Successful de novo protein design ideally targets specific folding kinetics, stability thermodynamics, and biochemical functionality, and the simultaneous achievement of all these criteria in a single step design is challenging. Protein design is potentially simplified by separating the problem into two steps: (a) an initial design of a protein "scaffold" having appropriate folding kinetics and stability thermodynamics, followed by (b) appropriate functional mutation-possibly involving insertion of a peptide functional "cassette." This stepwise approach can also separate the orthogonal effects of the "stability/function" and "foldability/function" tradeoffs commonly observed in protein design. If the scaffold is a protein architecture having an exact rotational symmetry, then there is the potential for redundant folding nuclei and multiple equivalent sites of functionalization; thereby enabling broader functional adaptation. We describe such a "scaffold" and functional "cassette" design strategy applied to a β-trefoil threefold symmetric architecture and a heparin ligand functionality. The results support the availability of redundant folding nuclei within this symmetric architecture, and also identify a minimal peptide cassette conferring heparin affinity. The results also identify an energy barrier of destabilization that switches the protein folding pathway from monomeric to trimeric, thereby identifying another potential advantage of symmetric protein architecture in de novo design.
DRUG target, DIAMINO amino acids, ENZYMES, ESSENTIAL amino acids
Abstract
Tantalizing implications The new paper demonstrates that ATE1 binds to clusters of iron and sulfur ions, and that the enzyme's activity increases two- to three-fold when it is bound to one of these iron-sulfur clusters. These enzymes add arginine (an amino acid) to proteins, which often flags the proteins for destruction in the cell. Keywords: Amino Acids; Arginine; Basic Amino Acids; Biochemistry; Chalcogens; Chemicals; Chemistry; Diamino Amino Acids; Drugs and Therapies; Enzymes and Coenzymes; Essential Amino Acids; Health and Medicine; Iron-sulfur Cluster; Peptides; Peptides and Proteins; Proteins; Sulfur; Therapeutics; Therapy; University of Maryland Baltimore County EN Amino Acids Arginine Basic Amino Acids Biochemistry Chalcogens Chemicals Chemistry Diamino Amino Acids Drugs and Therapies Enzymes and Coenzymes Essential Amino Acids Health and Medicine Iron-sulfur Cluster Peptides Peptides and Proteins Proteins Sulfur Therapeutics Therapy University of Maryland Baltimore County 534 534 1 03/27/23 20230331 NES 230331 2023 MAR 31 (NewsRx) -- By a News Reporter-Staff News Editor at Drug Week -- A new paper in Nature Communications illuminates how a previously poorly understood enzyme works in the cell. [Extracted from the article]
PROTEIN folding, RESEARCH personnel, DRUG therapy, SERPINS, PROTEINS
Abstract
Researchers at the University of Massachusetts Amherst have made a breakthrough in understanding how proteins fold, which could lead to new therapeutic options for various diseases. The study focused on a family of proteins called serpins, which are involved in several diseases. By using innovative techniques such as glycoproteomics, the researchers identified the carbohydrate-based code that determines how these proteins fold correctly. This discovery could pave the way for targeted drug therapies for a range of diseases caused by errors in protein folding. [Extracted from the article]
DENTAL enamel, DENTITION, ORGANOIDS, PROTEINS, HUMAN stem cells, CYTOLOGY
Abstract
Keywords: Biochemistry; Bioengineering; Biomedical Engineering; Biomedicine; Biotechnology; Chemistry; Dentistry; Genetics; Health and Medicine; Peptides; Peptides and Proteins; Proteins; Regenerative Medicine; Stem Cell Research; University of Washington School of Medicine/UW Medicine EN Biochemistry Bioengineering Biomedical Engineering Biomedicine Biotechnology Chemistry Dentistry Genetics Health and Medicine Peptides Peptides and Proteins Proteins Regenerative Medicine Stem Cell Research University of Washington School of Medicine/UW Medicine 512 512 1 08/28/23 20230901 NES 230901 2023 AUG 31 (NewsRx) -- By a News Reporter-Staff News Editor at Stem Cell Week -- Organoids have now been created from stem cells to secrete the proteins that form dental enamel, the substance that protects teeth from damage and decay. Biochemistry, Bioengineering, Biomedical Engineering, Biomedicine, Biotechnology, Chemistry, Dentistry, Genetics, Health and Medicine, Peptides, Peptides and Proteins, Proteins, Regenerative Medicine, Stem Cell Research, University of Washington School of Medicine/UW Medicine. [Extracted from the article]
