Computational Modeling of Protein Stability: Quantitative Analysis Reveals Solutions to Pervasive Problems

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Function2Form Bridge—Toward synthetic protein holistic performance prediction

Protein engineering and synthetic biology stand to benefit immensely from recent advances in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on individual parameters of a query protein, with output scores/metrics unique to each parameter. In reality, proteins feature multiple “parts”/functions and modification of a protein aimed at altering a given part, typically has collateral impact on other protein parts. A system for prediction of the combined effect of design parameters on the overall performance of the final protein does not exist. Function2Form Bridge (F2F-Bridge) attempts to address this by combining the scores of different design parameters pertaining to the protein being analyzed into a single easily interpreted output describing overall performance. The strategy comprises of (a) a mathematical strategy combining data from a myriad of in silico tools into an OP-score (a singular score informing on a user-defined overall performance) and (b) the F2F Plot, a graphical means of informing the wetlab biologist holistically on designed construct suitability in the context of multiple parameters, highlighting scope for improvement. F2F predictive output was compared with wetlab data from a range of synthetic proteins designed, built, and tested for this study. Statistical/machine learning approaches for predicting overall performance, for use alongside the F2F plot, were also examined. Comparisons between wetlab performance and F2F predictions demonstrated close and reliable correlations. This user-friendly strategy represents a pivotal enabler in increasing the accessibility of synthetic protein building and de novo protein design.     

What limits the primary sequence space of natural proteins?

Abstract

Number of naturally occurring primary sequences of proteins is an infinitesimally small subset of the possible number of primary sequences that can be synthesized using 20 amino acids. Prevailing views ascribe this to slow and incremental mutational/selection evolutionary mechanisms. However, considering the large number of avenues available in form of diversity of emerging/evolving and/or disappearing living systems for exploring the primary sequence space over the evolutionary time scale of ～3.5 billion years, this remains a conjecture. Therefore, to investigate primary sequence space limitations, we carried out a systematic study for finding primary sequences absent in nature. We report the discovery of the smallest peptide sequence “Cysteine-Glutamine-Tryptophan-Tryptophan” that is not found in over half-a-million curated protein sequences in the Uniprot (Swiss-Prot) database. Additionally, we report a library of 83605 pentapeptides that are not found in any of the known protein sequences. Compositional analyses of these absent primary sequences yield a remarkably strong power relationship between the percentage occurrence of individual amino acids in all known protein sequences and their respective frequency of occurrence in the absent peptides, regardless of their specific position in the sequences. If random evolutionary mechanisms were responsible for limitations to the primary sequence space, then one would not expect any relationship between compositions of available and absent primary sequences. Thus, we conclusively show that stoichiometric constraints on amino acids limit the primary sequence space of proteins in nature. We discuss the possibly profound implications of our findings in both evolutionary and synthetic biology.

Communicated by Ramaswamy H. Sarma     

The Exact Distribution of the Anderson-Kannemann Statistic

The Anderson-Kannemann test is a rank test for treatment effects in a randomized block design with K treatments and N blocks. In this paper, an algorithm for computing the exact distribution of the Anderson-Kannemann test statistic under the null hypothesis is deduced. Then, the exact distribution is compared with the asymptotic χ²-distribution, and it is shown that the exact distribution is approximated fairly well by the asymptotic distribution. Tables of the exact distribution are given for K = 3, N = 3(1)15; K = 4, N = 3(1)11; K = 5, N = 3(1)7; and K = 6, N = 3(1)5.     

Conjugation of N-acylhydrazone and 1,2,4-oxadiazole leads to the identification of active antimalarial agents

Malaria, caused by several Plasmodium species, is the major life-threatening parasitic infection worldwide. Due to the parasite resistance to quinoline based drugs, the search for antimalarial agents is necessary. Here, we report the structural design, synthesis and antiparasitic evaluation of two novel series of 1,2,4-oxadiazoles in conjugation to N-acylhydrazones, both groups recognized as privileged structures, as well as the studies on the antimalarial activity of 16 previous described analogues. By varying substituents attached to the phenyl ring, it was possible to retain, enhance or increase the antiparasitic activity in comparison to the nonsubstituted derivatives. Replacement of substituted aryl rings by ferrocenyl and cinnamyl moieties attached in the N-acylhydrazone ablated the antiparasitic response, evidencing the structural features associated with the activity. Active compounds exhibited in vitro potency similar to mefloquine, but not all inhibited β-hematin formation. Additionally, the active compounds displayed low cytotoxicity in HepG2 cells and did not cause hemolysis in uninfected erythrocytes. In Plasmodium berghei-infected mice, the compounds reduced parasitemia but exhibited limited efficacy in increasing mice survival when compared to chloroquine, suggesting that pharmacological improvement is still necessary.     

Finite element modelling of implant designs and cortical bone thickness on stress distribution in maxillary type IV bone

The aims of this study were to examine the effect of implant neck design and cortical bone thickness using 3D finite element analysis and to analyse the stability of clinical evidence based on micromotion and principal stress. Four commercial dental implants for a type IV bone and maxillary segments were created. Various parameters were considered, including the osseointegration condition, loading direction and cortical bone thickness. Micromotion and principal stresses were used to evaluate the failure of osseointegration and bone overloading, respectively. It was found that the maximum stress of the peri-implant bone decreased as cortical bone thickness increased. The micromotion level in full osseointegration is less than that in non-osseointegration and it also decreases as cortical bone thickness increases. The cortical bone thickness should be measured before surgery to help select a proper implant. In the early stage of implantation, the horizontal loading component induces stress concentration in bone around the implant neck more easily than does the vertical loading component, and this may result in crestal bone loss.     

On the PBB Designs for Multiresponse Experiments

We present the idea of using multiresponse incomplete block designs when not all responses can be observed in all experimental units. For a special class of such designs, in which partial designs are PBB designs, a method for estimating natural treatment contrast is given. We also consider the problem of testing the hypotheses concerning the natural and any estimable treatment contrasts. For testing this hypothesis the Wald statistics, being asymptotically chi-square distributed, is proposed.     

垂直绿化生态效益研究综述

全球气候变化和城市化背景下城市生态环境问题越发凸显，面对日趋紧张的土地资源现状，垂直绿化建设成为重要的城市绿地补充手段，对改善城市环境具有重要意义。垂直绿化具有多种生态效益，且其效益发挥受到多因素共同影响。如何统筹协调生态效益和影响因素之间的复杂关系，以使其综合生态效益最大化，是当前垂直绿化建设亟待解决的科学问题之一。基于文献综述法归纳了不同生态效益的机制及其关键影响因素，并对多效益和多影响因素进行了综合分析。结果表明，垂直绿化具有缓解城市热岛、建筑节能减排、固碳、净化空气、降噪、截留雨水和支持生物多样性等七种主要生态效益，并受到植被特征、设施结构特征、气象条件、空间格局等多方面因素的共同影响。基于对效益和影响因素的综合分析，进一步提出了两点规划思路：首先，关注环境需求和效益供给的耦合关系能够更加科学合理地指导区域垂直绿化建设布局。其次，关注生态效益间的关系，以区域关键生态环境问题为导向进行效益权衡并结合考虑其影响因素的重要性程度能为规划设计提供有效建议。