassailable foothold in the plant tissue from which the pathogen can pursue its destructive path. Dr. Daolong Dou, the lead author of the article, commented: “Our findings finally nail down that mechanism and enable us to focus on how to block the entry mechanism.”

Source: www.eurekalert.com

Biochemists at the University of Texas Medical School (UTMS), the United States, say the day may be coming when scientists will be able to fine-tune enzymes responsible for flavours in fruits and vegetables. In addition, it could lead to environmentally friendly pest control. UTMS Assistant Professor C.S. Raman and his colleagues report that they were able to manipulate flavour enzymes found in a popular plant model, Arabidopsis thaliana, by genetic means. The enzymes – allene oxide synthase (AOS) and hydroperoxide lyase (HPL) – produce jasmonate (responsible for the unique scent of jasmine flowers) and green leaf volatiles (GLV) respectively. GLVs confer characteristic aromas to fruits and vegetables.

Genetic modification of GLV production has many important implications. “For example, the aroma of virgin olive oil stems from the volatiles synthesized by olives. By modifying the activity of enzymes that generate these substances, it may be possible to alter the flavour of the resulting oils,” said Dr. Raman. “Our work shows how you can convert one enzyme to another and, more importantly, provides the needed information for modifying the GLV production in plants.”

The scientists made 3-D images of the enzymes, which allowed them to make a small, but specific, genetic change in AOS, leading to the generation of HPL. AOS and HPL are part of a super family of enzymes called cytochrome P450. Although AOS or HPL are not found in humans, there are related P450 family members that help metabolize nearly half of the pharmaceuticals currently in use. In plants, AOS and HPL break down naturally occurring, organic peroxides into GLV and jasmonate molecules.

“These insights led to the striking demonstration that a single amino acid substitution converts one enzyme into another, thereby showing how a single point mutation can contribute to the evolution of different biosynthetic pathways. This begins to answer a long-standing question, as to how the same starting molecule can be converted into different products by enzymes that look strikingly similar,” said Dr. Rodney E. Kellems, Chairman of the Department of Biochemistry & Molecular Biology at UTMS.

Source: www.newswise.com

In the United States, scientists at Rutgers University and the University of Texas at Austin (UTA) have reported a discovery that could help develop drugs to fight the much-feared bird flu and other virulent strains of influenza. They have determined the 3-D structure of a site on an influenza-A virus protein that binds to one of its human protein targets, thereby suppressing a person’s natural defences to the infection and paving the way for the virus to replicate efficiently. This NS1 virus protein is shared by all influenza-A viruses isolated from humans, including avian influenza and the 1918 pandemic influenza virus.

About 10 years ago, Prof. Robert M. Krug at UTA discovered that the NS1 protein binds a human protein known as CPSF30, which is important for protecting human cells from flu infection. Once bound to NS1, the human protein can no longer generate molecules needed to suppress flu virus replication. Now, scientists led by Rutgers’ Professor Gaetano T. Montelione and Prof. Krug have identified the novel NS1-binding pocket that grasps the human CPSF30 protein.

X-ray crystallography carried out at Rutgers identified the 3-D structure of the NS1-binding pocket and gave the research team unique insights into how the NS1 and human protein bind at the atomic level, and how that suppresses a crucial antiviral response. Scientists at UTA verified the key role of this binding pocket in flu replication by genetically engineering a change to a single amino acid in the NS1 protein’s binding pocket, which in turn eliminated the protein’s ability to grasp the human protein that is needed to generate antiviral molecules. These investigators then produced a flu virus with an NS1 pocket mutation and showed that this mutated virus doesn’t block host defences, and therefore has a much reduced ability to infect human cells.

Source: www.science daily.com