PARKINSON'S disease, MOVEMENT disorders, BASAL ganglia diseases, CENTRAL nervous system diseases, DARDARIN, PARKINSONIAN disorders
Abstract
Keywords: Basal Ganglia Diseases and Conditions; Biochemistry; Biomarkers; Brain Diseases and Conditions; Cancer; Central Nervous System Diseases and Conditions; Chemistry; Diagnostics and Screening; Genetics; Health and Medicine; Movement Disorders; Nervous System Diseases and Conditions; Neurodegenerative Diseases and Conditions; Oncology; Parkinson's Disease; Parkinsonian Disorders; Peptides; Peptides and Proteins; Proteins; Purdue University; Technology EN Basal Ganglia Diseases and Conditions Biochemistry Biomarkers Brain Diseases and Conditions Cancer Central Nervous System Diseases and Conditions Chemistry Diagnostics and Screening Genetics Health and Medicine Movement Disorders Nervous System Diseases and Conditions Neurodegenerative Diseases and Conditions Oncology Parkinson's Disease Parkinsonian Disorders Peptides Peptides and Proteins Proteins Purdue University Technology 602 602 1 05/29/23 20230529 NES 230529 2023 MAY 30 (NewsRx) -- By a News Reporter-Staff News Editor at Women's Health Weekly -- New liquid biopsy method offers potential for noninvasive Parkinson's disease testing EVtrap technology identifies proteins from brain cells in urine samples WEST LAFAYETTE, Ind. - A team led by researchers at Purdue University and Purdue spinoff company Tymora Analytical Operations has developed a technique that may reveal signs of Parkinson's disease in urine samples. Basal Ganglia Diseases and Conditions, Biochemistry, Biomarkers, Brain Diseases and Conditions, Cancer, Central Nervous System Diseases and Conditions, Chemistry, Diagnostics and Screening, Genetics, Health and Medicine, Movement Disorders, Nervous System Diseases and Conditions, Neurodegenerative Diseases and Conditions, Oncology, Parkinson's Disease, Parkinsonian Disorders, Peptides, Peptides and Proteins, Proteins, Purdue University, Technology. [Extracted from the article]
G protein coupled receptors, ANALGESICS, PEPTIDE drugs, OPIOIDS, SMALL molecules
Abstract
Certain naturally occurring, orendogenous, peptides bind to opioid receptors on thesurface of cells to create an analgesic effect, alsoknown as pain relief. Opioid drugs relieve pain by mimicking a naturallyoccurring pain-relief function within our nervoussymptoms. Opioids CHAPEL HILL, NC -- In the continuing effort to improveupon opioid pain relievers, American and Chinesescientists used cryoEM technology to solve the detailedstructures of the entire family of opioid receptors boundto their naturally occurring peptides. [Extracted from the article]
A patent application has been filed for a method of maintaining and culturing tissue slices in vitro or ex vivo. The method involves using a hydrogel with conjugated peptides as a culture substrate for the tissue slices. The hydrogel can be modulated to optimize the maintenance and culture of different types of tissue slices. This method has potential applications in studying cancer biology and evaluating the efficacy of tumor microenvironment-targeting strategies. The patent application provides detailed information on the composition and properties of the hydrogel, as well as the culture conditions and downstream analysis processes. [Extracted from the article]
BIPOLAR disorder, MENTAL illness, MENTAL depression, MEDICAL screening, THERAPEUTICS
Abstract
A preprint abstract from biorxiv.org discusses the challenge of differentiating between depression and bipolar disorder in clinical practice. The study focuses on urine proteomics and analyzes urine samples from two hospitals to identify potential biomarkers for distinguishing between the two conditions. The results show that there are differential proteins between the depressed and bipolar groups, with some proteins consistently associated with immunoglobulins. The study suggests that immune mechanisms may play a role in major depression and that drugs targeting the immune system could improve depressive symptoms. The findings highlight the potential of urine proteomics for differential diagnosis and precision treatment of depression and bipolar disorder. However, it is important to note that this preprint has not undergone peer review. [Extracted from the article]
