KAUST Discovery Associate Professor Stefan Arold has established KAUST's first structural biology lab specializing in determining the atomic 3D structure of proteins and other biological macromolecules. The lab setup involved challenges such as assembling instruments and continuing research, but the Bioscience Core Lab at KAUST and support from colleagues aided in the process. Arold's research focuses on understanding protein function through an integrated 'hybrid' approach to analyze 3D structure and function of proteins. Why it matters: This new lab enhances KAUST's capabilities in molecular biophysics and structural biology, enabling advanced research into the functions of proteins and their implications for health and disease.
KAUST researchers used cryogenic electron microscopy (cryo-EM) to study the 3D structure of protein complexes involved in DNA replication and repair. They investigated the interaction between the Y-family TLS polymerase Pol K and mono-ubiquitylated PCNA. The study revealed that DNA binding is required for Pol K to form a rigid, active complex with PCNA. Why it matters: Understanding these structural interactions may provide insights into cancer development and drug resistance mechanisms.
KAUST researchers have captured the initial unwinding of DNA using cryo-electron microscopy and deep learning. The study details 15 atomic states describing how the Simian Virus 40 Large Tumor Antigen helicase unwinds DNA, revealing the coordinated roles of DNA, helicases, and ATP. The research elucidates the fundamental mechanisms of DNA replication, a cornerstone of growth and reproduction. Why it matters: This detailed understanding of helicase function could lead to advances in nanotechnology and our understanding of genetic processes.
A DeepMind researcher presented work on incorporating symmetries into machine learning models, with applications to lattice-QCD and molecular dynamics. The work includes permutation and translation-invariant normalizing flows for free-energy estimation in molecular dynamics. They also presented U(N) and SU(N) Gauge-equivariant normalizing flows for pure Gauge simulations and its extensions to incorporate fermions in lattice-QCD. Why it matters: Applying symmetry principles to generative models could improve AI's ability to model complex physical systems relevant to materials science and other fields in the region.
Daisuke Kihara from Purdue University presented a seminar at MBZUAI on using deep learning for biomolecular structure modeling. His lab is developing 3D structure modeling methods, especially for cryo-electron microscopy (cryo-EM) data. They are also working on RNA structure prediction and peptide docking using deep neural networks inspired by AlphaFold2. Why it matters: Applying advanced deep learning techniques to biomolecular structure prediction can accelerate drug discovery and our understanding of molecular functions.
KAUST researchers developed a new single-molecule imaging method called the cumulative-area (CA) method. This method allows for simultaneous characterization of size, shape, and conformational dynamics of individual molecules, along with accurate determination of diffusion kinetics. The researchers demonstrated the CA method's effectiveness on nano- and micro-sized objects, extracting quantitative information about size, diffusion, and relaxation time. Why it matters: This advancement expands the capabilities of molecule imaging techniques in the region and has potential applications in polymer dynamics research and the study of molecular mechanisms within cells.
KAUST researchers have determined the atomic 3D structure of a key protein involved in plant stress signaling using X-ray crystallography at the SOLEIL synchrotron in France. Postdoctoral fellow Umar Farook Shahul Hameed optimized a tiny crystal of the plant enzyme for over six months. The team used the EIGER 9M detector to capture the weak diffraction pattern from the crystal. Why it matters: Understanding the interactions between proteins that communicate plant stress could lead to engineering more stress-tolerant crops, enhancing food security.
A conference at KAUST covered topics related to hydrophobic interfaces. The event brought together researchers and experts in the field. King Abdullah University of Science and Technology hosted the conference. Why it matters: Events like this foster collaboration and knowledge sharing in materials science and engineering.