Protein design using structure-based residue preferences

Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at individual residues-without accounting for mutation interactions-explain much and sometimes virtually all of the combinatorial mutation effects across 8 datasets (R2 ~ 78-98%). Hence, few observations (~100 times the number of mutated residues) enable accurate prediction of held-out variant effects (Pearson r > 0.80). We hypothesized that the local structural contexts around a residue could be sufficient to predict mutation preferences, and develop an unsupervised approach termed CoVES (Combinatorial Variant Effects from Structure). Our results suggest that CoVES outperforms not just model-free methods but also similarly to complex models for creating functional and diverse protein variants. CoVES offers an effective alternative to complicated models for identifying functional protein mutations.

Overcoming Immunological Challenges Limiting Capsid-Mediated Gene Therapy With Machine Learning

A key hurdle to making adeno-associated virus (AAV) capsid mediated gene therapy broadly beneficial to all patients is overcoming pre-existing and therapy-induced immune responses to these vectors. Recent advances in high-throughput DNA synthesis, multiplexing and sequencing technologies have accelerated engineering of improved capsid properties such as production yield, packaging efficiency, biodistribution and transduction efficiency. Here we outline how machine learning, advances in viral immunology, and high-throughput measurements can enable engineering of a new generation of de-immunized capsids beyond the antigenic landscape of natural AAVs, towards expanding the therapeutic reach of gene therapy.

Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design

Adeno-associated virus (AAV) capsids can deliver transformative gene therapies, but our understanding of AAV biology remains incomplete. We generated the complete first-order AAV2 capsid fitness landscape, characterizing all single-codon substitutions, insertions, and deletions across multiple functions relevant for in vivo delivery. We discovered a frameshifted gene in the VP1 region that expresses a membrane-associated accessory protein that limits AAV production through competitive exclusion. Mutant biodistribution revealed the importance of both surface-exposed and buried residues, with a few phenotypic profiles characterizing most variants. Finally, we algorithmically designed and experimentally verified a diverse in vivo targeted capsid library with viability far exceeding random mutagenesis approaches. These results demonstrate the power of systematic mutagenesis for deciphering complex genomes and the potential of empirical machine-guided protein engineering.

Primordial sex facilitates the emergence of evolution

Compartments are ubiquitous throughout biology, and they have very likely played a crucial role at the origin of life. Here we assume that a protocell, which is a compartment enclosing functional components, requires N such components in order to be evolvable. We calculate the timescale in which a minimal evolvable protocell is produced. We show that when protocells fuse and share information, the timescales polynomially in N By contrast, in the absence of fusion, the worst-case scenario is exponential in N We discuss the implications of this result for the origin of life and other biological processes.

Computer simulations of cellular group selection reveal mechanism for sustaining cooperation

We present a computer simulation of group selection that is inspired by proto-cell division. Two types of replicating molecules, cooperators and defectors, reside inside membrane bound compartments. Cooperators pay a cost for other replicators in the cell to receive a benefit. Defectors pay no cost and distribute no benefits. The total population size fluctuates as a consequence of births and deaths of individual replicators. Replication requires activated substrates that are generated at a constant rate. Our model includes mutation between cooperators and defectors and selection on two levels: within proto-cells and between proto-cells. We find surprising similarities and differences between models with and without cell death. In both cases, a necessary requirement for group selection to favor some level of cooperation is the continuous formation of a minimum fraction of pure cooperator groups. Subsequently these groups become undermined by defectors, because of mutation and selection within cells. Cell division mechanisms which generate pure cooperator groups more efficiently are stronger promoters of cooperation. For example, division of a proto-cell into many daughter cells is more powerful in enhancing cooperation than division into two daughter cells. Our model differs from previous studies of group selection in that we explore a variety of different features and relax several restrictive assumptions that would be needed for analytic calculations.

Burn care standards in Israel: lack of consensus

In recent years, the need for a national burn center based on ABA guidelines has emerged in Israel. The formation of such a center is now underway in the Chaim Sheba Medical Center. As a first step in the standardization of burn care in Israel, we have conducted a nation-wide survey among burn care personnel (physicians, nurses and other burn team members), regarding different aspects of the treatment of burn patients.

METHODS

A questionnaire comprised of 30 questions regarding the severity of burns admitted, the site of initial management, wound care (both burn/skin-graft sites and donor sites), dressing changes protocols, sterility precautions, hydrotherapy, and pressure dressings was presented to 70 health-care professionals involved in the treatment of burns.

RESULTS AND DISCUSSION

Seventy-seven percent of interviewed personnel participated in the survey. Consensus was found regarding most local (topical) wound care, (SSD for clean non-facial burns, Sulfamylon (mafenide-acetate) for contaminated non-facial burns, Threolone (chloramphenicol 3% and prednisolone 0.5%) or Bacitracin for facial burns, Paraffin gauzes with or without Sulfamylon for donor and graft sites). Dressing changes regimes were also agreed upon generally. However, there was no consensus regarding the ideal time for the removal of donor site dressings and this issue will need to be resolved. Other important findings are that both Edinborough University Solution of Lime (EUSOL), which has been deemed unsuitable for burn treatment due to toxic effects, and hydrotherapy, which has been proposed as a source of infection and contamination, are still widely used. We anticipate that these issues will be settled in our unified national burn care protocols (which are currently under development and revision).