Researchers from the University of Arizona have developed an innovative chemical strategy to combat mosquito-borne diseases such as malaria, dengue, zika, and chikungunya. By targeting the alkaline environment of larval mosquito guts, the team has selectively modified gut proteins using specially designed chemical compounds. These compounds release reactive molecules in the larval gut, which then bond with the proteins and modify them. The modified proteins are tagged with fluorescent markers, enabling their detection and isolation. The compounds are not acutely toxic to mosquito larvae and can be directly added to water without harming other aquatic animals. The researchers plan to further study the long-term effects of the compounds on larvae development and are considering attaching potentially toxic compounds to the chemical compound to test their effectiveness in killing mosquito larvae. [Extracted from the article]
LUNG volume, HEART, PULMONARY circulation, LUNGS, THERAPEUTICS, PROSTATECTOMY, LAPAROSCOPIC surgery, RESEARCH personnel, UNIVERSITY hospitals
Abstract
A recent report emphasizes the importance of optimizing anesthesia management during robotic-assisted laparoscopic radical prostatectomy to improve patient outcomes. The study suggests that different anesthesia techniques, such as total intravenous anesthesia (TIVA) and balanced general anesthesia (BGA), have similar outcomes in terms of postoperative complications and hospital stay. Other factors that can improve outcomes include maintaining appropriate positive end-expiratory pressure (PEEP) levels, restricting intravenous fluid administration, and using neuromuscular blocking agents and reversal agents. The report also highlights the potential cardiovascular changes that can occur during the procedure. Overall, careful intraoperative management is crucial for successful outcomes in this surgical procedure. [Extracted from the article]
Keywords: Biochemicals; Biochemistry; Biological Factors; Carotenoids; Chemicals; Clinical Research; Clinical Trials and Studies; Cytokines; Diagnostics and Screening; Drugs and Therapies; Drugs and Therapies - Phototherapy; Enzyme-Linked Immunosorbent Assay; Health and Medicine; Immunoenzyme Techniques; Immunologic Techniques; Immunologic Tests; Immunosorbent Techniques; Intercellular Signaling Peptides and Proteins; Interleukin-18; Interleukins; Investigative Techniques; Peptides; Photomedicine; Phototherapy; Proteins; Retinoids EN Biochemicals Biochemistry Biological Factors Carotenoids Chemicals Clinical Research Clinical Trials and Studies Cytokines Diagnostics and Screening Drugs and Therapies Drugs and Therapies - Phototherapy Enzyme-Linked Immunosorbent Assay Health and Medicine Immunoenzyme Techniques Immunologic Techniques Immunologic Tests Immunosorbent Techniques Intercellular Signaling Peptides and Proteins Interleukin-18 Interleukins Investigative Techniques Peptides Photomedicine Phototherapy Proteins Retinoids 468 468 1 10/16/23 20231016 NES 231016 2023 OCT 16 (NewsRx) -- By a News Reporter-Staff News Editor at Clinical Trials Week -- Staff editors report on the newly launched clinical trial, NCT06066554, which has the following summary description: "To compare tissue and serum level of NLRP1, NLRP3 inflammasomes and Interleukin (IL)-18 in mycosis fungoids patients and normal controls. To compare tissue and serum level of NLRP1, NLRP3 inflammasomes and Interleukin (IL)-18 in mycosis fungoids patients before and after different treatment modalities.
Detailed Description
Thirty patients with early stage mycosis fungoids and thirty normal healthy controls will be recruited. [Extracted from the article]
Chen Zhou, Shuaijian Dai, Yuanqiao Lin, Sheng Lian, Xiaodan Fan, Ning Li, and Weichuan Yu
Subjects
Cross-Linking Reagents, Proteins, General Chemistry, Peptides, Biochemistry, Mass Spectrometry, Feedback
Abstract
Improving the sensitivity of protein-protein interaction detection and protein structure probing is a principal challenge in cross-linking mass spectrometry (XL-MS) data analysis. In this paper, we propose an exhaustive cross-linking search method with protein feedback (ECL-PF) for cleavable XL-MS data analysis. ECL-PF adopts an optimized α/β mass detection scheme and establishes protein-peptide association during the identification of cross-linked peptides. Existing major scoring functions can all benefit from the ECL-PF workflow to a great extent. In comparisons using synthetic data sets and hybrid simulated data sets, ECL-PF achieved 3-fold higher sensitivity over standard techniques. In experiments using real data sets, it also identified 65.6% more cross-link spectrum matches and 48.7% more unique cross-links.
