David Baker
University of Washington
H-index: 209
North America-United States
Description
David Baker, With an exceptional h-index of 209 and a recent h-index of 128 (since 2020), a distinguished researcher at University of Washington, specializes in the field of Protein Design.
His recent articles reflect a diverse array of research interests and contributions to the field:
The Shortest History of Sex: Two Billion Years of Procreation and Recreation (Shortest History)
Blueprinting extendable nanomaterials with standardized protein blocks
Machine learning-guided engineering of genetically encoded fluorescent calcium indicators
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes
Expansive discovery of chemically diverse structured macrocyclic oligoamides
Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development
Genome editing reagents and their use
De novo design of obligate ABC heterotrimeric proteins
Professor Information
University | University of Washington |
---|---|
Position | ___ |
Citations(all) | 160879 |
Citations(since 2020) | 66819 |
Cited By | 119378 |
hIndex(all) | 209 |
hIndex(since 2020) | 128 |
i10Index(all) | 982 |
i10Index(since 2020) | 730 |
University Profile Page | University of Washington |
Research & Interests List
Protein Design
Top articles of David Baker
The Shortest History of Sex: Two Billion Years of Procreation and Recreation (Shortest History)
A wild—and satisfying!—ride through two billion years of sexual evolution. The Shortest History books deliver thousands of years of history in one riveting, fast-paced read. From the first microbial exchanges of DNA to Tinder and sexbots, how did sex begin, and how did it evolve to be so varied and complex in humans? What influence do our genetic ancestors have on our current love lives? And what might sex look like in the future? With acuity, humor, and respect for human diversity, The Shortest History of Sex reveals where the many facets of our sexuality—chemical, anatomical, behavioral, social—come from. Chasing down our evolutionary family tree, from the first aquatic creatures to primate societies, David Baker sheds light on our baffling array of passions, impulses, and fetishes, and guides us toward a clear understanding of one of the deepest, most abiding forces of human nature. The Shortest History of Sex also charts how sex changed for humans across the foraging, agrarian, and modern eras, showing how, even as our biology and sexual instincts have remained the same, the current nature of our sex lives has no historical or evolutionary precedent. The result is a revealing, utterly unique insight into history and human behavior—and the profound forces of nature and nurture compelling our most intimate relationships.
Authors
David Baker
Published Date
2024/2/6
Blueprinting extendable nanomaterials with standardized protein blocks
A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures 1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large …
Authors
Timothy F Huddy,Yang Hsia,Ryan D Kibler,Jinwei Xu,Neville Bethel,Deepesh Nagarajan,Rachel Redler,Philip JY Leung,Connor Weidle,Alexis Courbet,Erin C Yang,Asim K Bera,Nicolas Coudray,S John Calise,Fatima A Davila-Hernandez,Hannah L Han,Kenneth D Carr,Zhe Li,Ryan McHugh,Gabriella Reggiano,Alex Kang,Banumathi Sankaran,Miles S Dickinson,Brian Coventry,TJ Brunette,Yulai Liu,Justas Dauparas,Andrew J Borst,Damian Ekiert,Justin M Kollman,Gira Bhabha,David Baker
Journal
Nature
Published Date
2024/3
Machine learning-guided engineering of genetically encoded fluorescent calcium indicators
Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which …
Authors
Sarah J Wait,Marc Expòsit,Sophia Lin,Michael Rappleye,Justin Daho Lee,Samuel A Colby,Lily Torp,Anthony Asencio,Annette Smith,Michael Regnier,Farid Moussavi-Harami,David Baker,Christina K Kim,Andre Berndt
Journal
Nature Computational Science
Published Date
2024/3/21
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes
The organization of membrane proteins between and within membrane-bound compartments is critical to cellular function. Yet we lack approaches to regulate this organization in a range of membrane-based materials, such as engineered cells, exosomes, and liposomes. Uncovering and leveraging biophysical drivers of membrane protein organization to design membrane systems could greatly enhance the functionality of these materials. Towards this goal, we use de novo protein design, molecular dynamic simulations, and cell-free systems to explore how membrane-protein hydrophobic mismatch could be used to tune protein cotranslational integration and organization in synthetic lipid membranes. We find that membranes must deform to accommodate membrane-protein hydrophobic mismatch, which reduces the expression and co-translational insertion of membrane proteins into synthetic membranes. We …
Authors
Justin A Peruzzi,Jan Steinkühler,Timothy Q Vu,Taylor F Gunnels,Vivian T Hu,Peilong Lu,David Baker,Neha P Kamat
Journal
Nature Communications
Published Date
2024/4/11
Expansive discovery of chemically diverse structured macrocyclic oligoamides
Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug …
Authors
Patrick J Salveson,Adam P Moyer,Meerit Y Said,Gizem Gӧkçe,Xinting Li,Alex Kang,Hannah Nguyen,Asim K Bera,Paul M Levine,Gaurav Bhardwaj,David Baker
Journal
Science
Published Date
2024/4/26
Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development
We previously reported that the Plasmodium falciparum putative serine/threonine protein phosphatase 7 (PP7) is a high confidence substrate of the cAMP-dependent protein kinase (PKA). Here we explore the function of PP7 in asexual P. falciparum blood stage parasites. We show that conditional disruption of PP7 leads to a severe growth arrest. We show that PP7 is a calcium-dependent phosphatase which interacts with calmodulin and calcium-dependent protein kinase 1 (CDPK1), consistent with a role in calcium signalling. Notably, PP7 was found to be dispensable for erythrocyte invasion, but was crucial for ring-stage development, with PP7-null parasites arresting shortly following invasion and showing no transition to ameboid forms. Phosphoproteomic analysis revealed that PP7 may regulate dephosphorylation of PKAc substrates, particularly in the presence of Ca2+. Its interaction with calmodulin and CDPK1 further emphasise a role in calcium signalling, while its impact on early ring development and PKAc substrate phosphorylation underscores its importance in parasite development.
Authors
Avnish Patel,Joshua A Rey,Helen R Flynn,Konstantinos Kousis,Mark J Skehel,Mike Blackman,David A Baker
Journal
bioRxiv
Published Date
2024
Genome editing reagents and their use
The application discloses multimeric assemblies packaging one or more active component and their use to carry out nucleic acid regulation or gene editing.
Published Date
2024/1/9
De novo design of obligate ABC heterotrimeric proteins
Disclosed are polypeptides having an amino acid sequence at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence selected from the group consisting of the amino acid sequences listed in Tables 1, 2, and 3, and heteropolymers formed from such polypeptides.
Published Date
2024/1/25
Professor FAQs
What is David Baker's h-index at University of Washington?
The h-index of David Baker has been 128 since 2020 and 209 in total.
What are David Baker's top articles?
The articles with the titles of
The Shortest History of Sex: Two Billion Years of Procreation and Recreation (Shortest History)
Blueprinting extendable nanomaterials with standardized protein blocks
Machine learning-guided engineering of genetically encoded fluorescent calcium indicators
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes
Expansive discovery of chemically diverse structured macrocyclic oligoamides
Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development
Genome editing reagents and their use
De novo design of obligate ABC heterotrimeric proteins
...
are the top articles of David Baker at University of Washington.
What are David Baker's research interests?
The research interests of David Baker are: Protein Design
What is David Baker's total number of citations?
David Baker has 160,879 citations in total.
What are the co-authors of David Baker?
The co-authors of David Baker are Brian Kuhlman, Rhiju Das, Tanja Kortemme, Sarel Fleishman, Chu Wang, Possu Huang.