Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for chol
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Ochoa, Jessica M.↗
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Neural networks to learn protein sequence–function relationships from deep mutational scanning data
Understanding the relationship between protein sequence and function is necessary to design new and useful proteins with applications in bioenergy, medicine, and agriculture. The mapping from sequence to function is tremendously complex because it involves thousands of molecular interactions that are coupled over multiple lengths and timescales. We show that neural networks can learn the sequence–function mapping from large protein datasets. Neural networks are appealing for this task because they can learn complicated relationships from data, make few assumptions about the nature of the sequence–function relationship, and can learn general rules that apply across the length of the protein sequence. We demonstrate that learned models can be applied to design new proteins with properties that exceed natural sequences.
59 BASIC BIOLOGICAL SCIENCES↗
Temporal and contextual knowledge in model-based expert systems
A basic paradigm that allows representation of physical systems with a focus on context and time is presented. Paragon provides the capability to quickly capture an expert's knowledge in a cognitively resonant manner. From that description, Paragon creates a simulation model in LISP, which when executed, verifies that the domain expert did not make any mistakes. The Achille's heel of rule-based systems has been the lack of a systematic methodology for testing, and Paragon's developers are certain that the model-based approach overcomes that problem. The reason this testing is now possible is that software, which is very difficult to test, has in essence been transformed into hardware.
Toth-Fejel, Tihamer↗
On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations
The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.
59 BASIC BIOLOGICAL SCIENCES↗
Back stress in dislocation creep. Part 1: Basic concepts and measuring techniques
A theory is proposed whereby the plastic deformation of metal materials is determined by the difference between the applied stress and the back stress which characterizes the resistance of the material to plastic deformation. The back stress is usually equivalent to the internal stress or the friction stress and depends on the magnitude of the applied stress and temperature. The concept of back stress is applied to the case of the dislocation creep of precipitation-hardened or dispersion-strengthened metal materials. An additivity rule is formulated which can be useful in interpreting the creep behavior of such materials.
Cadek, J.↗
A de novo matrix for macroscopic living materials from bacteria
Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create materials with tailored functions. While bottom-up assembly of macroscopic ELMs with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. Here we report growth of ELMs from Caulobacter crescentus cells that display and secrete a self-interacting protein. This protein formed a de novo matrix and assembled cells into centimeter-scale ELMs. Discovery of design and assembly principles allowed us to tune the composition, mechanical properties, and catalytic function of these ELMs. This work provides genetic tools, design and assembly rules, and a platform for growing ELMs with control over both matrix and cellular structure and function.
59 BASIC BIOLOGICAL SCIENCES↗
Strangers in a foreign land: ‘Yeastizing’ plant enzymes
Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.
59 BASIC BIOLOGICAL SCIENCES↗
Gluonic Structure from Instantons
The instanton vacuum provides an effective description of chiral symmetry breaking by local topological fluctuations of the gauge fields, as observed in lattice QCD simulations. The resulting effective dynamics at momenta below 1/$\bar{ρ}$ ≈ 0.6 GeV explains the basic features of light-quark correlation functions and is used extensively in studies of hadron structure. The instanton fields also make definite contributions to the gluonic structure of light hadrons, as expressed in the matrix elements of composite quark– gluon or gluon operators. The article reviews the gluonic structure of light hadrons (nucleon, pion) induced by instantons. This includes: (i) twist-2 parton distributions and momentum sum rule; (ii) twist-3 angular momentum and spin-orbit interactions; (iii) twist-3 and twist-4 quark–gluon correlations and power corrections; (iv) trace anomaly and hadron mass decomposition; (v) scalar gluon form factors and mechanical properties; (vi) axial anomaly and pseudoscalar gluon form factors. It also discusses possible further applications of the methods and recent developments including gauge field configurations beyond instantons.
Weiss, C. [Thomas Jefferson National Accelerator F↗
On Slender-Body Theory at Transonic Speeds
The basic ideas of the slender-body approximation have been applied to the nonlinear transonic-flow equation for the velocity potential in order to obtain some of the essential features of slender-body theory at transonic speeds. The results of the investigation are presented from a unified point of view which demonstrates the similarity of slender-body solutions in the various Mach number ranges. The transonic area rule and some conditions concerning its validity follow from the analysis. (author)
Harder, Keith C↗
Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design
Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.
59 BASIC BIOLOGICAL SCIENCES↗
Real-time bioelectronic sensing of environmental contaminants
Real-time chemical sensing is crucial for applications in environmental and health monitoring. Biosensors can detect a variety of molecules through genetic circuits that use these chemicals to trigger the synthesis of a coloured protein, thereby producing an optical signal. However, the process of protein expression limits the speed of this sensing to approximately half an hour, and optical signals are often difficult to detect in situ. Here we combine synthetic biology and materials engineering to develop biosensors that produce electrical readouts and have detection times of minutes. Here we programmed Escherichia coli to produce an electrical current in response to specific chemicals using a modular, eight-component, synthetic electron transport chain. As designed, this strain produced current following exposure to thiosulfate, an anion that causes microbial blooms, within 2 min. This amperometric sensor was then modified to detect an endocrine disruptor. The incorporation of a protein switch into the synthetic pathway and encapsulation of the bacteria with conductive nanomaterials enabled the detection of the endocrine disruptor in urban waterway samples within 3 min. Our results provide design rules to sense various chemicals with mass-transport-limited detection times and a new platform for miniature, low-power bioelectronic sensors that safeguard ecological and human health.