Tatiana Martini, Beatriz Martines de Souza, Talita Mendes Oliveira Ventura, Ana Luiza Bogaz Debortolli, Flávio Henrique-Silva, Priscila Yumi Tanaka Shibao, Caroline Fernanda da Silva Ribeiro, Aline Dionizio, Even Akemi Taira, Thamyris de Souza Carvalho, Reinaldo Marchetto, Marília Afonso Rabelo Buzalaf, Heloisa Aparecida Pereira Barbosa, Tamara Teodoro Araujo, Chelsea Maria Vilas Boas Feitosa, Universidade de São Paulo (USP), São Carlos Federal University, and Universidade Estadual Paulista (UNESP)
Subjects
chemistry.chemical_classification, Proteomics, Proteins, Water, Peptide, PROTEÍNAS, CaneCPI-5, chemistry.chemical_compound, chemistry, Biochemistry, In vivo, Protein purification, Keratin, Humans, Hemoglobin, Cystatin, Dental Pellicle, Citric acid, Peptides, Acquired enamel pellicle, General Dentistry, Statherin
Abstract
Made available in DSpace on 2022-04-29T08:36:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-01 Objective: To study the proteomic alterations in the initial AEP after rinsing with CaneCPI-5, StN15 or Hb or their combination. Materials and methods: In five crossover phases, after prophylaxis, 10 volunteers in 5 consecutive days, rinsed (10 mL, 1 min) with the following solutions: deionized water (H2O- negative control- 1), 0.1 mg/mL CaneCPI-5 (2), 1.88×10−5 M StN15 (3), 1.0 mg/mL Hb (4) or their combination (5). The AEP formed after 3 min was collected with electrode filter papers soaked in 3% citric acid. After protein extraction, samples were analyzed by quantitative shotgun label-free proteomics. Results: Rinsing with the proteins/peptide increased the amounts of proteins in the AEP. The total numbers of proteins identified after rinsing with CaneCPI-5, StN15, Hb or their combination versus water, were 131, 167, 148 and 142, respectively. The treatment with the proteins/peptide or their combination increased proteins that bind calcium, phosphate and interact with distinct proteins, as well as proteins with antimicrobial and acid-resistant properties, such as, Cornifin-B (7.7, 12.6, and 4.3-fold for CaneCPI-5, StN15 and Hb, respectively), isoforms of Cystatin (2.2–2.4-fold for CaneCPI-5 and StN15), Proline-rich-protein 4 (4.3-fold; StN15), Histatin-1 (2.8-fold; StN15) and Hemoglobin (7.7–25-fold for Hb and Combination). Immunoglobulin, Keratin and Histone were exclusively identified upon treatment with the proteins/peptide, alone or combined. Conclusion: Rinsing with proteins/peptide, alone or combined, increased protective proteins in the initial AEP. Clinical Relevance: Our results suggest that rinsing with the proteins/peptide or their combination increases the proteins capable of enhancing the protective function of the basal layer of AEP. Department of Biological Sciences Bauru School of Dentistry University of São Paulo Department of Genetics and Evolution São Carlos Federal University Department of Biochemistry and Technology Institute of Chemistry São Paulo State University (UNESP) Department of Biochemistry and Technology Institute of Chemistry São Paulo State University (UNESP)
MALARIA, BLOOD proteins, PROTOZOAN diseases, NATURAL immunity, SICK people
Abstract
"What we've done is to create a library of all the components of all the proteins malaria could show to our immune system", said DeRisi, also a professor of biochemistry and biophysics at UCSF. Keywords: Antibodies; Biochemistry; Biophysics; Blood Proteins; Chan Zuckerberg Biohub; Chemistry; Genetics; Health and Medicine; Immunoglobulins; Immunology; Malaria; Mosquito-Borne Diseases; Pediatrics; Peptides; Peptides and Proteins; Physics; Plasmodium falciparum; Proteins; Protozoan Infections; Tropical Disease EN Antibodies Biochemistry Biophysics Blood Proteins Chan Zuckerberg Biohub Chemistry Genetics Health and Medicine Immunoglobulins Immunology Malaria Mosquito-Borne Diseases Pediatrics Peptides Peptides and Proteins Physics Plasmodium falciparum Proteins Protozoan Infections Tropical Disease 156 156 1 04/03/23 20230407 NES 230407 2023 APR 7 (NewsRx) -- By a News Reporter-Staff News Editor at Zika & Mosquito Week -- Plasmodium falciparum, the parasite that causes the deadliest form of malaria in humans, is a master evader, and has dodged all attempts at an effective and durable vaccine. [Extracted from the article]
Organic Chemistry, Proteins, Quantitative Structure-Activity Relationship, General Medicine, Amino Acid Sequence, Peptides, Biochemistry, Chromatography, High Pressure Liquid, Analytical Chemistry
Abstract
Peptide therapeutics plays a prominent role in medical practice. Both peptides and proteins have been used in several disease conditions like diabetes, cancer, bacterial infections etc. The optimization of a peptide library is a time consuming and expensive chore. The tools of computational chemistry offer a way to optimize the properties of peptides. Quantitative Structure Retention (Chromatographic) Relationships (QSRR) is a powerful tool which statistically derives relationships between chromatographic parameters and descriptors that characterize the molecular structure of analytes. In this paper, we show how Comparative Protein ModelingQuantitative Structure Retention Relationship (acronym ComProM-QSRR) can be used to predict the retention time of peptide sequences. This formalism is founded on our earlier published QSAR methodology HomoSAR. ComProM-QSRR can recognize and distinguish the contribution of amino acids at specific positions in the peptide sequences to the retention phenomena through their related physicochemical properties. This study firmly establishes the fact that this approach can be pragmatically used to predict the retention time to all classes of peptides regardless of size or sequence.
Published
2021
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