Review
Biochemical Research Methods
Joel Fauser, Aymelt Itzen, Burak Gulen
Summary: This review discusses the limitations of structural characterization of macromolecular assemblies due to transient interactions and highlights the importance of covalently tethering interacting proteins using specific chemical tools. Various protein engineering techniques and biochemical methodologies have been employed to stabilize macromolecular complexes for structural investigation, enabling advancements in diverse scientific fields.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Engineering, Environmental
Chen Cai, Yu Hua, Huiling Liu, Xiaohu Dai
Summary: This study demonstrates the potential of recycling cephalosporin fermentation residue (CFR) into plant biostimulants through partial acid hydrolysis. Two favorable hydrolysis conditions were identified, resulting in biostimulants with plant growth promotion and stress alleviation properties. The biostimulants derived from CFR showed differences in aminograms and profiles of low molecular weight compounds, indicating potential variability in their effects on plants.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Chemistry, Applied
Dezhi Yuan, Hua Lv, Tiantian Wang, Yulu Rao, Yibo Tang, Yiwen Chu, Xinrong Wang, Jiafu Lin, Peng Gao, Tao Song
Summary: This study reports the discovery of a novel alpha-agarase, AgaB, with an N-terminal CBM2 domain. AgaB exhibited activity against agarose and produced agarotetraose and agarohexaose. The study also found that CBM2 aids in substrate binding and identified possible catalytic amino acids, E468 and D333.
Article
Immunology
Stacey Orangi, Jessie Pinchoff, Daniel Mwanga, Timothy Abuya, Mainga Hamaluba, George Warimwe, Karen Austrian, Edwine Barasa
Summary: Kenya has a high rate of COVID-19 vaccine hesitancy at 36.5%, with factors such as rural regions, perceived difficulty in adhering to government regulations, no perceived infection risk, concerns about vaccine safety and effectiveness, and religious/cultural reasons being associated with hesitancy. Interventions to address vaccine hesitancy and improve vaccine confidence should prioritize holistic messaging targeting specific groups to communicate the risks and benefits of vaccines.
Review
Clinical Neurology
Aja Louise Murray, Marlena Vollmer, Ian J. Deary, Graciela Muniz-Terrera, Tom Booth
Summary: This review discusses the advantages and limitations of methods for assessing individual-level change, with a focus on factors such as imperfect reliability, differential reliability, and practice effects. The study concludes that IRT-based approaches hold promise for addressing a wide range of issues that influence accurate judgements of meaningful change.
ALZHEIMERS RESEARCH & THERAPY
(2021)
Article
Biochemistry & Molecular Biology
Isel Grau, Ann Nowe, Wim Vranken
Summary: This study investigates a novel approach to predict early folding residues (EFRs) from protein sequences to gain mechanistic residue-level insights into the sequence determinants of EFRs in proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Shengrong Liao, Nayeong Yuk, Yu Jin Kim, Huayan Xu, Xiaolin Li, Ling Wang, Yonghong Liu, Hye Jin Jung
Summary: Seventeen derivatives (1-17) with different L-amino acid side chains were designed and synthesized based on the natural product terpestacin. The anticancer activities of these derivatives against U87MG-derived glioblastoma stem cells (GSCs) were evaluated, and compounds 5, 11, 13, and 15 exhibited strong inhibitory effects on GSCs' proliferation and tumorsphere formation. In addition, compounds 13 and 15 effectively induced apoptosis and significantly hindered the invasion of GSCs. The levels of CD133, a marker in GSCs, also decreased in a dose-dependent manner after treatment with these active compounds. Compared to terpestacin and the positive control A1938, our derivatives demonstrated stronger activities, with compounds 13 and 15 considered promising candidates for further development as anticancer agents targeting GSCs.
BIOORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Elisabeth Rakiswende Ouedraogo, Kiessoun Konate, Abdoudramane Sanou, Hemayoro Sama, Ella Wendinpuikondo Raketa Compaore, Oksana Sytar, Adama Hilou, Marian Brestic, Mamoudou Hama Dicko
Summary: This study assessed the nutritional quality of soybeans and found variations in the fatty acid composition and pesticide residues among different varieties. The G197 variety had a better nutritional profile compared to G196.
Article
Agriculture, Dairy & Animal Science
Juan Zhang, Weizhen Wang, Ying Wang, Honghong Hu, Baojun Yu, Zihang Zhou, Ju Guo, Yaling Gu, Zhengyun Cai, Guosheng Xin
Summary: The addition of a certain proportion of lysine residue in diet for broilers can improve meat quality and reduce feed costs, but may also lower slaughter performance. The addition of lysine residue alters the metabolic pathways of broilers, affecting amino acid and fat metabolism.
JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION
(2022)
Article
Chemistry, Analytical
Yukuang Guo, Shaofei Ji, Wei Wang, Susan Wong, Chun-Wan Yen, Chloe Hu, Dennis H. Leung, Emile Plise, Shu Zhang, Chenghong Zhang, Uchenna A. Anene, Donglu Zhang, Christian N. Cunningham, S. Cyrus Khojasteh, Dian Su
Summary: Macrocyclic peptides (MCPs) are a promising class of drug modalities for targeting hard-to-drug targets, but their poor intestinal stability is a major obstacle for oral delivery. The study investigated the metabolic stability and biotransformation of MCPs in various matrices, revealing differences in metabolic pathways and identifying pancreatic enzymes as a primary barrier for oral delivery. Furthermore, lysosomal peptidase cathepsin B was found to be a major enzyme responsible for cleaving side-chain amide bonds in lysosomes, providing insights for lead candidate selection and optimization.
ANALYTICAL CHEMISTRY
(2022)
Article
Forestry
Maokai Cui, Qingyang Li, Zhanglin Ni, Yongxiang Han, Yuewen Zheng, Runhong Mo, Danyu Shen, Yihua Liu
Summary: This study collected 273 samples and corresponding soils from the main English walnut-producing areas in China to investigate the nutritional quality of Chinese walnuts and the influence of soil on their quality. The results showed that walnut oil is rich in linoleic acid and γ-tocopherol, while walnut flour contains high levels of macro-element K and various micro-elements. The amino acid profile of walnut flour is also highly nutritious. The content of trace elements in the soil, particularly Fe, Cu, and Zn, had the greatest impact on the nutritional qualities of walnuts. The pH of the soil also played a significant role in determining walnut quality.
Article
Biochemistry & Molecular Biology
Donghun Lee, Sanghoon Oh, HyeokJin Cho, Jungmin Yoo, Gwangrog Lee
Summary: Bacterial exonuclease III (ExoIII) is a multifunctional enzyme that has both apurinic/apyrimidinic (AP)-endonuclease and 3'->5' exonuclease activities. Through mutational analysis and single-molecule imaging, researchers have discovered the key amino acid residues that determine the functional selection between these two activities. Additionally, they found that stabilizing the melted state of the 3' terminal nucleobases is crucial for activating the exonuclease activity. Maintaining the DNA substrate as a B-form helix during the exonucleolytic cleavage process is also essential. This study provides insights into the mechanism of ExoIII's dual functionalities at the amino acid level.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Balint Biro, Bi Zhao, Lukasz Kurgan
Summary: This study explores the complementarity of different prediction methods, finding that combining structure-trained and disorder-trained predictions leads to improved quality, and demonstrating that predictions accurately reflect various relationships in experimental data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Ecology
Oliver N. Shipley, Gregory A. Henkes, James Gelsleichter, Clark R. Morgan, Eric V. Schneider, Brendan S. Talwar, Michael G. Frisk
Summary: The isotopic composition of tooth-bound collagen is used to reconstruct dietary patterns of animals, showing different isotopic values compared to other tissues and significant variability in isotopic values among teeth of different ages.
JOURNAL OF ANIMAL ECOLOGY
(2021)
Article
Multidisciplinary Sciences
Preeti Choudhary, Stephen Anyango, John Berrisford, James Tolchard, Mihaly Varadi, Sameer Velankar
Summary: More than 61,000 proteins have correspondence between their amino acid sequence (UniProtKB) and 3D structures (PDB) through the SIFTS resource. SIFTS incorporates residue-level annotations from various biological resources and is maintained separately from the structure data in the PDB archive.
