Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies

The CD4 binding site (CD4bs) of the HIV-1 envelope glycoprotein is susceptible to multiple lineages of broadly neutralizing antibodies (bnAbs) that are attractive to elicit with vaccines. The CH235 lineage (VH1-46) of CD4bs bnAbs is particularly attractive because the most mature members neutralize 90% of circulating strains, do not possess long HCDR3 regions, and do not contain insertions and deletions that may be difficult to induce. We used virus neutralization to measure the interaction of CH235 unmutated common ancestor (CH235 UCA) with functional Env trimers on infectious virions to guide immunogen design for this bnAb lineage. Two Env mutations were identified, one in loop D (N279K) and another in V5 (G458Y), that acted synergistically to render autologous CH505 transmitted/founder virus susceptible to neutralization by CH235 UCA. Man5-enriched N-glycans provided additional synergy for neutralization. CH235 UCA bound with nanomolar affinity to corresponding soluble native-like Env trimers as candidate immunogens. A cryo-EM structure of CH235 UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 revealed interactions of the antibody light chain complementarity determining region 3 (CDR L3) with the engineered Env loops D and V5. These results demonstrate that virus neutralization can directly inform vaccine design and suggest a germline targeting and reverse engineering strategy to initiate and mature the CH235 bnAb lineage

Potent and broad HIV-neutralizing antibodies in memory B cells and plasma

Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. Antibody 10E8, reactive with the distal portion of the membrane-proximal external region (MPER) of HIV-1 gp41, is broadly neutralizing. However, the ontogeny of distal MPER antibodies and the relationship of memory B cell to plasma bnAbs are poorly understood. HIV-1–specific memory B cell flow sorting and proteomic identification of anti-MPER plasma antibodies from an HIV-1–infected individual were used to isolate broadly neutralizing distal MPER bnAbs of the same B cell clonal lineage. Structural analysis demonstrated that antibodies from memory B cells and plasma recognized the envelope gp41 bnAb epitope in a distinct orientation compared with other distal MPER bnAbs. The unmutated common ancestor of this distal MPER bnAb was autoreactive, suggesting lineage immune tolerance control. Construction of chimeric antibodies of memory B cell and plasma antibodies yielded a bnAb that potently neutralized most HIV-1 strains

Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding

<b>Background</b> A key step in the development of an adaptive immune response to pathogens or vaccines is the binding of short peptides to molecules of the Major Histocompatibility Complex (MHC) for presentation to T lymphocytes, which are thereby activated and differentiate into effector and memory cells. The rational design of vaccines consists in part in the identification of appropriate peptides to effect this process. There are several algorithms currently in use for making such predictions, but these are limited to a small number of MHC molecules and have good but imperfect prediction power.<p></p> <b>Results</b> We have undertaken an exploration of the power gained by taking advantage of a natural representation of the amino acids in terms of their biophysical properties. We used several well-known statistical classifiers using either a naive encoding of amino acids by name or an encoding by biophysical properties. In all cases, the encoding by biophysical properties leads to substantially lower misclassification error.<p></p> <b>Conclusion</b> Representation of amino acids using a few important bio-physio-chemical property provide a natural basis for representing peptides and greatly improves peptide-MHC class I binding prediction

In silico analysis of the structure of variable domains of mouse single-chain antibodies specific to the human recombinant interferon β1b

In silico analysis of the DNA encoding singlechain Fv antibodies (ScFv) specific to the human recombinant interferon β1b and α2b (rhIFNβ1b, rhIFNα2b) has been carried out. The V, D and J-gene segments, the complementaritydetermining (CDR) and framework (FR) regions, n-nucleotides as well as mutation rates which take place during the affinity maturation of the examined sequences have been determined. For the panel of ScFv against rhIFNβ1b isolated from an immune combinatorial cDNA library uniqueness of the CDRH3 loop by the length and amino acid composition has been shown. Multiple alignments with the nearest homologies from the NCBI databases have revealed that the sequences of ScFv obtained are new.Проведен in silico анализ структуры последовательностей ДНК, кодирующих специфические к интерферону β1b и α2b человека (rhIFN β1b, rhIFN α2b) одноцепочечные антитела (ScFv – single chain Fv): определены V, D и J сегменты, границы антиген связывающих (CDR) и каркасных (FR) участков, n нуклеотиды, а также величина мутационных процессов, которые имели место при аффинном дозревании последовательностей in vivo. Для представителей панели ScFv против rhIFN β1b, изолированных из иммунной комбинаторной библиотеки кДНК V генов, показана уникальность участка CDRH3 как по длине, так и по аминокислотному составу. Множественное выравнивание с ближайшими гомологами базы данных NCBI показало, что полученные нами последовательности ScFv являются новыми.Проведено in silico аналіз структури послідовностей ДНК, які кодують специфічні до рекомбінантного інтерферону β1b та α2b людини (rhIFN β1b, rhIFN-α2b) одноланцюгові антитіла (ScFv – single chain Fv): визначено V , D та J генні сегменти, межі антигензв’язувальних (CDR) та каркасних (FR) ділянок, n- нуклеотиди, а також величину мутаційних процесів, що мали місце при афінному дозріванні даних послідовностей in vivo. Для представників панелі ScFv проти rhIFN β1b, ізольованих з імунної комбінаторної бібліотеки кДНК V генів, показано унікальність ділянки CDRH3 як за довжиною, так і за амінокислотним складом. Множинне вирівнювання з найближчими гомологами бази даних NCBI показало, що одержані нами послідовності ScFv є новими

On the Long-Term Fitness of Cells in Periodically Switching Environments

[[abstract]]Because all the cell populations are capable of making switches between different genetic expression states in response to the environmental change, Thattai and van Oudenaarden (Genetics 167, 523–530, 2004) have raised a very interesting question: In a constantly fluctuating environment, which type of cell population (heterogeneous or homogeneous) is fitter in the long term? This problem is very important to development and evolution biology. We thus take an extensive analysis about how the cell population evolves in a periodically switching environment either with symmetrical time-span or asymmetrical time-span. A complete picture of the phase diagrams for both cases is obtained. Furthermore, we find that the systems with time-dependent cellular transitions all collapse to the same set of dynamical equations with the modified parameters. Furthermore, we also explain in detail how the fitness problem bears much resemblance to the phenomenon, stochastic resonance, in physical sciences. Our results could be helpful for the biologists to design artificial evolution experiments and unveil the mystery of development and evolution.[[journaltype]]國內[[countrycodes]]US