59 BASIC BIOLOGICAL SCIENCES↗
Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective
The complexities of modern biomedicine are rapidly increasing. Thus, modeling and simulation have become increasingly important as a strategy to understand and predict the trajectory of pathophysiology, disease genesis, and disease spread in support of clinical and policy decisions. In such cases, inappropriate or ill-placed trust in the model and simulation outcomes may result in negative outcomes, and hence illustrate the need to formalize the execution and communication of modeling and simulation practices. Although verification and validation have been generally accepted as significant components of a model’s credibility, they cannot be assumed to equate to a holistic credible practice, which includes activities that can impact comprehension and in-depth examination inherent in the devel-opment and reuse of the models. For the past several years, the Committee on Credible Practice of Modeling and Simulation in Healthcare, an interdisciplinary group seeded from a U.S. interagency initiative, has worked to codify best practices. Here, we provide Ten Rules for credible practice of modeling and simulation in healthcare developed from a comparative analysis by the Committee’s multidisciplinary membership, followed by a large stakeholder com-munity survey. These rules establish a unified conceptual framework for modeling and simulation design, implementation, evaluation, dissemination and usage across the modeling and simulation life-cycle. While biomedical science and clinical care domains have somewhat different requirements and expectations for credible practice, our study converged on rules that would be useful across a broad swath of model types. In brief, the rules are: (1) Define context clearly. (2) Use contextually appropriate data. (3) Evaluate within context. (4) List limitations explicitly. (5) Use version control. (6) Document appropriately. (7) Disseminate broadly. (8) Get independent reviews. (9) Test competing imple-mentations. (10) Conform to standards. Although some of these are common sense guidelines, we have found that many are often missed or misconstrued, even by seasoned practitioners. Computational models are already widely used in basic science to generate new biomedical knowledge. As they penetrate clinical care and healthcare policy, contributing to personalized and precision medicine, clinical safety will require established guidelines for the credible practice of modeling and simulation in healthcare.
Credibility↗
Surface infrastructure functions, requirements and subsystems for a manned Mars mission
Planning and development for a permanently manned scientific outpost on Mars requires an in-depth understanding and analysis of the functions the outpost is expected to perform. The optimum configuration that accomplishes these functions then arises during the trade studies process. In a project this complex, it becomes necessary to use a formal methodology to document the design and planning process. The method chosen for this study is called top-down functional decomposition. This method is used to determine the functions that are needed to accomplish the overall mission, then determine what requirements and systems are needed to do each of the functions. This method facilitates automation of the trades and options process. In the example, this was done with an off-the shelf software package called TK! olver. The basic functions that a permanently manned outpost on Mars must accomplish are: (1) Establish the Life Critical Systems; (2) Support Planetary Sciences and Exploration; and (3) Develop and Maintain Long-term Support Functions, including those systems needed towards self-sufficiency. The top-down functional decomposition methology, combined with standard spread sheet software, offers a powerful tool to quickly assess various design trades and analyze options. As the specific subsystems, and the relational rule algorithms are further refined, it will be possible to very accurately determine the implications of continually evolving mission requirements.
Kyle Fairchild↗
Staggered solution procedures for multibody dynamics simulation
The numerical solution procedure for multibody dynamics (MBD) systems is termed a staggered MBD solution procedure that solves the generalized coordinates in a separate module from that for the constraint force. This requires a reformulation of the constraint conditions so that the constraint forces can also be integrated in time. A major advantage of such a partitioned solution procedure is that additional analysis capabilities such as active controller and design optimization modules can be easily interfaced without embedding them into a monolithic program. After introducing the basic equations of motion for MBD system in the second section, Section 3 briefly reviews some constraint handling techniques and introduces the staggered stabilized technique for the solution of the constraint forces as independent variables. The numerical direct time integration of the equations of motion is described in Section 4. As accurate damping treatment is important for the dynamics of space structures, we have employed the central difference method and the mid-point form of the trapezoidal rule since they engender no numerical damping. This is in contrast to the current practice in dynamic simulations of ground vehicles by employing a set of backward difference formulas. First, the equations of motion are partitioned according to the translational and the rotational coordinates. This sets the stage for an efficient treatment of the rotational motions via the singularity-free Euler parameters. The resulting partitioned equations of motion are then integrated via a two-stage explicit stabilized algorithm for updating both the translational coordinates and angular velocities. Once the angular velocities are obtained, the angular orientations are updated via the mid-point implicit formula employing the Euler parameters. When the two algorithms, namely, the two-stage explicit algorithm for the generalized coordinates and the implicit staggered procedure for the constraint Lagrange multipliers, are brought together in a staggered manner, they constitute a staggered explicit-implicit procedure which is summarized in Section 5. Section 6 presents some example problems and discussions concerning several salient features of the staggered MBD solution procedure are offered in Section 7.