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Periskova, Chris Randle, Alexander Rose, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva, Genji Kurisu, Haruki Nakamura, Yumiko Kengaku, Hasumi Cho, Junko Sato, Ju Yaen Kim, Yasuyo Ikegawa, Atsushi Nakagawa, Reiko Yamashita, Takahiro Kudou, Gert-Jan Bekker, Hirofumi Suzuki, Takeshi Iwata, Masashi Yokochi, Naohiro Kobayashi, Toshimichi Fujiwara, Sameer Velankar, Gerard J. Kleywegt, Stephen Anyango, David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Mandar Deshpande, Paul Gane, Romana Gaborova, Deepti Gupta, Aleksandras Gutmanas, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Ardan Patwardhan, Typhaine Paysan-Lafosse, Lukas Pravda, Osman Salih, David Sehnal, Mihaly Varadi, Radka Varekova, John L. Markley, Jeffrey C. Hoch, Pedro R. Romero, Kumaran Baskaran, Dimitri Maziuk, Eldon L. Ulrich, Jonathan R. Wedell, Hongyang Yao, Miron Livny, Yannis E. Ioannidis
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel K. Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlic, Chris Randle, Alexander Rose, Peter Rose, Raul Sala, Monica Sekharan, Chenghua Shao, Lihua Tan, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Marina Zhuravleva, Christine Zardecki
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
Christopher Markosian, Luigi Di Costanzo, Monica Sekharan, Chenghua Shao, Stephen K. Burley, Christine Zardecki
Article
Biochemistry & Molecular Biology
David S. Goodsell, Christine Zardecki, Luigi Di Costanzo, Jose M. Duarte, Brian P. Hudson, Irina Persikova, Joan Segura, Chenghua Shao, Maria Voigt, John D. Westbrook, Jasmine Y. Young, Stephen K. Burley
Article
Biochemistry & Molecular Biology
Jeffrey R. Wagner, Christopher P. Churas, Shuai Liu, Robert Swift, Michael Chiu, Chenghua Shao, Victoria A. Feher, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro
Article
Biochemistry & Molecular Biology
Conor D. Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2020)
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Chris Randle, Alexander Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Y. Young, Christine Zardecki, Marina Zhuravleva
Summary: RCSB PDB, as the US data center for the global PDB archive, provides free access to 3D macromolecular structure data for millions of users worldwide, including educators, students, and the general public, integrating over 40 external biodata resources. The redesigned website now features improved search functionality and easier access to PDB data, showcasing new structures relevant to the understanding and addressing of the COVID-19 pandemic.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg Crichlow, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai J. Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, John D. Westbrook, Shamara Whetstone, Jasmine Y. Young, Christine Zardecki
Summary: RCSB PDB, funded by several US government agencies, has been providing service to structural biologists and PDB data consumers worldwide since 1999. It is a founding member of the worldwide Protein Data Bank partnership, serving as the US data center for the global PDB archive. RCSB PDB also develops new tools and features for 3D structure analysis and visualization.
Article
Biochemistry & Molecular Biology
Chenghua Shao, John D. Westbrook, Changpeng Lu, Charmi Bhikadiya, Ezra Peisach, Jasmine Y. Young, Jose M. Duarte, Robert Lowe, Sijian Wang, Yana Rose, Zukang Feng, Stephen K. Burley
Summary: This study analyzed quality indicators of small-molecule ligands in experimentally determined macromolecular structures in the Protein Data Bank (PDB). It found that ligand quality varies greatly in terms of fit to experimental data, deviations from known chemical structures, and interatomic clashes. A composite ranking score was constructed based on these quality indicators, allowing for comparison of chemically identical ligands in different PDB structures. Two-dimensional ligand quality plots were used to assess ligand structure quality and select the best exemplars.
Review
Biochemistry & Molecular Biology
John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach
Summary: PDBx/mmCIF is a data standard for structural biology, used for storing and disseminating three-dimensional structures of biological macromolecules. Developed collaboratively over three decades, involving contributions from multiple scientific disciplines, it accelerates the pace of scientific discovery.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben Webb, John D. Westbrook, Shamara Whetstone, Jasmine Y. Young, Arthur Zalevsky, Christine Zardecki
Summary: The Protein Data Bank (PDB) is an open-access global archive that houses three-dimensional biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the US data center for wwPDB and is responsible for processing and ensuring the security of PDB data. It provides free access to PDB data and supports training and education through its web portals.
Review
Biochemistry & Molecular Biology
Stephen K. Burley, Helen M. Berman, Jose M. Duarte, Zukang Feng, Justin W. Flatt, Brian P. Hudson, Robert Lowe, Ezra Peisach, Dennis W. Piehl, Yana Rose, Andrej Sali, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, John D. Westbrook, Jasmine Y. Young, Christine Zardecki
Summary: RCSB PDB, funded by multiple US agencies, is a global support center for structural biologists and PDB data users. It serves as the US data center and archive keeper for the worldwide PDB, providing storage and updating services. RCSB PDB serves thousands of depositors annually and offers free data access and education resources to millions of users worldwide.
Article
Biochemistry & Molecular Biology
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Igor Khokhriakov, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben Webb, John D. Westbrook, Shamara Whetstone, Jasmine Y. Young, Arthur Zalevsky, Christine Zardecki
Summary: The RCSB PDB is a founding member of the wwPDB and serves as the US data center for the open-access PDB archive. The upgraded RCSB.org web portal provides a one-stop-shop for open access to a large number of experimentally-determined PDB structures and computationally-predicted CSMs, along with related functional annotations.
NUCLEIC ACIDS RESEARCH
(2023)
Meeting Abstract
Chemistry, Multidisciplinary
Stephen K. Burley
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2021)