Park, K. C.↗
Evolving Design Criteria for Very Large Aperture Space Based Telescopes and Their Influence on the Need for Integrated Tools in the Optimization Process
NASA's Advanced Mirror Technology Development (AMTD) program has been developing the means to design and build the future generations of space based telescopes. With the nearing completion of the James Webb Space Telescope (JWST), the astrophysics community is already starting to define the requirements for follow-on observatories. The restrictions of available launch vehicles and the possibilities of planned future vehicles have fueled the competition between monolithic primaries (with better optical quality) and segmented primaries (with larger apertures, but with diffraction, costs and figure control issues). Regardless of the current shroud sizes and lift capacities, these competing architectures share the need for rapid design tools. As part of the AMTD program a number of tools have been developed and tested to speed up the design process. Starting with the Arnold Mirror Modeler (which creates Finite Element Models (FEM) for structural analysis) and now also feeds these models into thermal stability analyses. They share common file formats and interchangeable results. During the development of the program, numerous trade studies were created for 4-meter and 8-meter monolithic primaries, complete with support systems. Evaluation of these results has led to a better understanding of how the specification drives the results. This paper will show some of the early trade studies for typical specification requirements such as lowest mirror bending frequency and suspension system lowest frequency. The results use representative allowable stress values for each mirror substrate material and construction method and generic material properties. These studies lead to some interesting relationships between feasible designs and the realities of actually trying to build these mirrors. Much of the traditional specifications were developed for much smaller systems, where the mass and volume of the primary where a small portion of the overall satellite. JWST shows us that as the aperture grows, the primary takes up the majority of the mass and volume and the established rules need to be adjusted. For example, a small change in lowest frequency requirement can change the cost by millions of dollars. The paper uses numerous trade studies created during the software development phase of the Arnold Mirror Modeler to illustrate the influences of system specifications on the design space. The future telescopes will require better performance, stability and documented feasibility to meet the hurdles of today's budget and schedules realities. AMTD is developing the tools, but the basic system planning mentality also has to adopt to the requirements of these very large and complex physical structures.
Arnold, William R., Sr.↗
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.
59 BASIC BIOLOGICAL SCIENCES↗
Application of multi-criteria decision analysis techniques and decision support framework for informing plant select agent designation and decision making
The United States Department of Agriculture (USDA) Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents (Select Agents List) that threaten crops of economic importance to the United States and regulates the procedures governing containment, incident response, and the security of entities working with them. Every 2 years the USDA DASAT reviews their select agent list, utilizing assessments by subject matter experts (SMEs) to rank the agents. We explored the applicability of multi-criteria decision analysis (MCDA) techniques and a decision support framework (DSF) to support the USDA DASAT biennial review process. The evaluation includes both current and non-select agents to provide a robust assessment. We initially conducted a literature review of 16 pathogens against 9 criteria for assessing plant health and bioterrorism risk and documented the findings to support this analysis. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for ensuring accuracy. Scoring criteria were adopted to ensure consistency. The MCDA supported the expectation that select agents would rank high on the relative risk scale when considering the agricultural consequences of a bioterrorism attack; however, application of analytical thresholds as a basis for designating select agents led to some exceptions to current designations. A second analytical approach used agent-specific data to designate key criteria in a DSF logic tree format to identify pathogens of low concern that can be ruled out for further consideration as select agents. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making.
59 BASIC BIOLOGICAL SCIENCES↗
Sensitivity of transport aircraft performance and economics to advanced technology and cruise Mach number
Sensitivity data for advanced technology transports has been systematically collected. This data has been generated in two separate studies. In the first of these, three nominal, or base point, vehicles designed to cruise at Mach numbers .85, .93, and .98, respectively, were defined. The effects on performance and economics of perturbations to basic parameters in the areas of structures, aerodynamics, and propulsion were then determined. In all cases, aircraft were sized to meet the same payload and range as the nominals. This sensitivity data may be used to assess the relative effects of technology changes. The second study was an assessment of the effect of cruise Mach number. Three families of aircraft were investigated in the Mach number range 0.70 to 0.98: straight wing aircraft from 0.70 to 0.80; sweptwing, non-area ruled aircraft from 0.80 to 0.95; and area ruled aircraft from 0.90 to 0.98. At each Mach number, the values of wing loading, aspect ratio, and bypass ratio which resulted in minimum gross takeoff weight were used. As part of the Mach number study, an assessment of the effect of increased fuel costs was made.
Ardema, M. D.↗